1
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Irie N, Warita K, Tashiro J, Zhou Y, Ishikawa T, Oltvai ZN, Warita T. Expression of housekeeping genes varies depending on mevalonate pathway inhibition in cancer cells. Heliyon 2023; 9:e18017. [PMID: 37501994 PMCID: PMC10368838 DOI: 10.1016/j.heliyon.2023.e18017] [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: 01/19/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/29/2023] Open
Abstract
Statins have anticancer effects and may be used as anticancer agents via drug repositioning. In reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays, the internal reference gene must not be affected by any experimental conditions. As statins exert a wide range of effects on cells by inhibiting the mevalonate pathway, it is possible that statin treatment might alter the expression of housekeeping genes used as internal reference genes, thereby misleading the assessment of obtained gene expression data. Here, we evaluated the expression stability of internal reference genes in atorvastatin-treated cancer cell lines. We treated both statin-sensitive and statin-resistant cancer cell lines with atorvastatin at seven different concentrations and performed RT-qPCR on 15 housekeeping genes whose expression stability was then assessed using five different algorithms. In both statin-sensitive and statin-resistant cancer cell lines, atorvastatin affected the expression of certain internal reference genes in a dose-dependent and cancer cell line-dependent manner; therefore, caution should be exercised when comparing target gene expression between cells. Our findings emphasize the importance of the validation of internal reference genes in gene expression analyses in drug treatment-based cancer research.
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Affiliation(s)
- Nanami Irie
- Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669‐1330, Japan
| | - Katsuhiko Warita
- Department of Veterinary Anatomy, School of Veterinary Medicine, Tottori University, 4-101 Koyama Minami, Tottori, Tottori 680-8553, Japan
| | - Jiro Tashiro
- Department of Veterinary Anatomy, School of Veterinary Medicine, Tottori University, 4-101 Koyama Minami, Tottori, Tottori 680-8553, Japan
| | - Yaxuan Zhou
- Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669‐1330, Japan
| | - Takuro Ishikawa
- Department of Anatomy, School of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi 480-1195, Japan
| | - Zoltán N. Oltvai
- Department of Pathology and Laboratory Medicine, University of Rochester, 601 Elmwood Ave., Rochester, NY 14642, USA
| | - Tomoko Warita
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669‐1330, Japan
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2
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Cirrincione AM, Reimonn CA, Harrison BJ, Rieger S. Longitudinal RNA Sequencing of Skin and DRG Neurons in Mice with Paclitaxel-Induced Peripheral Neuropathy. DATA 2022; 7. [PMID: 36248261 PMCID: PMC9564132 DOI: 10.3390/data7060072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Paclitaxel-induced peripheral neuropathy is a condition of nerve degeneration induced by chemotherapy, which afflicts up to 70% of treated patients. Therapeutic interventions are unavailable due to an incomplete understanding of the underlying mechanisms. We previously discovered that major physiological changes in the skin underlie paclitaxel-induced peripheral neuropathy in zebrafish and rodents. The precise molecular mechanisms are only incompletely understood. For instance, paclitaxel induces the upregulation of MMP-13, which, when inhibited, prevents axon degeneration. To better understand other gene regulatory changes induced by paclitaxel, we induced peripheral neuropathy in mice following intraperitoneal injection either with vehicle or paclitaxel every other day four times total. Skin and dorsal root ganglion neurons were collected based on distinct behavioural responses categorised as “pain onset” (d4), “maximal pain” (d7), “beginning of pain resolution” (d11), and “recovery phase” (d23) for comparative longitudinal RNA sequencing. The generated datasets validate previous discoveries and reveal additional gene expression changes that warrant further validation with the goal to aid in the development of drugs that prevent or reverse paclitaxel-induced peripheral neuropathy.
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Affiliation(s)
| | - Cassandra A. Reimonn
- Department of Biomedical Sciences, University of New England, Biddeford, ME 04005, USA
| | - Benjamin J. Harrison
- Department of Biomedical Sciences, University of New England, Biddeford, ME 04005, USA
- Correspondence: (B.J.H.); (S.R.)
| | - Sandra Rieger
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Correspondence: (B.J.H.); (S.R.)
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3
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Lee YM, Cho H, Kim RO, In S, Kim SJ, Won EJ. Validation of reference genes for quantitative real-time PCR in chemical exposed and at different age's brackish water flea Diaphanosoma celebensis. Sci Rep 2021; 11:23691. [PMID: 34880360 PMCID: PMC8654955 DOI: 10.1038/s41598-021-03098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), a primary approach for evaluating gene expression, requires an appropriate normalization strategy to confirm relative gene expression levels by comparison, and rule out variations that might occur in analytical procedures. The best option is to use a reference gene whose expression level is stable across various experimental conditions to compare the mRNA levels of a target gene. However, there is limited information on how the reference gene is differentially expressed at different ages (growth) in small invertebrates with notable changes such as molting. In this study, expression profiles of nine candidate reference genes from the brackish water flea, Diaphanosoma celebensis, were evaluated under diverse exposure to toxicants and according to growth. As a result, four different algorithms showed similar stabilities of genes for chemical exposures in the case of limited conditions using the same developmental stage (H2A was stable, whereas Act was fairly unstable in adults), while the results according to age showed a significantly different pattern in suite of candidate reference genes. This affected the results of genes EcRA and GST, which are involved in development and detoxification mechanisms, respectively. Our finding is the first step towards establishing a standardized real-time qRT-PCR analysis of this environmentally important invertebrate that has potential for aquatic ecotoxicology, particularly in estuarine environments.
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Affiliation(s)
- Young-Mi Lee
- Department of Biotechnology, College of Convergence Engineering, Sangmyung University, Seoul, 03016, Republic of Korea.
| | - Hayoung Cho
- Department of Biotechnology, College of Convergence Engineering, Sangmyung University, Seoul, 03016, Republic of Korea
| | - Ryeo-Ok Kim
- Department of Biotechnology, College of Convergence Engineering, Sangmyung University, Seoul, 03016, Republic of Korea.,Division of Chemical Research, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Korea
| | - Soyeon In
- Department of Biotechnology, College of Convergence Engineering, Sangmyung University, Seoul, 03016, Republic of Korea
| | - Se-Joo Kim
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Eun-Ji Won
- Department of Marine Science and Convergent Technology, Hanyang University, Ansan, 15588, Republic of Korea.
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4
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Development of a 3':5' digital PCR assay to determine horse mRNA integrity. Anal Biochem 2021; 626:114217. [PMID: 33939972 DOI: 10.1016/j.ab.2021.114217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Accurate tools to measure RNA integrity are essential to obtain reliable gene expression data. The reverse transcription quantitative PCR (RT-qPCR) based 3':5' assay permits a direct determination of messenger RNA (mRNA) integrity. However, the use of standard curves and the possible effect of PCR inhibitors make this method cumbersome and prone to variation, especially in small samples. Here we developed a triplex digital PCR (dPCR) 3':5' assay for assessing RNA integrity in equine samples as rapid and simple alternative to RT-qPCR. This dPCR assay not only provides a straight forward analysis of the mRNA integrity, but also of its quantity.
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The exon junction complex core factor eIF4A3 is a key regulator of HPV16 gene expression. Biosci Rep 2021; 41:228142. [PMID: 33760064 PMCID: PMC8026852 DOI: 10.1042/bsr20203488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/04/2021] [Accepted: 03/24/2021] [Indexed: 01/06/2023] Open
Abstract
High-risk human papillomavirus (hrHPVs), particularly HPV16 and HPV18, are the etiologic factors of ano-genital cancers and some head and neck squamous cell carcinomas (HNSCCs). Viral E6 and E7 oncoproteins, controlled at both transcriptional and post-transcriptional levels, drive hrHPVs-induced carcinogenesis. In the present study, we investigated the implication of the DEAD-box helicase eukaryotic translation initiation factor 4A3 (eIF4A3,) an Exon Junction Complex factor, in the regulation of HPV16 gene expression. Our data revealed that the depletion of the factor eIF4A3 up-regulated E7 oncoprotein levels. We also showed that the inhibition of the nonsense-mediated RNA decay (NMD) pathway, resulted in the up-regulation of E7 at both RNA and protein levels. We therefore proposed that HPV16 transcripts might present different susceptibilities to NMD and that this pathway could play a key role in the levels of expression of these viral oncoproteins during the development of HPV-related cancers.
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de Waard AA, Verkerk T, Hoefakker K, van der Steen DM, Jongsma ML, Melamed Kadosh D, Bliss S, de Ru AH, Admon A, van Veelen PA, Griffioen M, Heemskerk MH, Spaapen RM. Healthy cells functionally present TAP-independent SSR1 peptides: implications for selection of clinically relevant antigens. iScience 2021; 24:102051. [PMID: 33554062 PMCID: PMC7847959 DOI: 10.1016/j.isci.2021.102051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/27/2020] [Accepted: 01/07/2021] [Indexed: 01/02/2023] Open
Abstract
Tumors with an impaired transporter associated with antigen processing (TAP) present several endoplasmic reticulum-derived self-antigens on HLA class I (HLA-I) which are absent on healthy cells. Selection of such TAP-independent antigens for T cell-based immunotherapy should include analysis of their expression on healthy cells to prevent therapy-induced adverse toxicities. However, it is unknown how the absence of clinically relevant antigens on healthy cells needs to be validated. Here, we monitored TAP-independent antigen presentation on various healthy cells after establishing a T cell tool recognizing a TAP-independent signal sequence receptor 1-derived antigen. We found that most but not all healthy cells present this antigen under normal and inflammatory conditions, indicating that TAP-independent antigen presentation is a variable phenomenon. Our data emphasize the necessity of extensive testing of a wide variety of healthy cell types to define clinically relevant TAP-independent antigens that can be safely targeted by immunotherapy. The ER-resident SSR1 holds an antigenic peptide that is processed independently of TAP TAP-independent peptide presentation is functional in healthy cell types TAP-independent SSR1-derived antigen presentation varies between healthy cells This exposes safety and efficacy risks of clinical TAP-independent peptide targeting
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Affiliation(s)
- Antonius A. de Waard
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
| | - Tamara Verkerk
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
| | - Kelly Hoefakker
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
| | | | - Marlieke L.M. Jongsma
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, ZA 2333, The Netherlands
| | | | - Sophie Bliss
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, LUMC, Leiden, ZA 2333, The Netherlands
| | - Arie Admon
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, LUMC, Leiden, ZA 2333, The Netherlands
| | | | | | - Robbert M. Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, CX 1066, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, CX 1066, The Netherlands
- Corresponding author
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7
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Yonker LM, Neilan AM, Bartsch Y, Patel AB, Regan J, Arya P, Gootkind E, Park G, Hardcastle M, St John A, Appleman L, Chiu ML, Fialkowski A, De la Flor D, Lima R, Bordt EA, Yockey LJ, D'Avino P, Fischinger S, Shui JE, Lerou PH, Bonventre JV, Yu XG, Ryan ET, Bassett IV, Irimia D, Edlow AG, Alter G, Li JZ, Fasano A. Pediatric Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Clinical Presentation, Infectivity, and Immune Responses. J Pediatr 2020; 227:45-52.e5. [PMID: 32827525 PMCID: PMC7438214 DOI: 10.1016/j.jpeds.2020.08.037] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVES As schools plan for re-opening, understanding the potential role children play in the coronavirus infectious disease 2019 (COVID-19) pandemic and the factors that drive severe illness in children is critical. STUDY DESIGN Children ages 0-22 years with suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection presenting to urgent care clinics or being hospitalized for confirmed/suspected SARS-CoV-2 infection or multisystem inflammatory syndrome in children (MIS-C) at Massachusetts General Hospital were offered enrollment in the Massachusetts General Hospital Pediatric COVID-19 Biorepository. Enrolled children provided nasopharyngeal, oropharyngeal, and/or blood specimens. SARS-CoV-2 viral load, ACE2 RNA levels, and serology for SARS-CoV-2 were quantified. RESULTS A total of 192 children (mean age, 10.2 ± 7.0 years) were enrolled. Forty-nine children (26%) were diagnosed with acute SARS-CoV-2 infection; an additional 18 children (9%) met the criteria for MIS-C. Only 25 children (51%) with acute SARS-CoV-2 infection presented with fever; symptoms of SARS-CoV-2 infection, if present, were nonspecific. Nasopharyngeal viral load was highest in children in the first 2 days of symptoms, significantly higher than hospitalized adults with severe disease (P = .002). Age did not impact viral load, but younger children had lower angiotensin-converting enzyme 2 expression (P = .004). Immunoglobulin M (IgM) and Immunoglobulin G (IgG) to the receptor binding domain of the SARS-CoV-2 spike protein were increased in severe MIS-C (P < .001), with dysregulated humoral responses observed. CONCLUSIONS This study reveals that children may be a potential source of contagion in the SARS-CoV-2 pandemic despite having milder disease or a lack of symptoms; immune dysregulation is implicated in severe postinfectious MIS-C.
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Key Words
- ace2, angiotensin-converting enzyme
- covid-19, coronavirus disease-19
- ipo8, importin-8
- irb, institutional review board
- mgh, massachusetts general hospital
- mis-c, multisystem inflammatory syndrome in children
- nt-probnb, n-terminal pro b-type natriuretic peptide
- rbd, receptor binding domain
- rsv, respiratory syncytial virus
- sars-cov-2, severe acute respiratory syndrome coronavirus 2
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Affiliation(s)
- Lael M Yonker
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA.
| | - Anne M Neilan
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA; Department of Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Yannic Bartsch
- Harvard Medical School, Boston, MA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA
| | - Ankit B Patel
- Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Department of Medicine, Renal Division, Boston, MA
| | - James Regan
- Department of Infectious Diseases, Brigham and Women's Hospital, Boston, MA
| | - Puneeta Arya
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | | | - Grace Park
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Margot Hardcastle
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Anita St John
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Lori Appleman
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Michelle L Chiu
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | | | - Denis De la Flor
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Rosiane Lima
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Evan A Bordt
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Laura J Yockey
- Department of Internal Medicine, Massachusetts General Hospital, Boston, MA; Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA
| | - Paolo D'Avino
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA
| | - Stephanie Fischinger
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA
| | - Jessica E Shui
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Paul H Lerou
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Joseph V Bonventre
- Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Department of Medicine, Renal Division, Boston, MA
| | - Xu G Yu
- Harvard Medical School, Boston, MA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA; Department of Infectious Diseases, Brigham and Women's Hospital, Boston, MA
| | - Edward T Ryan
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA; Department of Internal Medicine, Massachusetts General Hospital, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Ingrid V Bassett
- Harvard Medical School, Boston, MA; Department of Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Daniel Irimia
- Harvard Medical School, Boston, MA; Center for Engineering in Medicine, Department of Surgery, Boston, MA
| | - Andrea G Edlow
- Harvard Medical School, Boston, MA; Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA; Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Massachusetts General Hospital Boston, Boston, MA
| | - Galit Alter
- Harvard Medical School, Boston, MA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA
| | - Jonathan Z Li
- Harvard Medical School, Boston, MA; Department of Infectious Diseases, Brigham and Women's Hospital, Boston, MA
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
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8
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Ogorevc J, Poklukar K, Dovč P. Establishment and characterization of proliferating primary cultures of equine epidermal keratinocytes. Anim Biotechnol 2019; 32:282-291. [PMID: 31736400 DOI: 10.1080/10495398.2019.1687091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Skin-derived tissue cultures are a useful model to study molecular mechanisms of skin renewal and pathogenesis of dermal diseases. Horses often suffer from skin diseases, skin trauma and problems with proper wound healing, which could be improved by in vitro grown keratinocyte grafts. Herein we describe establishment and characterization of equine skin-derived primary cell cultures, using enzymatic and explant methods. The established cell lines of primary equine keratinocytes (peK) maintained high proliferative capacity for over five passages and expressed different epithelial/keratinocyte-specific markers. Characterization of the primary culture was performed in parallel with localization studies of the markers in the skin histological sections, using commercially available antibodies. Relative expression of typical differentiation stage-specific markers was determined in the established cell lines, using RT-qPCR. Basal (proliferating) keratinocytes were the predominant cell type in the established cell lines, but low expression of post-mitotic keratinocyte markers was also detected. Differences in marker expression were observed neither between the peK originating from two different animals nor between the peK established with two different methods (enzymatically or by explanting). The described methods in combination with the suggested characterization and differentiation markers are suitable for establishment of proliferating peK and evaluation of their differentiation status.
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Affiliation(s)
- Jernej Ogorevc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Klavdija Poklukar
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia.,Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
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9
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Reliable Reference Genes for Gene Expression Assessment in Tendon-Derived Cells under Inflammatory and Pro-Fibrotic/Healing Stimuli. Cells 2019; 8:cells8101188. [PMID: 31581587 PMCID: PMC6830081 DOI: 10.3390/cells8101188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 01/04/2023] Open
Abstract
Tendon cells (TCs) are important for homeostatic maintenance in the healthy tendon and to promote tissue healing after injury. Further, resident and rare populations of tendon stem/progenitor cells, located at various sites within the tendon, contribute to tendon recovery by differentiating into repairing TCs. Gene expression analysis, through quantitative reverse-transcription polymerase chain reaction (qRT-PCR), constitutes a useful tool to study cellular responses, including the transition from initial inflammation to healing processes. A critical step required for data normalization is the choice of reliable reference genes (RGs), a process highly underestimated in tendon biology. In this study, the suitability of five commonly used RGs (ACTB, B2M, GAPDH, HPRT1, and RPLP0) was evaluated using TCs samples cultured in both standard and progenitor-enriching conditions, as well as under either inflammatory (IFNγ + TNFα) or pro-fibrotic/healing (CTGF) stimulation. The stability of the candidate RGs was computationally determined using NormFinder, geNorm, BestKeeper, and DeltaCt applets. Overall, ACTB resulted as the most stable RG on the basis of the integration of each gene weight, whereas B2M and RPLP0 performed poorly. To further validate ACTB’s optimal performance, we evaluated the expression of ICAM1, coding for an immune-related cell surface glycoprotein, and COL1A1, encoding collagen type I that is the main component of the tendon extracellular matrix (ECM), both known to be modulated by inflammation. The expression of both genes was heavily affected by the RGs used. Consequently, when analyzing gene expression in tendon-derived cells subjected to various stimulatory protocols, the use of a suitable RG should be considered carefully. On the basis of our results, ACTB can be reliably used when analyzing different TC types exposed to pathological conditions.
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10
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Tarrant AM, Nilsson B, Hansen BW. Molecular physiology of copepods - from biomarkers to transcriptomes and back again. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:230-247. [DOI: 10.1016/j.cbd.2019.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 12/31/2022]
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11
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El-Sherbiny YM, Psarras A, Md Yusof MY, Hensor EMA, Tooze R, Doody G, Mohamed AAA, McGonagle D, Wittmann M, Emery P, Vital EM. A novel two-score system for interferon status segregates autoimmune diseases and correlates with clinical features. Sci Rep 2018; 8:5793. [PMID: 29643425 PMCID: PMC5895784 DOI: 10.1038/s41598-018-24198-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/23/2018] [Indexed: 11/10/2022] Open
Abstract
Measurement of type I interferon (IFN-I) has potential to diagnose and stratify autoimmune diseases, but existing results have been inconsistent. Interferon-stimulated-gene (ISG) based methods may be affected by the modularity of the ISG transcriptome, cell-specific expression, response to IFN-subtypes and bimodality of expression. We developed and clinically validated a 2-score system (IFN-Score-A and -B) using Factor Analysis of 31 ISGs measured by TaqMan selected from 3-IFN-annotated modules. We evaluated these scores using in-vitro IFN stimulation as well as in sorted cells then clinically validated in a cohort of 328 autoimmune disease patients and healthy controls. ISGs varied in response to IFN-subtypes and both scores varied between cell subsets. IFN-Score-A differentiated Systemic Lupus Erythematosus (SLE) from both Rheumatoid Arthritis (RA) and Healthy Controls (HC) (both p < 0.001), while IFN-Score-B differentiated SLE and RA from HC (both p < 0.001). In SLE, both scores were associated with cutaneous and hematological (all p < 0.05) but not musculoskeletal disease activity. Comparing with bimodal (IFN-high/low) classification, significant differences in IFN-scores were found between diagnostic groups within the IFN-high group. Our continuous 2-score system is more clinically relevant than a simple bimodal classification of IFN status. This system should allow improvement in diagnosis, stratification, and therapy in IFN-mediated autoimmunity.
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Affiliation(s)
- Y M El-Sherbiny
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - A Psarras
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - M Y Md Yusof
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - E M A Hensor
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - R Tooze
- Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - G Doody
- Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - A A A Mohamed
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Department of Rheumatology and Rehabilitation, Faculty of Medicine, Assiut University, Asyut, Egypt
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - D McGonagle
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - M Wittmann
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - P Emery
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - E M Vital
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK.
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12
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Dzaki N, Azzam G. Assessment of Aedes albopictus reference genes for quantitative PCR at different stages of development. PLoS One 2018; 13:e0194664. [PMID: 29554153 PMCID: PMC5858815 DOI: 10.1371/journal.pone.0194664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/07/2018] [Indexed: 11/23/2022] Open
Abstract
Members of the Aedes genus of mosquitoes are widely recognized as vectors of viral diseases. Ae.albopictus is its most invasive species, and are known to carry viruses such as Dengue, Chikugunya and Zika. Its emerging importance puts Ae.albopictus on the forefront of genetic interaction and evolution studies. However, a panel of suitable reference genes specific for this insect is as of now undescribed. Nine reference genes, namely ACT, eEF1-γ, eIF2α, PP2A, RPL32, RPS17, PGK1, ILK and STK were evaluated. Expression patterns of the candidate reference genes were observed in a total of seventeen sample types, separated by stage of development and age. Gene stability was inferred from obtained quantification data through three widely cited evaluation algorithms i.e. BestKeeper, geNorm, and NormFinder. No single gene showed a satisfactory degree of stability throughout all developmental stages. Therefore, we propose combinations of PGK and ILK for early embryos; RPL32 and RPS17 for late embryos, all four larval instars, and pupae samples; eEF1-γ with STK for adult males; eEF1-γ with RPS17 for non-blood fed females; and eEF1-γ with eIF2α for both blood-fed females and cell culture. The results from this study should be able to provide a more informed selection of normalizing genes during qPCR in Ae.albopictus.
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Affiliation(s)
- Najat Dzaki
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Vector Control and Research Unit, School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- * E-mail:
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13
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Kong F, Zhang W, Qiao L, Li Q, Li H, Cao J, He W, Dong C, He Y, He L, Liu L, Fu W, Liu L, Li Z, Wang Y. Establishment and quality evaluation of a glioma biobank in Beijing Tiantan Hospital. PeerJ 2018; 6:e4450. [PMID: 29576945 PMCID: PMC5855883 DOI: 10.7717/peerj.4450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/13/2018] [Indexed: 01/01/2023] Open
Abstract
Background We established a glioma biobank at Beijing Tiantan Hospital in November, 2010. Specialized residents have been trained to collect, store and manage the biobank in accordance with standard operating procedures. Methods One hundred samples were selected to evaluate the quality of glioma samples stored in the liquid nitrogen tank during different periods (from 2011 to 2015) by morphological examination, RNA integrity determination, DNA integrity determination and housekeeping gene expression determination. Results The majority of samples (95%) had high RNA quality for further analysis with RIN ≥6. Quality of DNA of all samples were stable without significant degradation. Conclusion Storage conditions of our biobank are suitable for long-term (at least five years) sample preservation with high molecular quality.
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Affiliation(s)
- Fanhong Kong
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenli Zhang
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin Qiao
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qi Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Haowen Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jingli Cao
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenyan He
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chengya Dong
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanjiao He
- Neuropathological department, Beijing Neurosugical Institute, Capital Medical University, Beijing, China
| | - Lu He
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Li Liu
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Weilun Fu
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lijun Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zirui Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yajie Wang
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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14
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Steinbach A, Winter J, Reuschenbach M, Blatnik R, Klevenz A, Bertrand M, Hoppe S, von Knebel Doeberitz M, Grabowska AK, Riemer AB. ERAP1 overexpression in HPV-induced malignancies: A possible novel immune evasion mechanism. Oncoimmunology 2017; 6:e1336594. [PMID: 28811980 DOI: 10.1080/2162402x.2017.1336594] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 01/17/2023] Open
Abstract
Immune evasion of tumors poses a major challenge for immunotherapy. For human papillomavirus (HPV)-induced malignancies, multiple immune evasion mechanisms have been described, including altered expression of antigen processing machinery (APM) components. These changes can directly influence epitope presentation and thus T-cell responses against tumor cells. To date, the APM had not been studied systematically in a large array of HPV+ tumor samples. Therefore in this study, systematic expression analysis of the APM was performed on the mRNA and protein level in a comprehensive collection of HPV16+ cell lines. Subsequently, HPV+ cervical tissue samples were examined by immunohistochemistry. ERAP1 (endoplasmic reticulum aminopeptidase 1) was the only APM component consistently altered - namely overexpressed - in HPV16+ tumor cell lines. ERAP1 was also found to be overexpressed in cervical intraepithelial neoplasia and cervical cancer samples; expression levels were increasing with disease stage. On the functional level, the influence of ERAP1 expression levels on HPV16 E7-derived epitope presentation was investigated by mass spectrometry and in cytotoxicity assays with HPV16-specific T-cell lines. ERAP1 overexpression did not cause a complete destruction of any of the HPV epitopes analyzed, however, an influence of ERAP1 overexpression on the presentation levels of certain HPV epitopes could be demonstrated by HPV16-specific CD8+ T-cells. These showed enhanced killing toward HPV16+ CaSki cells whose ERAP1 expression had been attenuated to normal levels. ERAP1 overexpression may thus represent a novel immune evasion mechanism in HPV-induced malignancies, in cases when presentation of clinically relevant epitopes is reduced by overactivity of this peptidase.
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Affiliation(s)
- Alina Steinbach
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Jan Winter
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miriam Reuschenbach
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Renata Blatnik
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Alexandra Klevenz
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miriam Bertrand
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie Hoppe
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | | | - Agnieszka K Grabowska
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika B Riemer
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
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15
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Lima L, Gaiteiro C, Peixoto A, Soares J, Neves M, Santos LL, Ferreira JA. Reference Genes for Addressing Gene Expression of Bladder Cancer Cell Models under Hypoxia: A Step Towards Transcriptomic Studies. PLoS One 2016; 11:e0166120. [PMID: 27835695 PMCID: PMC5106008 DOI: 10.1371/journal.pone.0166120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/24/2016] [Indexed: 11/18/2022] Open
Abstract
Highly aggressive, rapidly growing tumors contain significant areas of hypoxia or anoxia as a consequence of inadequate and/or irregular blood supply. During oxygen deprivation, tumor cells withstand a panoply of adaptive responses, including a shift towards anaerobic metabolism and the reprogramming of the transcriptome. One of the major mediators of the transcriptional hypoxic response is the hypoxia-inducible factor 1 (HIF-1), whose stabilization under hypoxia acts as an oncogenic stimulus contributing to chemotherapy resistance, invasion and metastasis. Gene expression analysis by qRT-PCR is a powerful tool for cancer cells phenotypic characterization. Nevertheless, as cells undergo a severe transcriptome remodeling.in response to oxygen deficit, the precise identification of reference genes poses a significant challenge for hypoxic studies. Herein, we aim to establish the best reference genes for studying the effects of hypoxia on bladder cancer cells. Accordingly, three bladder cancer cell lines (T24, 5637, and HT1376) representative of two distinct carcinogenesis pathways to invasive cancer (FGFR3/CCND1 and E2F3/RB1) were used. Additionally, we have explored the most suitable control gene when addressing the influence of Deferoxamine Mesilate salt (DFX), an iron chelator often used to avoid the proteasomal degradation of HIF-1α, acting as an hypoxia-mimetic agent. Using bioinformatics tools (GeNorm and NormFinder), we have elected B2M and HPRT as the most stable genes for all cell lines and experimental conditions out of a panel of seven putative candidates (HPRT, ACTB, 18S, GAPDH, TBP, B2M, and SDHA). These observations set the molecular basis for future studies addressing the effect of hypoxia and particularly HIF-1α in bladder cancer cells.
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Affiliation(s)
- Luís Lima
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- * E-mail:
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
| | - Manuel Neves
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- Health School of University of Fernando Pessoa, 4249-004, Porto, Portugal
- Department of Surgical Oncology, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group – Research Center, Portuguese Institute of Oncology of Porto (IPO-Porto), 4200-072, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
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16
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Woollard WJ, Kalaivani NP, Jones CL, Roper C, Tung L, Lee JJ, Thomas BR, Tosi I, Ferreira S, Beyers CZ, McKenzie RCT, Butler RM, Lorenc A, Whittaker SJ, Mitchell TJ. Independent Loss of Methylthioadenosine Phosphorylase (MTAP) in Primary Cutaneous T-Cell Lymphoma. J Invest Dermatol 2016; 136:1238-1246. [PMID: 26872600 DOI: 10.1016/j.jid.2016.01.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 12/07/2015] [Accepted: 01/20/2016] [Indexed: 10/22/2022]
Abstract
Methylthioadenosine phosphorylase (MTAP) and the tumor suppressor genes CDKN2A-CDKN2B are frequently deleted in malignancies. The specific role of MTAP in cutaneous T-cell lymphoma subgroups, mycosis fungoides (MF) and Sézary syndrome (SS), is unknown. In 213 skin samples from patients with MF/SS, MTAP copy number loss (34%) was more frequent than CDKN2A (12%) in all cutaneous T-cell lymphoma stages using quantitative reverse transcription PCR. Importantly, in early stage MF, MTAP loss occurred independently of CDKN2A loss in 37% of samples. In peripheral blood mononuclear cells from patients with SS, codeletion with CDKN2A occurred in 18% of samples but loss of MTAP alone was uncommon. In CD4(+) cells from SS, reduced MTAP mRNA expression correlated with MTAP copy number loss (P < 0.01) but reduced MTAP expression was also detected in the absence of copy number loss. Deep sequencing of MTAP/CDKN2A-CDKN2B loci in 77 peripheral blood mononuclear cell DNA samples from patients with SS did not show any nonsynonymous mutations, but read-depth analysis suggested focal deletions consistent with MTAP and CDKN2A copy number loss detected with quantitative reverse transcription PCR. In a cutaneous T-cell lymphoma cell line, promoter hypermethylation was shown to downregulate MTAP expression and may represent a mechanism of MTAP inactivation. In conclusion, our findings suggest that there may be selection in early stages of MF for MTAP deletion within the cutaneous tumor microenvironment.
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Affiliation(s)
- Wesley J Woollard
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Nithyha P Kalaivani
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Christine L Jones
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Catherine Roper
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Lam Tung
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jae Jin Lee
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Bjorn R Thomas
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Isabella Tosi
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Silvia Ferreira
- Viapath, Skin Tumour Unit, St John's Institute of Dermatology, Guy's Hospital, London, UK
| | - Carl Z Beyers
- Viapath, Skin Tumour Unit, St John's Institute of Dermatology, Guy's Hospital, London, UK
| | - Robert C T McKenzie
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Rosie M Butler
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Anna Lorenc
- Transformational Bioinformatics, NIHR Research Biomedical Research Center at Guy's and St Thomas' Hospital Foundation Trust and Kings College London, London, UK
| | - Sean J Whittaker
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Tracey J Mitchell
- St John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK.
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17
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Borowska D, Rothwell L, Bailey RA, Watson K, Kaiser P. Identification of stable reference genes for quantitative PCR in cells derived from chicken lymphoid organs. Vet Immunol Immunopathol 2016; 170:20-4. [PMID: 26872627 DOI: 10.1016/j.vetimm.2016.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 12/20/2022]
Abstract
Quantitative polymerase chain reaction (qPCR) is a powerful technique for quantification of gene expression, especially genes involved in immune responses. Although qPCR is a very efficient and sensitive tool, variations in the enzymatic efficiency, quality of RNA and the presence of inhibitors can lead to errors. Therefore, qPCR needs to be normalised to obtain reliable results and allow comparison. The most common approach is to use reference genes as internal controls in qPCR analyses. In this study, expression of seven genes, including β-actin (ACTB), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-glucuronidase (GUSB), TATA box binding protein (TBP), α-tubulin (TUBAT) and 28S ribosomal RNA (r28S), was determined in cells isolated from chicken lymphoid tissues and stimulated with three different mitogens. The stability of the genes was measured using geNorm, NormFinder and BestKeeper software. The results from both geNorm and NormFinder were that the three most stably expressed genes in this panel were TBP, GAPDH and r28S. BestKeeper did not generate clear answers because of the highly heterogeneous sample set. Based on these data we will include TBP in future qPCR normalisation. The study shows the importance of appropriate reference gene normalisation in other tissues before qPCR analysis.
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Affiliation(s)
- D Borowska
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom.
| | - L Rothwell
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - R A Bailey
- Aviagen Ltd., Edinburgh EH28 8SZ, United Kingdom
| | - K Watson
- Aviagen Ltd., Edinburgh EH28 8SZ, United Kingdom
| | - P Kaiser
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
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18
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dos Santos O, de Vargas Rigo G, Frasson AP, Macedo AJ, Tasca T. Optimal Reference Genes for Gene Expression Normalization in Trichomonas vaginalis. PLoS One 2015; 10:e0138331. [PMID: 26393928 PMCID: PMC4579074 DOI: 10.1371/journal.pone.0138331] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 08/28/2015] [Indexed: 01/13/2023] Open
Abstract
Trichomonas vaginalis is the etiologic agent of trichomonosis, the most common non-viral sexually transmitted disease worldwide. This infection is associated with several health consequences, including cervical and prostate cancers and HIV acquisition. Gene expression analysis has been facilitated because of available genome sequences and large-scale transcriptomes in T. vaginalis, particularly using quantitative real-time polymerase chain reaction (qRT-PCR), one of the most used methods for molecular studies. Reference genes for normalization are crucial to ensure the accuracy of this method. However, to the best of our knowledge, a systematic validation of reference genes has not been performed for T. vaginalis. In this study, the transcripts of nine candidate reference genes were quantified using qRT-PCR under different cultivation conditions, and the stability of these genes was compared using the geNorm and NormFinder algorithms. The most stable reference genes were α-tubulin, actin and DNATopII, and, conversely, the widely used T. vaginalis reference genes GAPDH and β-tubulin were less stable. The PFOR gene was used to validate the reliability of the use of these candidate reference genes. As expected, the PFOR gene was upregulated when the trophozoites were cultivated with ferrous ammonium sulfate when the DNATopII, α-tubulin and actin genes were used as normalizing gene. By contrast, the PFOR gene was downregulated when the GAPDH gene was used as an internal control, leading to misinterpretation of the data. These results provide an important starting point for reference gene selection and gene expression analysis with qRT-PCR studies of T. vaginalis.
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Affiliation(s)
- Odelta dos Santos
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Amanda Piccoli Frasson
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Alexandre José Macedo
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tiana Tasca
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- * E-mail:
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19
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Mound A, Malaisse J, De Vuyst É, Hayez A, Lambert de Rouvroit C, Pittelkow MR, Poumay Y. Epidermal reference genes at the forefront of data interpretation. Exp Dermatol 2015; 24:738-9. [PMID: 26186391 DOI: 10.1111/exd.12811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Yves Poumay
- URPHYM-Narilis, University of Namur, Namur, Belgium
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20
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Beer L, Mlitz V, Gschwandtner M, Berger T, Narzt MS, Gruber F, Brunner PM, Tschachler E, Mildner M. Bioinformatics approach for choosing the correct reference genes when studying gene expression in human keratinocytes. Exp Dermatol 2015; 24:742-7. [PMID: 25980460 DOI: 10.1111/exd.12759] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2015] [Indexed: 12/27/2022]
Abstract
Reverse transcription polymerase chain reaction (qRT-PCR) has become a mainstay in many areas of skin research. To enable quantitative analysis, it is necessary to analyse expression of reference genes (RGs) for normalization of target gene expression. The selection of reliable RGs therefore has an important impact on the experimental outcome. In this study, we aimed to identify and validate the best suited RGs for qRT-PCR in human primary keratinocytes (KCs) over a broad range of experimental conditions using the novel bioinformatics tool 'RefGenes', which is based on a manually curated database of published microarray data. Expression of 6 RGs identified by RefGenes software and 12 commonly used RGs were validated by qRT-PCR. We assessed whether these 18 markers fulfilled the requirements for a valid RG by the comprehensive ranking of four bioinformatics tools and the coefficient of variation (CV). In an overall ranking, we found GUSB to be the most stably expressed RG, whereas the expression values of the commonly used RGs, GAPDH and B2M were significantly affected by varying experimental conditions. Our results identify RefGenes as a powerful tool for the identification of valid RGs and suggest GUSB as the most reliable RG for KCs.
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Affiliation(s)
- Lucian Beer
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Veronika Mlitz
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Maria Gschwandtner
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Tanja Berger
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Marie-Sophie Narzt
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory for Biotechnology of Skin Aging, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Florian Gruber
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory for Biotechnology of Skin Aging, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Patrick M Brunner
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Michael Mildner
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
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21
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Gapdh gene expression is modulated by inflammatory arthritis and is not suitable for qPCR normalization. Inflammation 2015; 37:1059-69. [PMID: 24493325 DOI: 10.1007/s10753-014-9829-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gene expression studies are fundamental for the understanding of complex diseases, providing new insights into the pathogenic process and new tools for diagnostic and patient stratification. Gene profiling studies by real-time PCR require the use of reference genes for normalization and an appropriate validation is essential for accurate results. We performed a comprehensive assessment of six common housekeeping genes in the K/BxN serum-induced arthritis model in mice. Classical statistics and NormFinder analyses pointed out Gapdh as the less stable and therefore unsuitable as a reference control. Gapdh was considerably down-regulated in arthritic joints and therefore produced an overestimation of transcriptional changes. Hptr, B2m, and Rpl13a showed the most constant expression. Collectively our data advise against the use of Gapdh in gene expression studies in the acute phase of the K/BxN model and adds a cautionary note on the need to validate the reference genes for reliable, comparable, and reproducible results.
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22
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Lohoefer F, Reeps C, Lipp C, Rudelius M, Haertl F, Matevossian E, Zernecke A, Eckstein HH, Pelisek J. Quantitative expression and localization of cysteine and aspartic proteases in human abdominal aortic aneurysms. Exp Mol Med 2014; 46:e95. [PMID: 24833013 PMCID: PMC3972792 DOI: 10.1038/emm.2014.20] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 10/24/2013] [Accepted: 12/26/2013] [Indexed: 11/17/2022] Open
Abstract
Cysteine and aspartic proteases possess high elastolytic activity and might contribute to the degradation of the abdominal aortic aneurysm (AAA) wall. The aim of this study was to analyze, in detail, the proteases (cathepsins B, D, K, L and S, and inhibitor cystatin C) found in human AAA and healthy aortic tissue samples. The vessel walls from AAA patients (n=36) and nonaneurysmal aortae (n=10) were retrieved using conventional surgical repair and autopsy methods. Serum samples from the same AAA patients and 10 healthy volunteers were also collected. Quantitative expression analyses were performed at the mRNA level using real-time reverse transcriptase-PCR (RT–PCR). Furthermore, analyses at the protein level included western blot and immunoprecipitation analyses. Cellular sources of cysteine/aspartic proteases and cystatin C were identified by immunohistochemistry (IHC). All cysteine/aspartic proteases and cystatin C were detected in the AAA and control samples. Using quantitative RT–PCR, a significant increase in expression was observed for cathepsins B (P=0.021) and L (P=0.018), compared with the controls. Cathepsin B and cystatin C were also detected in the serum of AAA patients. Using IHC, smooth muscle cells (SMCs) and macrophages were positive for all of the tested cathepsins, as well as cystatin C; in addition, the lymphocytes were mainly positive for cathepsin B, followed by cathepsins D and S. All cysteine/aspartic proteases analyzed in our study were detected in the AAA and healthy aorta. The highest expression was found in macrophages and SMCs. Consequently, cysteine/aspartic proteases might play a substantial role in AAA.
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Affiliation(s)
- Fabian Lohoefer
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Christian Reeps
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Christina Lipp
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Martina Rudelius
- Institute of Pathology, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Felix Haertl
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Edouard Matevossian
- Department of Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Alma Zernecke
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Hans-Henning Eckstein
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Jaroslav Pelisek
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
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Schildberg T, Rauh J, Bretschneider H, Stiehler M. Identification of suitable reference genes in bone marrow stromal cells from osteoarthritic donors. Stem Cell Res 2013; 11:1288-98. [PMID: 24080205 DOI: 10.1016/j.scr.2013.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 08/20/2013] [Accepted: 08/31/2013] [Indexed: 12/28/2022] Open
Abstract
Bone marrow stromal cells (BMSCs) are key cellular components for musculoskeletal tissue engineering strategies. Furthermore, recent data suggest that BMSCs are involved in the development of Osteoarthritis (OA) being a frequently occurring degenerative joint disease. Reliable reference genes for the molecular evaluation of BMSCs derived from donors exhibiting OA as a primary co-morbidity have not been reported on yet. Hence, the aim of the study was to identify reference genes suitable for comparative gene expression analyses using OA-BMSCs. Passage 1 bone marrow derived BMSCs were isolated from n=13 patients with advanced stage idiopathic hip osteoarthritis and n=15 age-matched healthy donors. The expression of 31 putative reference genes was analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using a commercially available TaqMan(®) assay. Calculating the coefficient of variation (CV), mRNA expression stability was determined and afterwards validated using geNorm and NormFinder algorithms. Importin 8 (IPO8), TATA box binding protein (TBP), and cancer susceptibility candidate 3 (CASC3) were identified as the most stable reference genes. Notably, commonly used reference genes, e.g. beta-actin (ACTB) and beta-2-microglobulin (B2M) were among the most unstable genes. For normalization of gene expression data of OA-BMSCs the combined use of IPO8, TBP, and CASC3 gene is recommended.
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Affiliation(s)
- Theresa Schildberg
- University Centre for Orthopaedics & Trauma Surgery and Centre for Translational Bone, Joint & Soft Tissue Research, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany.
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Pestov NB, Korneenko TV, Shakhparonov MI, Modyanov NN. Postnatal regulation of X,K-ATPases in rat skin and conserved lateroapical polarization of Na,K-ATPase in vertebrate epidermis. Exp Dermatol 2013; 22:423-5. [PMID: 23651441 DOI: 10.1111/exd.12149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2013] [Indexed: 11/26/2022]
Abstract
Development of epidermis creates stratified epithelium with different sets of ion-transporting enzymes in its layers. We have characterized expression of Na,K- and H,K-ATPase α and β subunits and FXYD isoforms in rat skin. Maturation of rat skin from newborn to adult is associated with an increase in FXYD4 and a decrease of Na,K-ATPase α1-isoform, ATP1B4 and FXYD6 transcripts. Na,K-ATPase of rat epidermis is represented predominantly by α1 and β3 isoforms. Keratinization is associated with the loss of the Na,K-ATPase α-subunit and an enrichment of αng. Na,K-ATPase α1 is abundant in the innermost layer, stratum basale, where it is lacking in basal membranes, thus indicating lateroapical polarization of Na,K-ATPase. Immunocytochemical detection of Na,K-ATPase in Xenopus laevis skin shows that cellular and subcellular localization of the enzyme has a pattern highly similar to that of mammals: basolateral in glandular epithelium and lateroapical in epidermis.
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