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Tavares LS, Oliveira-Silva RL, Moura MT, da Silva JB, Benko-Iseppon AM, Lima-Filho JV. Reference genes for gene expression profiling in mouse models of Listeria monocytogenes infection. Biotechniques 2024; 76:104-113. [PMID: 38112054 DOI: 10.2144/btn-2023-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
RT-qPCR dissects transcription-based processes but requires reference genes (RGs) for data normalization. This study prospected RGs for mouse macrophages (pMØ) and spleen infected with Listeria monocytogenes. The pMØ were infected in vitro with L. monocytogenes or vehicle for 4 h. Mice were injected with L. monocytogenes (or vehicle) and euthanized 24 h post-injection. The RGs came from a multispecies primer set, from the literature or designed here. The RG ranking relied on GeNorm, NormFinder, BestKeeper, Delta-CT and RefFinder. B2m-H3f3a-Ppia were the most stable RGs for pMØ, albeit RG indexes fine-tuned estimations of cytokine relative expression. Actβ-Ubc-Ppia were the best RGs for spleen but modestly impacted the cytokine relative expression. Hence, mouse models of L. monocytogenes require context-specific RGs for RT-qPCR, thus reinforcing its paramount contribution to accurate gene expression profiling.
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Affiliation(s)
| | | | - Marcelo Tigre Moura
- Departamento de Biologia Celular e Molecular, Centro de Biotecnologia, Campus I, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | | | | | - José Vitor Lima-Filho
- Departamento de Biologia, Universidade Federal Rural de Pernambuco, Recife, PE, Brasil
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Davies KA, Welch SR, Sorvillo TE, Coleman-McCray JD, Martin ML, Brignone JM, Montgomery JM, Spiropoulou CF, Spengler JR. Optimal reference genes for RNA tissue analysis in small animal models of hemorrhagic fever viruses. Sci Rep 2023; 13:19384. [PMID: 37938597 PMCID: PMC10632498 DOI: 10.1038/s41598-023-45740-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Reverse-transcription quantitative polymerase chain reaction assays are frequently used to evaluate gene expression in animal model studies. Data analyses depend on normalization using a suitable reference gene (RG) to minimize effects of variation due to sample collection, sample processing, or experimental set-up. Here, we investigated the suitability of nine potential RGs in laboratory animals commonly used to study viral hemorrhagic fever infection. Using tissues (liver, spleen, gonad [ovary or testis], kidney, heart, lung, eye, brain, and blood) collected from naïve animals and those infected with Crimean-Congo hemorrhagic fever (mice), Nipah (hamsters), or Lassa (guinea pigs) viruses, optimal species-specific RGs were identified based on five web-based algorithms to assess RG stability. Notably, the Ppia RG demonstrated stability across all rodent tissues tested. Optimal RG pairs that include Ppia were determined for each rodent species (Ppia and Gusb for mice; Ppia and Hrpt for hamsters; and Ppia and Gapdh for guinea pigs). These RG pair assays were multiplexed with viral targets to improve assay turnaround time and economize sample usage. Finally, a pan-rodent Ppia assay capable of detecting Ppia across multiple rodent species was developed and successfully used in ecological investigations of field-caught rodents, further supporting its pan-species utility.
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Affiliation(s)
- Katherine A Davies
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
- U.S. Department of Agriculture, Agricultural Research Service, Zoonotic and Emerging Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS, USA
| | - Stephen R Welch
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Teresa E Sorvillo
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - JoAnn D Coleman-McCray
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - María Laura Martin
- Departamento Investigación, Instituto Nacional de Enfermedades Virales Humanas (INEVH) "Dr. Julio I. Maiztegui", Pergamino, Argentina
| | - Julia M Brignone
- Departamento Investigación, Instituto Nacional de Enfermedades Virales Humanas (INEVH) "Dr. Julio I. Maiztegui", Pergamino, Argentina
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Brizić I, Lisnić B, Krstanović F, Brune W, Hengel H, Jonjić S. Mouse Models for Cytomegalovirus Infections in Newborns and Adults. Curr Protoc 2022; 2:e537. [PMID: 36083111 DOI: 10.1002/cpz1.537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article describes procedures for infecting adult mice with murine cytomegalovirus (MCMV) and for infecting newborn mice to model congenital CMV infection. Methods are included for propagating MCMV in cell cultures and preparing a more virulent form of MCMV from the salivary glands of infected mice. A plaque assay is provided for determining MCMV titers of infected tissues or virus stocks. Also, methods are described for preparing the murine embryonic fibroblasts used for propagating MCMV, and for the plaque assay. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Berislav Lisnić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Fran Krstanović
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | | | - Hartmut Hengel
- Institute of Virology, Medical Center-University of Freiburg, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stipan Jonjić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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nanoString evaluation of murine Cytomegalovirus transcription in vivo and in vitro. J Virol Methods 2021; 301:114436. [PMID: 34929204 DOI: 10.1016/j.jviromet.2021.114436] [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: 10/14/2021] [Revised: 11/28/2021] [Accepted: 12/15/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Next Generation Sequencing allows for deep analysis of transcriptional activity in cells and tissues, however it is still a cost intensive method that demands well versed data handling. Reverse transcription quantitative PCR (RT-qPCR) is the most commonly used method to measure gene expression levels, however the information gathered is quite small in comparison to NGS. A newer method called nanoString allows for highly multiplexed gene expression analysis by detecting mRNAs without the use of enzymes for reverse transcription or amplification even for single cells or low input material. The method can be done in 1.5 days and data are quickly analyzed by the accompanied user friendly software. Our aim was to investigate this new method and compare it to the existing alternatives, while investigating murine Cytomegalovirus (mCMV) infection and latency. METHODS mCMV infected murine embryonic fibroblasts (MEF), lung and salivary glands from BALB/c mice were evaluated at different stages of infection. A set of 30 custom designed nanoString probes were tested, 20 probes specific for mCMV genes, 6 probes for host genes known to be influenced by viral infection and 4 reference gene specific probes. nanoString counts were compared to published RNA-Seq RPKM. RESULTS We found that nanoString can be used for analysis of cytomegalovirus gene expression during acute infection in vitro and in vivo, both for virus specific and host genes. Although some transcripts show different expression rates in comparison to NGS data, the most abundant transcripts are comparable. When tissues are infected, there are significantly fewer transcripts than in MEFs, and consistent with previous work there are significant differences in relevant abundance between MEF and tissues. We were unable to detect our viral transcripts of interest in latently infected tissue. CONCLUSIONS For viruses with annotated transcriptomes, nanoString allows simultaneous quantitation of multiple virus and host genes. One huge advantage of the platform is rapid turnaround and simplicity of analysis. It should prove to be very useful to explore host virus interactions during acute infection, but it is unclear if it has adequate sensitivity for analysis during latency in immunocompetent mice.
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Fragoulis A, Biller K, Fragoulis S, Lex D, Uhlig S, Reiss LK. Reference Gene Selection for Gene Expression Analyses in Mouse Models of Acute Lung Injury. Int J Mol Sci 2021; 22:ijms22157853. [PMID: 34360619 PMCID: PMC8346155 DOI: 10.3390/ijms22157853] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/12/2021] [Accepted: 07/19/2021] [Indexed: 12/21/2022] Open
Abstract
qRT-PCR still remains the most widely used method for quantifying gene expression levels, although newer technologies such as next generation sequencing are becoming increasingly popular. A critical, yet often underappreciated, problem when analysing qRT-PCR data is the selection of suitable reference genes. This problem is compounded in situations where up to 25% of all genes may change (e.g., due to leukocyte invasion), as is typically the case in ARDS. Here, we examined 11 widely used reference genes for their suitability in commonly used models of acute lung injury (ALI): ventilator-induced lung injury (VILI), in vivo and ex vivo, lipopolysaccharide plus mechanical ventilation (MV), and hydrochloric acid plus MV. The stability of reference gene expression was determined using the NormFinder, BestKeeper, and geNorm algorithms. We then proceeded with the geNorm results because this is the only algorithm that provides the number of reference genes required to achieve normalisation. We chose interleukin-6 (Il-6) and C-X-C motif ligand 1 (Cxcl-1) as the genes of interest to analyse and demonstrate the impact of inappropriate normalisation. Reference gene stability differed between the ALI models and even within the subgroup of VILI models, no common reference gene index (RGI) could be determined. NormFinder, BestKeeper, and geNorm produced slightly different, but comparable results. Inappropriate normalisation of Il-6 and Cxcl1 gene expression resulted in significant misinterpretation in all four ALI settings. In conclusion, choosing an inappropriate normalisation strategy can introduce different kinds of bias such as gain or loss as well as under- or overestimation of effects, affecting the interpretation of gene expression data.
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Affiliation(s)
- Athanassios Fragoulis
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen University, 52074 Aachen, Germany;
| | - Kristina Biller
- Department of Pharmacology and Toxicology, Uniklinik RWTH Aachen University, 52074 Aachen, Germany; (K.B.); (S.F.); (D.L.); (S.U.)
| | - Stephanie Fragoulis
- Department of Pharmacology and Toxicology, Uniklinik RWTH Aachen University, 52074 Aachen, Germany; (K.B.); (S.F.); (D.L.); (S.U.)
| | - Dennis Lex
- Department of Pharmacology and Toxicology, Uniklinik RWTH Aachen University, 52074 Aachen, Germany; (K.B.); (S.F.); (D.L.); (S.U.)
| | - Stefan Uhlig
- Department of Pharmacology and Toxicology, Uniklinik RWTH Aachen University, 52074 Aachen, Germany; (K.B.); (S.F.); (D.L.); (S.U.)
| | - Lucy Kathleen Reiss
- Department of Pharmacology and Toxicology, Uniklinik RWTH Aachen University, 52074 Aachen, Germany; (K.B.); (S.F.); (D.L.); (S.U.)
- Correspondence:
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Mansfield SA, Dwivedi V, Elgharably H, Griessl M, Zimmerman PD, Limaye AP, Cook CH. Cytomegalovirus immunoglobulin G titers do not predict reactivation risk in immunocompetent hosts. J Med Virol 2019; 91:836-844. [PMID: 30609051 DOI: 10.1002/jmv.25389] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/07/2018] [Indexed: 11/06/2022]
Abstract
Cytomegalovirus (CMV) reactivation occurs in roughly one-third of immunocompetent patients during critical illness, and is associated with worse outcomes. These outcomes have prompted consideration of early antiviral prophylaxis, but two-third of patients would receive unnecessary treatment. Tissue viral load has been associated with risk of reactivation in murine models, and recent work has suggested a relationship between immune responses to CMV and underlying viral load. We, therefore, sought to confirm the hypothesis that serum CMV-specific immunoglobulin G (IgG) correlates with tissue viral load, and might be used to predict the risk of reactivation during critical illness. We confirm that there is a good correlation between tissue viral load and serum CMV-specific IgG after laboratory infection of inbred mice. Further, we show that naturally infected outbred hosts have variable tissue viral DNA loads that do not correlate well with serum IgG. Perhaps as a consequence, CMV-specific IgG was not predictive of reactivation events in immunocompetent humans. When reactivation did occur, those with the lowest IgG levels had longer durations of reactivation, but IgG quartiles were not associated with differing peak DNAemia. Together our data suggest that CMV-specific IgG titers diverge from tissue viral loads in outbred immunocompetent hosts, and their importance for the control of reactivation events remains unclear.
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Affiliation(s)
- Sara A Mansfield
- Department of Surgery, The Ohio State University, Columbus, Ohio
| | - Varun Dwivedi
- Department of Surgery, The Ohio State University, Columbus, Ohio
| | | | - Marion Griessl
- Department of Surgery, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts
| | | | - Ajit P Limaye
- Department of Medicine, University of Washington, Seattle, Washington
| | - Charles H Cook
- Department of Surgery, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts
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Brizić I, Lisnić B, Brune W, Hengel H, Jonjić S. Cytomegalovirus Infection: Mouse Model. CURRENT PROTOCOLS IN IMMUNOLOGY 2018; 122:e51. [PMID: 30044539 PMCID: PMC6347558 DOI: 10.1002/cpim.51] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This unit describes procedures for infecting newborn and adult mice with murine cytomegalovirus (MCMV). Methods are included for propagating MCMV in cell cultures and for preparing a more virulent form of MCMV from salivary glands of infected mice. A plaque assay is provided for determining MCMV titers of infected tissues or virus stocks. Also, a method is described for preparing the murine embryonic fibroblasts used for propagating MCMV and for the plaque assay. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ilija Brizić
- Department of Histology and Embryology and Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Berislav Lisnić
- Department of Histology and Embryology and Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Wolfram Brune
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Hartmut Hengel
- Institute of Virology, Medical Center-University of Freiburg, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stipan Jonjić
- Department of Histology and Embryology and Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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