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Englisch CN, Kirstein E, Diebolt CM, Wagner M, Tschernig T. Distribution of TRPC3 and TRPC6 in the human exocrine and endocrine pancreas. Pathol Res Pract 2024; 260:155403. [PMID: 38870712 DOI: 10.1016/j.prp.2024.155403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/03/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Expression and function of TRPC3 and TRPC6 in the pancreas is a controversial topic. Investigation in human tissue is seldom. We aimed to provide here a detailed description of the distribution of TRPC3 and TRPC6 in the human exocrine and endocrine pancreas. METHODS We collected healthy samples from cadavers (n = 4) and visceral surgery (n = 4) to investigate the respective expression profiles using immunohistochemical tracing with knockout-validated antibodies. RESULTS TRPC3- and TRPC6-proteins were detected in different pancreatic structures including acinar cells, as well as epithelial ductal cells from intercalate, intralobular, and interlobular ducts. Respective connective tissue layers appeared unstained. Endocrine islets of Langerhans were clearly and homogenously immunolabeled by the anti-TRPC3 and anti-TRPC6 antibodies. Insular α, β, γ, and δ cells were conclusively stained, although no secure differentiation of cell types was performed. CONCLUSIONS Due to aforementioned antibody specificity verification, protein expression in the immunolabeled localizations can be accepted. Our study in human tissue supports previous investigations especially with respect to acinar and insular α and β cells, while other localizations are here reported for the first time to express TRPC3 and TRPC6, ultimately warranting further research.
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Affiliation(s)
- Colya N Englisch
- Institute for Anatomy and Cell Biology, Saarland University, 66421 Homburg, Saarland, Germany.
| | - Emilie Kirstein
- Institute for Anatomy and Cell Biology, Saarland University, 66421 Homburg, Saarland, Germany
| | - Coline M Diebolt
- Institute for Anatomy and Cell Biology, Saarland University, 66421 Homburg, Saarland, Germany
| | - Mathias Wagner
- Department of General and Special Pathology, Saarland University Medical Center, 66421 Homburg, Saarland, Germany
| | - Thomas Tschernig
- Institute for Anatomy and Cell Biology, Saarland University, 66421 Homburg, Saarland, Germany
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2
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Thompson SD, Pichika R, Lieber RL, Lavasani M. Extracting high-quality RNA from formaldehyde-fixed naturally aged neuromusculoskeletal tissues. Biotechniques 2024; 76:153-160. [PMID: 38334498 PMCID: PMC10988388 DOI: 10.2144/btn-2023-0092] [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: 09/12/2023] [Accepted: 12/22/2023] [Indexed: 02/10/2024] Open
Abstract
Modern approaches to discovering molecular mechanisms and validating treatments for age-related neuromusculoskeletal dysfunction typically rely on high-throughput transcriptome analysis. Previously harvested and fixed tissues offer an incredible reservoir of untapped molecular information. However, obtaining RNA from such formaldehyde-fixed neuromusculoskeletal tissues, especially fibrotic aged tissues, is technically challenging and often results in RNA degradation, chemical modification and yield reduction, prohibiting further analysis. Therefore, we developed a protocol to extract high-quality RNA from formaldehyde-fixed brain, cartilage, muscle and peripheral nerve isolated from naturally aged mice. Isolated RNA produced reliable gene expression data comparable to fresh and flash-frozen tissues and was sensitive enough to detect age-related changes, making our protocol valuable to researchers in the field of aging.
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Affiliation(s)
- Seth D Thompson
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Graduate Program, Northwestern University, Chicago, IL 60611, USA
| | - Rajeswari Pichika
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr VA Medical Center, Maywood, IL 60153, USA
| | - Richard L Lieber
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr VA Medical Center, Maywood, IL 60153, USA
| | - Mitra Lavasani
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Graduate Program, Northwestern University, Chicago, IL 60611, USA
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3
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Kaul NL, Diebolt CM, Meier C, Tschernig T. Transient receptor potential channel 3 in human liver and gallbladder - An investigation in body donors. Ann Anat 2023; 250:152150. [PMID: 37633502 DOI: 10.1016/j.aanat.2023.152150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/28/2023]
Abstract
Since the discovery of TRP proteins in 1969, during studies of the fruit fly Drosophila melanogaster, interest around them and the subfamily of TRPC channels has remained high. TRPC3 was able to be detected in a number of organs in rodents, such as rats and mice, and also in various human tissues. For the most part, these investigations were carried out using gene expression of TRPC3. Further work has already confirmed the relevance of TRPC3 in the context of neurodegenerative diseases, such as spinocerebellar ataxia, and carcinogenic entities, such as ovarian carcinoma. An association with TRPC3 has also been demonstrated for diseases that affect the liver. In order to confirm the expression of TRPC3 in the human liver, this study uses samples taken from eight (n = 8) fixated human body donors and analyzed with immunohistochemistry. In accordance with the macroscopic anatomy of the organs, six samples (n = 6) of liver tissue and three (n = 3) of gallbladder tissue were obtained. TRPC3 was clearly detected in all liver and gallbladder samples examined. Thus, it is not unlikely that TRPC3 plays a role in the extensive metabolic processes of the liver and could also serve as a target for pharmacological interventions in an imbalance of calcium homeostasis.
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Affiliation(s)
- Nele Leonie Kaul
- Institute of Anatomy and Cell Biology, Saarland University, Medical Campus, Homburg, Saar, Germany
| | - Coline M Diebolt
- Institute of Anatomy and Cell Biology, Saarland University, Medical Campus, Homburg, Saar, Germany
| | - Carola Meier
- Institute of Anatomy and Cell Biology, Saarland University, Medical Campus, Homburg, Saar, Germany
| | - Thomas Tschernig
- Institute of Anatomy and Cell Biology, Saarland University, Medical Campus, Homburg, Saar, Germany.
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4
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Deepa PR, Nalini V, Surianarayanan M, Krishnakumar S. Towards safer non-volatile tissue fixatives: Evaluation of choline-based ionic liquids for fixing ocular tissues. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111777. [PMID: 33352431 DOI: 10.1016/j.ecoenv.2020.111777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/19/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Volatile organic chemicals (VOCs) are routinely used for processing biological tissue samples in clinical laboratories. Recognizing their serious health and environmental impacts, a few non-volatile green solvents (choline based ionic liquids, ILs) were evaluated as tissue fixatives here. Microscopic evaluation of histo-morphology, fixation and staining quality, and macromolecular integrity (DNA and proteins) were assessed in human eye tissues (sclera, choroid, retinal layers and retinal pigmented epithelium, eyelid and orbit) after IL-fixation. Formalin-fixed tissues were used as standard reference. Microscopic examination revealed favorable histomorphology, tissue fixation and staining characteristics in most tissues immersed in ILs. Time taken to fix, and stability over a period of time (24 h, 48 h, 1 week, 1 month) was also recorded. Electrophoretic analysis revealed stability of cellular proteins and nucleic acids in IL-fixed scleral tissues. Heterogeneity in tissue fixation property relative to the type of ocular tissue, duration of fixation and storage, warrant further design and optimization of ILs to fix biological tissues. The simple cholinium salts based ILs tested here show favorable potential for tissue fixation application, and as an alternative approach to the use of VOCs, towards sustainable biomedical practice.
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Affiliation(s)
- P R Deepa
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani 333 031, Rajasthan, India.
| | - V Nalini
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani 333 031, Rajasthan, India; L&T Department of Ocular Pathology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, 18, College Road, 600 006 Chennai, India
| | - M Surianarayanan
- Cell for Industrial Safety and Risk Analysis (CISRA), Central Leather Research Institute (CSIR-CLRI), Adyar, Chennai, India
| | - S Krishnakumar
- L&T Department of Ocular Pathology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, 18, College Road, 600 006 Chennai, India.
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Restoration of an academic historical gross pathology collection—refreshed impact on current medical teaching? Virchows Arch 2018; 473:219-228. [DOI: 10.1007/s00428-018-2369-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/07/2018] [Accepted: 04/29/2018] [Indexed: 01/19/2023]
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Ceciliani F, Roccabianca P, Giudice C, Lecchi C. Application of post-genomic techniques in dog cancer research. MOLECULAR BIOSYSTEMS 2017; 12:2665-79. [PMID: 27345606 DOI: 10.1039/c6mb00227g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Omics techniques have been widely applied to veterinary science, although mostly on farm animal productions and infectious diseases. In canine oncology, on the contrary, the use of omics methodologies is still far behind. This review presents the most recent achievement in the application of postgenomic techniques, such as transcriptomics, proteomics, and metabolomics, to canine cancer research. The protocols to recover material suitable for omics analyses from formalin-fixed, paraffin-embedded tissues are presented, and omics applications for biomarker discovery and their potential for cancer diagnostics in veterinary medicine are highlighted.
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Affiliation(s)
- F Ceciliani
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - P Roccabianca
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - C Giudice
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - C Lecchi
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
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Daud S, Nambiar P, Hossain MZ, Saub R, Ab Murat N, Mohamed A, Abdul Razak F, Bakri MM. Removal of the apical one-third of the root improves the fixation process of the dental pulp in teeth. J Histotechnol 2016. [DOI: 10.1080/01478885.2016.1164377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Gress V, Wolfesberger B, Fuchs-Baumgartinger A, Nedorost N, Saalmüller A, Schwendenwein I, Rütgen BC, Hammer SE. Characterization of the T-cell receptor gamma chain gene rearrangements as an adjunct tool in the diagnosis of T-cell lymphomas in the gastrointestinal tract of cats. Res Vet Sci 2016; 107:261-266. [DOI: 10.1016/j.rvsc.2016.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/01/2016] [Accepted: 07/02/2016] [Indexed: 02/09/2023]
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Korzhevskii DE, Sukhorukova EG, Kirik OV, Grigorev IP. Immunohistochemical demonstration of specific antigens in the human brain fixed in zinc-ethanol-formaldehyde. Eur J Histochem 2015; 59:2530. [PMID: 26428887 PMCID: PMC4598599 DOI: 10.4081/ejh.2015.2530] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/20/2015] [Accepted: 07/23/2015] [Indexed: 11/25/2022] Open
Abstract
Tissue fixation is critical for immunohistochemistry. Recently, we developed a zinc-ethanol-formalin fixative (ZEF), and the present study was aimed to assess the applicability of the ZEF for the human brain histology and immunohistochemistry and to evaluate the detectability of different antigens in the human brain fixed with ZEF. In total, 11 antigens were tested, including NeuN, neuron-specific enolase, GFAP, Iba-1, calbindin, calretinin, choline acetyltransferase, glutamic acid decarboxylase (GAD65), tyrosine hydroxylase, synaptophysin, and α-tubulin. The obtained data show that: i) the ZEF has potential for use in general histological practice, where detailed characterization of human brain morphology is needed; ii) the antigens tested are well-preserved in the human brain specimens fixed in the ZEF.
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Affiliation(s)
- D E Korzhevskii
- Laboratory of Functional Morphology of the Central and Peripheral Nervous System, Institute of Experimental Medicine.
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10
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Koch A, Saran S, Tran DDH, Klebba-Färber S, Thiesler H, Sewald K, Schindler S, Braun A, Klopfleisch R, Tamura T. Murine precision-cut liver slices (PCLS): a new tool for studying tumor microenvironments and cell signaling ex vivo. Cell Commun Signal 2014; 12:73. [PMID: 25376987 PMCID: PMC4226874 DOI: 10.1186/s12964-014-0073-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/23/2014] [Indexed: 11/29/2022] Open
Abstract
Background One of the most insidious characteristics of cancer is its spread to and ability to compromise distant organs via the complex process of metastasis. Communication between cancer cells and organ-resident cells via cytokines/chemokines and direct cell-cell contacts are key steps for survival, proliferation and invasion of metastasized cancer cells in organs. Precision-cut liver slices (PCLS) are considered to closely reflect the in vivo situation and are potentially useful for studying the interaction of cancer cells with liver-resident cells as well as being a potentially useful tool for screening anti-cancer reagents. Application of the PCLS technique in the field of cancer research however, has not yet been well developed. Results We established the mouse PCLS system using perfluorodecalin (PFD) as an artificial oxygen carrier. Using this system we show that the adherence of green fluorescent protein (GFP) labeled MDA-MB-231 (highly invasive) cells to liver tissue in the PCLS was 5-fold greater than that of SK-BR-3 (less invasive) cells. In addition, we generated PCLS from THOC5, a member of transcription/export complex (TREX), knockout (KO) mice. The PCLS still expressed Gapdh or Albumin mRNAs at normal levels, while several chemokine/growth factor or metalloprotease genes, such as Cxcl12, Pdgfa, Tgfb, Wnt11, and Mmp1a genes were downregulated more than 2-fold. Interestingly, adhesion of cancer cells to THOC5 KO liver slices was far less (greater than 80% reduction) than to wild-type liver slices. Conclusion Mouse PCLS cultures in the presence of PFD may serve as a useful tool for screening local adherence and invasiveness of individual cancer cells, since single cells can be observed. This method may also prove useful for identification of genes in liver-resident cells that support cancer invasion by using PCLS from transgenic liver.
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Affiliation(s)
- Alexandra Koch
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Shashank Saran
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Doan Duy Hai Tran
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Sabine Klebba-Färber
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Hauke Thiesler
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Katherina Sewald
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin Atemwegspharmakologie, Nikolai-Fuchs-Str.1, D-30625, Hannover, Germany.
| | - Susann Schindler
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin Atemwegspharmakologie, Nikolai-Fuchs-Str.1, D-30625, Hannover, Germany.
| | - Armin Braun
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin Atemwegspharmakologie, Nikolai-Fuchs-Str.1, D-30625, Hannover, Germany.
| | - Robert Klopfleisch
- Institute of Veterinary Pathology, Freie Universitaet Berlin, Robert-von-Ostertag- Str. 15, D-14163, Berlin, Germany.
| | - Teruko Tamura
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
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11
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Granato A, Giantin M, Ariani P, Carminato A, Baratto C, Zorzan E, Vascellari M, Bozzato E, Dacasto M, Mutinelli F. DNA and RNA isolation from canine oncologic formalin-fixed, paraffin-embedded tissues for downstream "-omic" analyses: possible or not? J Vet Diagn Invest 2014; 26:117-24. [PMID: 24398906 DOI: 10.1177/1040638713509378] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues represent a unique source of archived biological material, but obtaining suitable DNA and RNA for retrospective "-omic" investigations is still challenging. In the current study, canine tumor FFPE blocks were used to 1) compare common commercial DNA and RNA extraction kits; 2) compare target gene expression measured in FFPE blocks and biopsies stored in a commercial storage reagent; 3) assess the impact of fixation time; and 4) perform biomolecular investigations on archival samples chosen according to formalin fixation times. Nucleic acids yield and quality were determined by spectrophotometer and capillary electrophoresis, respectively. Quantitative real-time polymerase chain reaction assays for the following genes: BCL-2-associated X protein, B-cell lymphoma extra large, antigen identified by monoclonal antibody Ki-67, proto-oncogene c-KIT (c-kit). Two internal control genes (Golgin A1 and canine transmembrane BAX inhibitor motif containing 4), together with direct sequencing of c-kit exons 8, 9, 11, and 17, were used as end points. Differences in DNA/RNA yield and purity were noticed among the commercial kits. Nucleic acids (particularly RNA) extracted from paraffin blocks were degraded, even at lower fixation times. Compared to samples held in the commercial storage reagent, archived tissues showed a poorer amplification. Therefore, a gold standard protocol for DNA/RNA isolation from canine tumor FFPE blocks for molecular investigations is still troublesome. More standardized storage conditions, including time between sample acquisition and fixation, fixation time, and sample thickness, are needed to guarantee the preservation of nucleic acids and, then, their possible use in retrospective transcriptomic analysis.
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Affiliation(s)
- Anna Granato
- 1Anna Granato, Veterinary and Public Health Institute, viale Università 10, 35020 Legnaro, Padua, Italy.
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Ostrowski A, Nordmeyer D, Mundhenk L, Fluhr JW, Lademann J, Graf C, Rühl E, Gruber AD. AHAPS-functionalized silica nanoparticles do not modulate allergic contact dermatitis in mice. NANOSCALE RESEARCH LETTERS 2014; 9:524. [PMID: 25276110 PMCID: PMC4177380 DOI: 10.1186/1556-276x-9-524] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/16/2014] [Indexed: 05/16/2023]
Abstract
Allergic contact dermatitis (ACD) is a common skin disease in people and may become a potential site of exposure to nanoparticles (NP). Silica nanoparticles (SiO2-NP) possess a promising potential for various medical and non-medical applications, including normal and diseased skin as target organs. However, it has been shown that negatively charged SiO2-NP may act as proinflammatory adjuvant in allergic diseases. The effect of topical SiO2-NP exposure on preexisting ACD has not been studied to date although this reflects a common in vivo situation. Of particular interest are the potential effects of positively charged N-(6-aminohexyl)-aminopropyltrimethoxysilane (AHAPS)-functionalized SiO2-NP which are promising candidates for delivery systems, including gene delivery into the skin. Here, the effects of such AHAPS-functionalized SiO2-NP (55 ± 6 nm in diameter) were studied in an oxazolone-induced ACD model in SKH1 mice and compared to ACD mice treated with vehicle only. The clinical course of the disease was assessed by monitoring of the transepidermal water loss (TEWL) and the erythema. In histologic and morphometric analyses, the distribution of particles, the degree of inflammation, epidermal thickness, and the inflammatory infiltrate were characterized and quantified by standard and special histological stains as well as immunohistochemistry for CD3+ lymphocytes. To assess possible systemic effects, serum immunoglobulin E (IgE) was determined by enzyme-linked immunosorbent assay. Following administration of AHAPS-SiO2-NP for five consecutive days, no effects were observed in all clinical, histologic, morphometric, and molecular parameters investigated. In conclusion, positively charged AHAPS-SiO2-NP seem not to affect the course of ACD during exposure for 5 days.
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Affiliation(s)
- Anja Ostrowski
- Institute of Veterinary Pathology, Freie Universität Berlin, Robert-von-Ostertag-Str. 15, 14163 Berlin, Germany
| | - Daniel Nordmeyer
- Institute of Chemistry and Biochemistry - Physical and Theoretical Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Lars Mundhenk
- Institute of Veterinary Pathology, Freie Universität Berlin, Robert-von-Ostertag-Str. 15, 14163 Berlin, Germany
| | - Joachim W Fluhr
- Department of Dermatology, Venerology and Allergology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jürgen Lademann
- Department of Dermatology, Venerology and Allergology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christina Graf
- Institute of Chemistry and Biochemistry - Physical and Theoretical Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Eckart Rühl
- Institute of Chemistry and Biochemistry - Physical and Theoretical Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Robert-von-Ostertag-Str. 15, 14163 Berlin, Germany
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13
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Saran S, Tran DDH, Klebba-Färber S, Moran-Losada P, Wiehlmann L, Koch A, Chopra H, Pabst O, Hoffmann A, Klopfleisch R, Tamura T. THOC5, a member of the mRNA export complex, contributes to processing of a subset of wingless/integrated (Wnt) target mRNAs and integrity of the gut epithelial barrier. BMC Cell Biol 2013; 14:51. [PMID: 24267292 PMCID: PMC4222586 DOI: 10.1186/1471-2121-14-51] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/19/2013] [Indexed: 11/26/2022] Open
Abstract
Background THO (Suppressors of the transcriptional defects of hpr1 delta by overexpression) complex 5 (THOC5), an mRNA export protein, is involved in the expression of only 1% of all genes. Using an interferon inducible knockout mouse system, we have previously shown that THOC5 is an essential element in the maintenance of hematopoietic stem cells and cytokine-mediated hematopoiesis in adult mice. Here we interrogate THOC5 function in cell differentiation beyond the hematopoietic system and study pathological changes caused by THOC5 deficiency. Results To examine whether THOC5 plays a role in general differentiation processes, we generated tamoxifen inducible THOC5 knockout mice. We show here that the depletion of THOC5 impaired not only hematopoietic differentiation, but also differentiation and self renewal of the gut epithelium. Depletion of the THOC5 gene did not cause pathological alterations in liver or kidney. We further show that THOC5 is indispensable for processing of mRNAs induced by Wnt (wingless/integrated) signaling which play key roles in epithelial cell differentiation/proliferation. A subset of Wnt target mRNAs, SRY-box containing gene 9 (Sox9), and achaete-scute complex homolog 2 (Ascl2), but not Fibronectin 1 (Fn1), were down-regulated in THOC5 knockout intestinal cells. The down-regulated Wnt target mRNAs were able to bind to THOC5. Furthermore, pathological alterations in the gastrointestinal tract induced translocation of intestinal bacteria and caused sepsis in mice. The bacteria translocation may cause Toll-like receptor activation. We identified one of the Toll-like receptor inducible genes, prostaglandin-endoperoxidase synthase 2 (Ptgs2 or COX2) transcript as THOC5 target mRNA. Conclusion THOC5 is indispensable for processing of only a subset of mRNAs, but plays a key role in processing of mRNAs inducible by Wnt signals. Furthermore, THOC5 is dispensable for general mRNA export in terminally differentiated organs, indicating that multiple mRNA export pathways exist. These data imply that THOC5 may be a useful tool for studying intestinal stem cells, for modifying the differentiation processes and for cancer therapy.
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Affiliation(s)
- Shashank Saran
- Institut fuer Biochemie, Medizinische Hochschule Hannover, OE4310 Carl-Neuberg-Str, 1, Hannover D-30623, Germany.
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Ramos-Vara JA, Miller MA. When tissue antigens and antibodies get along: revisiting the technical aspects of immunohistochemistry--the red, brown, and blue technique. Vet Pathol 2013; 51:42-87. [PMID: 24129895 DOI: 10.1177/0300985813505879] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Once focused mainly on the characterization of neoplasms, immunohistochemistry (IHC) today is used in the investigation of a broad range of disease processes with applications in diagnosis, prognostication, therapeutic decisions to tailor treatment to an individual patient, and investigations into the pathogenesis of disease. This review addresses the technical aspects of immunohistochemistry (and, to a lesser extent, immunocytochemistry) with attention to the antigen-antibody reaction, optimal fixation techniques, tissue processing considerations, antigen retrieval methods, detection systems, selection and use of an autostainer, standardization and validation of IHC tests, preparation of proper tissue and reagent controls, tissue microarrays and other high-throughput systems, quality assurance/quality control measures, interpretation of the IHC reaction, and reporting of results. It is now more important than ever, with these sophisticated applications, to standardize the entire IHC process from tissue collection through interpretation and reporting to minimize variability among laboratories and to facilitate quantification and interlaboratory comparison of IHC results.
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Affiliation(s)
- J A Ramos-Vara
- Animal Disease Diagnostic Laboratory and Department of Comparative Pathobiology, Purdue University, 406 South University, West Lafayette, IN 47907, USA.
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15
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Farztdinov V, McDyer F. Distributional fold change test - a statistical approach for detecting differential expression in microarray experiments. Algorithms Mol Biol 2012; 7:29. [PMID: 23122055 PMCID: PMC3526407 DOI: 10.1186/1748-7188-7-29] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/22/2012] [Indexed: 11/10/2022] Open
Abstract
Background Because of the large volume of data and the intrinsic variation of data intensity observed in microarray experiments, different statistical methods have been used to systematically extract biological information and to quantify the associated uncertainty. The simplest method to identify differentially expressed genes is to evaluate the ratio of average intensities in two different conditions and consider all genes that differ by more than an arbitrary cut-off value to be differentially expressed. This filtering approach is not a statistical test and there is no associated value that can indicate the level of confidence in the designation of genes as differentially expressed or not differentially expressed. At the same time the fold change by itself provide valuable information and it is important to find unambiguous ways of using this information in expression data treatment. Results A new method of finding differentially expressed genes, called distributional fold change (DFC) test is introduced. The method is based on an analysis of the intensity distribution of all microarray probe sets mapped to a three dimensional feature space composed of average expression level, average difference of gene expression and total variance. The proposed method allows one to rank each feature based on the signal-to-noise ratio and to ascertain for each feature the confidence level and power for being differentially expressed. The performance of the new method was evaluated using the total and partial area under receiver operating curves and tested on 11 data sets from Gene Omnibus Database with independently verified differentially expressed genes and compared with the t-test and shrinkage t-test. Overall the DFC test performed the best – on average it had higher sensitivity and partial AUC and its elevation was most prominent in the low range of differentially expressed features, typical for formalin-fixed paraffin-embedded sample sets. Conclusions The distributional fold change test is an effective method for finding and ranking differentially expressed probesets on microarrays. The application of this test is advantageous to data sets using formalin-fixed paraffin-embedded samples or other systems where degradation effects diminish the applicability of correlation adjusted methods to the whole feature set.
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