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Velderrain-Armenta F, González-Ochoa G, Tamez-Guerra P, Romero-Arguelles R, Romo-Sáenz CI, Gomez-Flores R, Flores-Mendoza L, Icedo-García R, Soñanez-Organis JG. Bifidobacterium longum and Chlorella sorokiniana Combination Modulates IFN-γ, IL-10, and SOCS3 in Rotavirus-Infected Cells. Int J Mol Sci 2024; 25:5514. [PMID: 38791551 PMCID: PMC11122607 DOI: 10.3390/ijms25105514] [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: 04/01/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Rotavirus is the main cause of acute diarrhea in children up to five years of age. In this regard, probiotics are commonly used to treat or prevent gastroenteritis including viral infections. The anti-rotavirus effect of Bifidobacterium longum and Chlorella sorokiniana, by reducing viral infectivity and improving IFN-type I response, has been previously reported. The present study aimed to study the effect of B. longum and/or C. sorokiniana on modulating the antiviral cellular immune response mediated by IFN-γ, IL-10, SOCS3, STAT1, and STAT2 genes in rotavirus-infected cells. To determine the mRNA relative expression of these genes, HT-29 cells were treated with B. longum and C. sorokiniana alone or in combination, followed by rotavirus infection. In addition, infected cells were treated with B. longum and/or C. sorokiniana. Cellular RNA was purified, used for cDNA synthesis, and amplified by qPCR. Our results demonstrated that the combination of B. longum and C. sorokiniana stimulates the antiviral cellular immune response by upregulating IFN-γ and may block pro-inflammatory cytokines by upregulating IL-10 and SOCS3. The results of our study indicated that B. longum, C. sorokiniana, or their combination improve antiviral cellular immune response and might modulate pro-inflammatory responses.
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Affiliation(s)
- Felizardo Velderrain-Armenta
- Department of Chemistry-Biology and Agriculture, Interdisciplinary Faculty of Biology Sciences and Health, University of Sonora, Navojoa C.P. 85880, Mexico; (F.V.-A.); (L.F.-M.); (R.I.-G.); (J.G.S.-O.)
| | - Guadalupe González-Ochoa
- Department of Chemistry-Biology and Agriculture, Interdisciplinary Faculty of Biology Sciences and Health, University of Sonora, Navojoa C.P. 85880, Mexico; (F.V.-A.); (L.F.-M.); (R.I.-G.); (J.G.S.-O.)
| | - Patricia Tamez-Guerra
- Laboratory of Immunology and Virology, Falculty of Biological Sciences, Autonomous University of Nuevo Leon, San Nicolás de los Garza C.P. 66455, Mexico; (R.R.-A.); (C.I.R.-S.); (R.G.-F.)
| | - Ricardo Romero-Arguelles
- Laboratory of Immunology and Virology, Falculty of Biological Sciences, Autonomous University of Nuevo Leon, San Nicolás de los Garza C.P. 66455, Mexico; (R.R.-A.); (C.I.R.-S.); (R.G.-F.)
| | - César I. Romo-Sáenz
- Laboratory of Immunology and Virology, Falculty of Biological Sciences, Autonomous University of Nuevo Leon, San Nicolás de los Garza C.P. 66455, Mexico; (R.R.-A.); (C.I.R.-S.); (R.G.-F.)
| | - Ricardo Gomez-Flores
- Laboratory of Immunology and Virology, Falculty of Biological Sciences, Autonomous University of Nuevo Leon, San Nicolás de los Garza C.P. 66455, Mexico; (R.R.-A.); (C.I.R.-S.); (R.G.-F.)
| | - Lilian Flores-Mendoza
- Department of Chemistry-Biology and Agriculture, Interdisciplinary Faculty of Biology Sciences and Health, University of Sonora, Navojoa C.P. 85880, Mexico; (F.V.-A.); (L.F.-M.); (R.I.-G.); (J.G.S.-O.)
| | - Ramona Icedo-García
- Department of Chemistry-Biology and Agriculture, Interdisciplinary Faculty of Biology Sciences and Health, University of Sonora, Navojoa C.P. 85880, Mexico; (F.V.-A.); (L.F.-M.); (R.I.-G.); (J.G.S.-O.)
| | - José G. Soñanez-Organis
- Department of Chemistry-Biology and Agriculture, Interdisciplinary Faculty of Biology Sciences and Health, University of Sonora, Navojoa C.P. 85880, Mexico; (F.V.-A.); (L.F.-M.); (R.I.-G.); (J.G.S.-O.)
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Abot A, Pomié N, Astre G, Cani PD, Aussant J, Barrat E, Knauf C. Effect of the dietary supplement PERMEAPROTECT+ TOLERANCE© on gut permeability in a human co-culture epithelial and immune cells model. Heliyon 2024; 10:e28320. [PMID: 38586362 PMCID: PMC10998107 DOI: 10.1016/j.heliyon.2024.e28320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Background and objective The leaky gut syndrome is characterized by an intestinal hyperpermeability observed in multiple chronic disorders. Alterations of the gut barrier are associated with translocation of bacterial components increasing inflammation, oxidative stress and eventually dysfunctions of cellular interactions at the origin pathologies. Therapeutic and/or preventive approaches have to focus on the identification of novel targets to improve gut homeostasis. In this context, this study aims to identify the role of PERMEAPROTECT + TOLERANE©, known as PERMEA, a food complement composed of a combination of factors (including l-Glutamine) known to improve gut physiology. Methods We tested the effects of PERMEA or l-Glutamine alone (as reference) on gut permeability (FITC dextran method, expression of tight junctions) and its inflammatory/oxidative consequences (cytokines and redox assays, RT-qPCR) in a co-culture of human cells (peripheral blood mononuclear cells and intestinal epithelial cells) challenged with TNFα. Results PERMEA prevented intestinal hyperpermeability induced by inflammation. This was linked with its antioxidant and immunomodulatory properties showing a better efficacity than l-Glutamine alone on several parameters including permeability, global antioxidant charge and production of cytokines. Conclusion PERMEA is more efficient to restore intestinal physiology, reinforcing the concept that combination of food constituents could be used to prevent the development of numerous diseases.
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Affiliation(s)
| | | | | | - Patrice D. Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute LDRI, UCLouvain, Université catholique de Louvain, Brussels, Belgium
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, WELBIO department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
- NeuroMicrobiota, International Research Program (IRP) INSERM/UCLouvain, France Belgium
- UCLouvain, Université catholique de Louvain, Institute of Experimental and Clinical Research IREC, 1200, Brussels, Belgium
| | - Justine Aussant
- Laboratoire Lescuyer, Research Department, 15 rue Le Corbusier, 17440, Aytré, France
| | - Emmanuel Barrat
- Laboratoire Lescuyer, Research Department, 15 rue Le Corbusier, 17440, Aytré, France
| | - Claude Knauf
- NeuroMicrobiota, International Research Program (IRP) INSERM/UCLouvain, France Belgium
- INSERM U1220, Institut de Recherche en Santé Digestive IRSD, Université Paul Sabatier, Toulouse III, CHU Purpan, Place Du Docteur Baylac, CS 60039, CEDEX 3, 31024 Toulouse, France
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Popescu MC, Haddock NL, Burgener EB, Rojas-Hernandez LS, Kaber G, Hargil A, Bollyky PL, Milla CE. The Inovirus Pf4 Triggers Antiviral Responses and Disrupts the Proliferation of Airway Basal Epithelial Cells. Viruses 2024; 16:165. [PMID: 38275975 PMCID: PMC10818373 DOI: 10.3390/v16010165] [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: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The inovirus Pf4 is a lysogenic bacteriophage of Pseudomonas aeruginosa (Pa). People with Cystic Fibrosis (pwCF) experience chronic airway infection with Pa and a significant proportion have high numbers of Pf4 in their airway secretions. Given the known severe damage in the airways of Pa-infected pwCF, we hypothesized a high Pf4 burden can affect airway healing and inflammatory responses. In the airway, basal epithelial cells (BCs) are a multipotent stem cell population critical to epithelium homeostasis and repair. We sought to investigate the transcriptional responses of BCs under conditions that emulate infection with Pa and exposure to high Pf4 burden. METHODS Primary BCs isolated from pwCF and wild-type (WT) donors were cultured in vitro and exposed to Pf4 or bacterial Lipopolysaccharide (LPS) followed by transcriptomic and functional assays. RESULTS We found that BCs internalized Pf4 and this elicits a strong antiviral response as well as neutrophil chemokine production. Further, we found that BCs that take up Pf4 demonstrate defective migration and proliferation. CONCLUSIONS Our findings are highly suggestive of Pf4 playing a role in the pathogenicity of Pa in the airways. These findings provide additional evidence for the ability of inoviruses to interact with mammalian cells and disrupt cell function.
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Affiliation(s)
- Medeea C. Popescu
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
- Immunology Program, Stanford University, Stanford, CA 94305, USA
| | - Naomi L. Haddock
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
- Immunology Program, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura S. Rojas-Hernandez
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gernot Kaber
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Aviv Hargil
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Paul L. Bollyky
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Carlos E. Milla
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Romero-Arguelles R, Tamez-Guerra P, González-Ochoa G, Romo-Sáenz CI, Gomez-Flores R, Flores-Mendoza L, Aros-Uzarraga E. Bifidobacterium longum and Chlorella sorokiniana Improve the IFN Type I-Mediated Antiviral Response in Rotavirus-Infected Cells. Microorganisms 2023; 11:1237. [PMID: 37317211 DOI: 10.3390/microorganisms11051237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 06/16/2023] Open
Abstract
Probiotics are effective to treat or prevent gastrointestinal infections, and microalgae have demonstrated important health-promoting effects and in some cases function as prebiotics. In this regard, the anti-rotavirus effect of Bifidobacterium longum and Chlorella sorokiniana by reducing viral infectivity is well known. However, their effect on immune response against rotavirus has not yet been investigated. Therefore, the aim of this study was to determine the role of Bifidobacterium longum and/or Chlorella sorokiniana in influencing an IFN type I-mediated antiviral response in rotavirus-infected cells. In pre-infection experiments, HT-29 cells were treated with B. longum and C. sorokiniana alone or in combination, followed by rotavirus infection, whereas in post-infection assays, HT-29 cells were treated after infection. The cells' mRNA was then purified to determine the relative expression level of IFN-α, IFN-β, and precursors of interferons such as RIG-I, IRF-3, and IRF-5 by qPCR. We showed that combination of B. longum and C. sorokiniana significantly increased IFN-α levels in pre-infection and IFN-β in post-infection assays, as compared with individual effects. Results indicate that B. longum, C. sorokiniana, or their combination improve cellular antiviral immune response.
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Affiliation(s)
- Ricardo Romero-Arguelles
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Patricia Tamez-Guerra
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Guadalupe González-Ochoa
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Navojoa 85880, Mexico
| | - César I Romo-Sáenz
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Ricardo Gomez-Flores
- Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | - Lilian Flores-Mendoza
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Navojoa 85880, Mexico
| | - Elizama Aros-Uzarraga
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Navojoa 85880, Mexico
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Zhu S, Liu Y, Liao M, Yang Y, Bai Y, Li N, Li S, Luan Y, Chen N. Evaluation of Reference Genes for Transcriptional Profiling in Two Cockroach Models. Genes (Basel) 2021; 12:genes12121880. [PMID: 34946836 PMCID: PMC8701133 DOI: 10.3390/genes12121880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 02/02/2023] Open
Abstract
The German cockroach, Blattella germanica, and the American cockroach, Periplaneta americana are the most common and synanthropic household pests of interest to public health. While they have increasingly served as model systems in hemimetabolous insects for studying many biological issues, there is still a lack of stable reference gene evaluation for reliable quantitative real-time PCR (qPCR) outputs and functional genomics. Here, we evaluated the expression variation of common insect reference genes, including the historically used actin, across various tissues and developmental stages, and also under experimental treatment conditions in these two species by using three individual algorithms (geNorm, BestKeeper, and NormFinder) and a comprehensive program (RefFinder). RPL32 in B. germanica and EF1α in P. americana showed the overall lowest variation among all examined samples. Based on the stability rankings by RefFinder, the optimal but varied reference genes under specific conditions were selected for qPCR normalization. In addition, the combination of RPL32 and EF1α was recommended for all the tested tissues and stages in B. germanica, whereas the combination of multiple reference genes was unfavorable in P. americana. This study provides a condition-specific resource of reference gene selection for accurate gene expression profiling and facilitating functional genomics in these two important cockroaches.
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Affiliation(s)
- Shen Zhu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514000, China
| | - Yongjun Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
| | - Mingtao Liao
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
| | - Yang Yang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
| | - Yu Bai
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
| | - Na Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514000, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514000, China
| | - Yunxia Luan
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514000, China
| | - Nan Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (S.Z.); (Y.L.); (M.L.); (Y.Y.); (Y.B.); (N.L.); (S.L.); (Y.L.)
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514000, China
- Correspondence:
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Ahannach S, Delanghe L, Spacova I, Wittouck S, Van Beeck W, De Boeck I, Lebeer S. Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples. iScience 2021; 24:103306. [PMID: 34765924 PMCID: PMC8571498 DOI: 10.1016/j.isci.2021.103306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/09/2021] [Accepted: 10/15/2021] [Indexed: 12/17/2022] Open
Abstract
Few validated protocols are available for large-scale collection, storage, and analysis of microbiome samples from the vagina, skin, and mouth. To prepare for a large-scale study on the female microbiome by remote self-sampling, we investigated the impact of sample collection, storage, and host DNA depletion on microbiome profiling. Vaginal, skin, and saliva samples were analyzed using 16S rRNA gene amplicon and metagenomic shotgun sequencing, and qPCR. Of the two tested storage buffers, the eNAT buffer could keep the microbial composition stable during various conditions. All three tested host DNA-depletion approaches showed a bias against Gram-negative taxa. However, using the HostZERO Microbial DNA and QIAamp DNA Microbiome kits, samples still clustered according to body site and not by depletion approach. Therefore, our study showed the effectiveness of these methods in depleting host DNA. Yet, a suitable approach is recommended for each habitat studied based on microbial composition. Lysis buffer keeps the microbial composition stable during various storage conditions Host DNA depletion introduces a larger bias toward Gram-negative taxa The HostZERO Microbial DNA kit performed best in human DNA depletion for metagenomics Body site-specific approach based on microbial composition is needed to minimize bias
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Affiliation(s)
- Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lize Delanghe
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Stijn Wittouck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Wannes Van Beeck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ilke De Boeck
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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Sasaki N, Takeuchi H, Kitano S, Irie S, Amano A, Matsusaki M. Dynamic analysis of Porphyromonas gingivalis invasion into blood capillaries during the infection process in host tissues using a vascularized three-dimensional human gingival model. Biomater Sci 2021; 9:6574-6583. [PMID: 34582534 DOI: 10.1039/d1bm00831e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Porphyromonas gingivalis, the pathogen of periodontal disease, is thought to be involved in various diseases throughout the body via gingival tissue blood capillaries. However, the dynamic analysis of the infection mechanism, particularly the deep invasion process of the gingival tissue, has not yet been elucidated because of the lack of both in vivo and in vitro models. In this study, we developed a vascularized three-dimensional (3D) gingival model with an epithelial barrier expressing cell-cell junctions using collagen microfibers (CMFs) to enable the dynamic analysis of the P. gingivalis invasion process. Lipid raft disruption experiments in the gingival epithelial cell layer demonstrated that P. gingivalis migrates into the deeper epithelium via the intercellular pathway rather than intracellular routes. P. gingivalis was shown to invade the 3D gingival model, being found inside blood capillaries during two days of culture. Notably, the number of bacteria had increased greatly at least two days later, whereas the mutant P. gingivalis lacking the cysteine proteases, gingipains, showed a significantly lower number of survivors. The secretion of interleukin-6 (IL-6) from the gingival tissue decreased during the two days of infection with the wild type P. gingivalis, but the opposite was found for the mutant suggesting that P. gingivalis infection disturbs IL-6 secretion at an early stage. By allowing the dynamic observation of the P. gingivalis invasion from the epithelial cell layer into the blood capillaries for the first time, this model will be a powerful tool for the development of novel therapeutics against periodontal infection related diseases.
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Affiliation(s)
- Naoko Sasaki
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroki Takeuchi
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Shiro Kitano
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. .,TOPPAN PRINTING CO., LTD, Japan
| | - Shinji Irie
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. .,TOPPAN PRINTING CO., LTD, Japan
| | - Atsuo Amano
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Michiya Matsusaki
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Rafieenia F, Nikkhah E, Nourmohammadi F, Hosseini S, Abdollahi A, Sharifi N, Aliakbarian M, Forghani Fard MM, Gholamin M, Abbaszadegan MR. Allogeneic tumor cell line-based vaccines: A good alternative to autologous and cancer stem cell vaccines in colorectal cancer. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1231-1239. [PMID: 35083010 PMCID: PMC8751741 DOI: 10.22038/ijbms.2021.56732.12671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/27/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Besides the uncertainty about colorectal cancer stem cell (CCSC) markers, isolating, purifying, and enriching CCSCs to produce CCSC vaccines is highly challenging. However, allogeneic vaccines developed from CRC cell lines can provide universal, comprehensive, inexpensive, simple, and fast approach to cancer treatment. MATERIALS AND METHODS CCSCs were isolated from human CRC tissue using the in vitro sphere formation assay and then characterized through gene expression analysis, in vivo and in vitro tumor formation assay, karyotyping, and surface marker detection. Subsequently, CCSCs and two CRC cell lines (HT-29 and SW-480) were inactivated with cisplatin (CDDP) and administrated as vaccines to the three groups of athymic C57BL/6 nude mice. Afterward, tumorigenesis was challenged with HT-29 cells. The antitumor effect of vaccines was evaluated by tumor and spleen examination and immune response analysis. The cytotoxic activity of splenocytes and serum levels of TGF-β and IFN-γ were measured by Calcein-AM cytotoxicity assay and enzyme-linked immunosorbent assay (ELISA), respectively. RESULTS The results of gene expression analysis showed that CCSCs are CD44+CD133-LGR5-. All vaccinations resulted in decreased tumor growth, spleen enlargement, enhanced serum level of IFN-γ and TGF-β, and increased cytotoxic activity of natural killer (NK) cells. The antitumor efficacy of the CCSC vaccine was not more than CRC cell line-based vaccines. Interestingly, the allogeneic SW-480 vaccine could effectively inhibit tumorigenesis. CONCLUSION Despite the great challenge in developing CCSC vaccines, allogeneic vaccines based on CRC cell lines can efficiently induce antitumor immunity in CRC.
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Affiliation(s)
- Fatemeh Rafieenia
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elham Nikkhah
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Susan Hosseini
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Abdollahi
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nurieh Sharifi
- Department of Pathology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Aliakbarian
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mehran Gholamin
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Fulvio F, Martinelli T, Paris R. Selection and validation of reference genes for RT-qPCR normalization in different tissues of milk thistle (Silybum marianum, Gaert.). Gene 2021; 768:145272. [PMID: 33122080 DOI: 10.1016/j.gene.2020.145272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/06/2020] [Accepted: 10/21/2020] [Indexed: 12/31/2022]
Abstract
Quantitative reverse transcription PCR is a sensitive technique for evaluating transcriptional profiles in different experimental datasets. To obtain a reliable quantification of the transcripts level, data normalization with stable reference genes is required. Stable reference genes are identified after analysis of their transcripts profile in every new experiment and species of interest. In Silybum marianum, a widely cultivated officinal plant, only few gene expression studies exist, and reference genes for RT-qPCR studies in the diverse plant tissues have never been investigated before. In this work, the expression stability of 10 candidate reference genes was evaluated in leaves, roots, stems and fruits of S. marianum grown under physiological environmental condition. The stability values for each candidate reference gene were calculated by four canonical statistical algorithms GeNorm, NormFinder, Bestkeeper and ΔCt method in different subsets of samples, then they were ranked with RefFinder from the most to the least suitable for normalization. Best combinations of reference genes are finally proposed for different experimental data sets, including all tissues, vegetative, and reproductive tissues separately. Three target genes putatively involved in important biosynthetic pathway leading to key metabolites in the fruits of milk thistle, such as silymarin and fatty acids, were analyzed with the chosen panels of reference genes, in comparison to the ones used in previous papers. To the best of our knowledge, this is the first report on a reliable and systematic identification and validation of the reference genes for RT-qPCR normalization to study gene expression in S. marianum.
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Affiliation(s)
- Flavia Fulvio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy
| | - Tommaso Martinelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy; Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Difesa e Certificazione, Via di Lanciola 12/A, Loc. Cascine del Riccio, 50125 Firenze, Italy
| | - Roberta Paris
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca Cerealicoltura e Colture Industriali, Via di Corticella 133, 40128 Bologna, Italy.
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10
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Reference gene selection for transcriptional profiling in Cryptocercus punctulatus, an evolutionary link between Isoptera and Blattodea. Sci Rep 2020; 10:22169. [PMID: 33335167 PMCID: PMC7746730 DOI: 10.1038/s41598-020-79030-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/26/2020] [Indexed: 11/21/2022] Open
Abstract
The subsocial life style and wood-feeding capability of Cryptocercus gives us an evolutionary key to unlock some outstanding questions in biology. With the advent of the Genomics Era, there is an unprecedented opportunity to address the evolution of eusociality and the acquisition of lignocellulases at the genetic level. However, to quantify gene expression, an appropriate normalization strategy is warranted to control for the non-specific variations among samples across different experimental conditions. To search for the internal references, 10 housekeeping genes from a gut transcriptome of a wood-feeding cockroach, Cryptocercus punctulatus, were selected as the candidates for the RT-qPCR analysis. The expression profiles of these candidates, including ACT, EF1α, GAPDH, HSP60, HSP70, αTUB, UBC, RPS18, ATPase and GST, were analyzed using a panel of analytical tools, including geNorm, NormFinder, BestKeeper, and comparative ΔCT method. RefFinder, a comprehensive ranking system integrating all four above-mentioned algorithms, rated ACT as the most stable reference gene for different developmental stages and tissues. Expression analysis of the target genes, Hex-1 and Cell-1, using the most or the least appropriate reference genes and a single or multiple normalizers signified this research. Our finding is the first step toward establishing a standardized RT-qPCR analysis in Cryptocercus.
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11
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Xu L, Luo H, Wang R, Wu WW, Phue JN, Shen RF, Juhl H, Wu L, Alterovitz WL, Simonyan V, Pelosof L, Rosenberg AS. Novel reference genes in colorectal cancer identify a distinct subset of high stage tumors and their associated histologically normal colonic tissues. BMC MEDICAL GENETICS 2019; 20:138. [PMID: 31409279 PMCID: PMC6693228 DOI: 10.1186/s12881-019-0867-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Background Reference genes are often interchangeably called housekeeping genes due to 1) the essential cellular functions their proteins provide and 2) their constitutive expression across a range of normal and pathophysiological conditions. However, given the proliferative drive of malignant cells, many reference genes such as beta-actin (ACTB) and glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) which play critical roles in cell membrane organization and glycolysis, may be dysregulated in tumors versus their corresponding normal controls Methods Because Next Generation Sequencing (NGS) technology has several advantages over hybridization-based technologies, such as independent detection and quantitation of transcription levels, greater sensitivity, and increased dynamic range, we evaluated colorectal cancers (CRC) and their histologically normal tissue counterparts by NGS to evaluate the expression of 21 “classical” reference genes used as normalization standards for PCR based methods. Seventy-nine paired tissue samples of CRC and their patient matched healthy colonic tissues were subjected to NGS analysis of their mRNAs. Results We affirmed that 17 out of 21 classical reference genes had upregulated expression in tumors compared to normal colonic epithelial tissue and dramatically so in some cases. Indeed, tumors were distinguished from normal controls in both unsupervised hierarchical clustering analyses (HCA) and principal component analyses (PCA). We then identified 42 novel potential reference genes with minimal coefficients of variation (CV) across 79 CRC tumor pairs. Though largely consistently expressed across tumors and normal control tissues, a subset of high stage tumors (HSTs) as well as some normal tissue samples (HSNs) located adjacent to these HSTs demonstrated dysregulated expression, thus identifying a subset of tumors with a potentially distinct and aggressive biological profile. Conclusion While classical CRC reference genes were found to be differentially expressed between tumors and normal controls, novel reference genes, identified via NGS, were more consistently expressed across malignant and normal colonic tissues. Nonetheless, a subset of HST had profound dysregulation of such genes as did many of the histologically normal tissues adjacent to such HSTs, indicating that the HSTs so distinguished may have unique biological properties and that their histologically normal tissues likely harbor a small population of microscopically undetected but metabolically active tumors. Electronic supplementary material The online version of this article (10.1186/s12881-019-0867-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lai Xu
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA. .,Office of Hematology and Oncology Products CDER, FDA, Silver Spring, MD, 20993, USA. .,, Silver Spring, USA.
| | - Helen Luo
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA
| | - Rong Wang
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA
| | - Wells W Wu
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | - Je-Nie Phue
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | | | - Leihong Wu
- OCS/NCTR/DBB, FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | | | | | - Lorraine Pelosof
- Office of Hematology and Oncology Products CDER, FDA, Silver Spring, MD, 20993, USA
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12
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Marin M, Holani R, Shah CB, Odeón A, Cobo ER. Cathelicidin modulates synthesis of Toll-like Receptors (TLRs) 4 and 9 in colonic epithelium. Mol Immunol 2017; 91:249-258. [PMID: 28988039 DOI: 10.1016/j.molimm.2017.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/12/2017] [Accepted: 09/21/2017] [Indexed: 12/13/2022]
Abstract
Cathelicidin are innate antimicrobial peptides with broad immunomodulatory functions; however, their role in regulating intestinal defenses is not well characterized. This study aimed to investigate the role of cathelicidin modulating expression of Toll-like receptors (TLRs) 4 and 9 in colonic epithelium in response to bacterial patterns. We demonstrated herein that intestinal epithelial cells, when primed by bacterial lipopolysaccharide (LPS), responded to cathelicidin by increased transcription and protein synthesis of TLR4. This cathelicidin-induced response required the interaction of LPS-TLR4 and activation of MAPK signalling pathways. However, cathelicidin blocked TLR9 responses induced by TLR9 ligand CpG oligodeoxynucleotide (CpG ODN) in these colonic epithelial cells. Modulations of TLRs triggered by cathelicidin in intestinal epithelium occurred mainly in the apical compartment of intestinal cells. Activation of TLR4 by ligands in combination with cathelicidin promoted CXCL8 chemokine secretion and epithelial antimicrobial defenses against Escherichia coli. We concluded that cathelicidin selectively modulated synthesis of TLR4 and 9 in intestinal epithelium, but only when cells were exposed to virulence factors, mostly from apical surfaces. Enhanced TLR4 expression promoted by cathelicidin in intestinal epithelium may be crucial for controlling enteric infectious diseases.
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Affiliation(s)
- Maia Marin
- National Scientific and Technical Research Council (CONICET), Argentina
| | - Ravi Holani
- Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Canada
| | | | - Anselmo Odeón
- Animal Production, Balcarce Experimental Station, National Institute of Agricultural Technology (INTA), Argentina
| | - Eduardo R Cobo
- Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Canada.
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Ruhe F, Olling A, Abromeit R, Rataj D, Grieschat M, Zeug A, Gerhard R, Alekov A. Overexpression of the Endosomal Anion/Proton Exchanger ClC-5 Increases Cell Susceptibility toward Clostridium difficile Toxins TcdA and TcdB. Front Cell Infect Microbiol 2017; 7:67. [PMID: 28348980 PMCID: PMC5346576 DOI: 10.3389/fcimb.2017.00067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 02/21/2017] [Indexed: 12/30/2022] Open
Abstract
Virulent C. difficile toxins TcdA and TcdB invade host intestinal epithelia by endocytosis and use the acidic environment of intracellular vesicles for further processing and activation. We investigated the role of ClC-5, a chloride/proton exchanger expressed in the endosomes of gastrointestinal epithelial cells, in the activation and processing of C. difficile toxins. Enhanced intoxication by TcdA and TcdB was observed in cells expressing ClC-5 but not ClC-4, another chloride/proton exchanger with similar function but different localization. In accordance with the established physiological function of ClC-5, its expression lowered the endosomal pH in HEK293T cells by approximately 0.6 units and enhanced approximately 5-fold the internalization of TcdA. In colon HT29 cells, 34% of internalized TcdA localized to ClC-5-containing vesicles defined by colocalization with Rab5, Rab4a, and Rab7 as early and early-to-late of endosomes but not as Rab11-containing recycling endosomes. Impairing the cellular uptake of TcdA by deleting the toxin CROPs domain did not abolish the effects of ClC-5. In addition, the transport-incompetent mutant ClC-5 E268Q similarly enhanced both endosomal acidification and intoxication by TcdA but facilitated the internalization of the toxin to a lower extent. These data suggest that ClC-5 enhances the cytotoxic action of C. difficile toxins by accelerating the acidification and maturation of vesicles of the early and early-to-late endosomal system. The dispensable role of electrogenic ion transport suggests that the voltage-dependent nonlinear capacitances of mammalian CLC transporters serve important physiological functions. Our data shed light on the intersection between the endocytotic cascade of host epithelial cells and the internalization pathway of the large virulence C. difficile toxins. Identifying ClC-5 as a potential specific host ion transporter hijacked by toxins produced by pathogenic bacteria widens the horizon of possibilities for novel therapies of life-threatening gastrointestinal infections.
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Affiliation(s)
- Frederike Ruhe
- Institute for Neurophysiology, Hannover Medical SchoolHannover, Germany
| | - Alexandra Olling
- Institute for Toxicology, Hannover Medical SchoolHannover, Germany
| | - Rasmus Abromeit
- Institute for Neurophysiology, Hannover Medical SchoolHannover, Germany
| | - Dennis Rataj
- Institute for Toxicology, Hannover Medical SchoolHannover, Germany
| | | | - Andre Zeug
- Institute for Neurophysiology, Hannover Medical SchoolHannover, Germany
| | - Ralf Gerhard
- Institute for Toxicology, Hannover Medical SchoolHannover, Germany
| | - Alexi Alekov
- Institute for Neurophysiology, Hannover Medical SchoolHannover, Germany
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14
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Wen S, Chen X, Xu F, Sun H. Validation of Reference Genes for Real-Time Quantitative PCR (qPCR) Analysis of Avibacterium paragallinarum. PLoS One 2016; 11:e0167736. [PMID: 27942007 PMCID: PMC5152862 DOI: 10.1371/journal.pone.0167736] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/18/2016] [Indexed: 11/18/2022] Open
Abstract
Real-time quantitative reverse transcription PCR (qRT-PCR) offers a robust method for measurement of gene expression levels. Selection of reliable reference gene(s) for gene expression study is conducive to reduce variations derived from different amounts of RNA and cDNA, the efficiency of the reverse transcriptase or polymerase enzymes. Until now reference genes identified for other members of the family Pasteurellaceae have not been validated for Avibacterium paragallinarum. The aim of this study was to validate nine reference genes of serovars A, B, and C strains of A. paragallinarum in different growth phase by qRT-PCR. Three of the most widely used statistical algorithms, geNorm, NormFinder and ΔCT method were used to evaluate the expression stability of reference genes. Data analyzed by overall rankings showed that in exponential and stationary phase of serovar A, the most stable reference genes were gyrA and atpD respectively; in exponential and stationary phase of serovar B, the most stable reference genes were atpD and recN respectively; in exponential and stationary phase of serovar C, the most stable reference genes were rpoB and recN respectively. This study provides recommendations for stable endogenous control genes for use in further studies involving measurement of gene expression levels.
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Affiliation(s)
- Shuxiang Wen
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaoling Chen
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fuzhou Xu
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Huiling Sun
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- * E-mail:
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15
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Krzystek-Korpacka M, Hotowy K, Czapinska E, Podkowik M, Bania J, Gamian A, Bednarz-Misa I. Serum availability affects expression of common house-keeping genes in colon adenocarcinoma cell lines: implications for quantitative real-time PCR studies. Cytotechnology 2016; 68:2503-2517. [PMID: 27339468 PMCID: PMC5101321 DOI: 10.1007/s10616-016-9971-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/18/2016] [Indexed: 11/29/2022] Open
Abstract
Careful selection of housekeeping genes (HKG) is prerequisite to yield sound qPCR results. HKG expression varies in response to hypoxia but the effect of manipulations of serum availability, a common experimental procedure, remains unknown. Also, no data on HKG expression stability across colon adenocarcinoma lines that would aid selection of normalizers suitable for studies involving several lines are available. Thus, we evaluated the effect of serum availability on the expression of commonly used HKG (ACTB, B2M, GAPDH, GUSB, HPRT1, IPO8, MRPL19, PGK1, PPIA, RPLP0, RPS23, SDHA, TBP, UBC, and YWHAZ) in seven colon adenocarcinoma cell lines (Caco-2, DLD-1, HCT116, HT29, Lovo, SW480, and SW620). Sets of stably expressed line-specific and pan-line HKG were validated against absolutely quantified CDKN1A, TP53, and MDK transcripts. Both serum availability and line type affected HKG expression. UBC was fourfold down-regulated and HPRT1 1.75-fold up-regulated in re-fed HT29 cultures. Line-to-line variability in HKG expression was more pronounced than that caused by altering serum availability and could be found even between isogenic cell lines. PPIA, RPLP0, YWHAZ, and IPO8 were repeatedly highly ranked while ACTB, B2M, UBC, and PGK1 were ranked poorly. Normalization against PPIA/RPLP0/SDHA was found optimal for studies involving various colon adenocarcinoma cell lines subjected to manipulations of serum availability. We found HKG expression to vary, more pronouncedly by line type than growth conditions with significant differences also between isogenic cell lines. Although using line-specific normalizers remains optimal, a set of pan-line HKG that yields good estimation of relative expression of target genes was proposed.
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Affiliation(s)
| | - Katarzyna Hotowy
- Department of Medical Biochemistry, Wroclaw Medical University, ul. Chalubinskiego 10, 50-368, Wroclaw, Poland
| | - Elzbieta Czapinska
- Department of Medical Biochemistry, Wroclaw Medical University, ul. Chalubinskiego 10, 50-368, Wroclaw, Poland
| | - Magdalena Podkowik
- Department of Food Hygiene and Consumer Health, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Andrzej Gamian
- Department of Medical Biochemistry, Wroclaw Medical University, ul. Chalubinskiego 10, 50-368, Wroclaw, Poland.,Wroclaw Research Center EIT+, Wroclaw, Poland
| | - Iwona Bednarz-Misa
- Department of Medical Biochemistry, Wroclaw Medical University, ul. Chalubinskiego 10, 50-368, Wroclaw, Poland
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Chapman JR, Waldenström J. With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies. PLoS One 2015; 10:e0141853. [PMID: 26555275 PMCID: PMC4640531 DOI: 10.1371/journal.pone.0141853] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/13/2015] [Indexed: 12/20/2022] Open
Abstract
The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with β-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.
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Affiliation(s)
- Joanne R. Chapman
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
- * E-mail:
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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