1
|
Wehr MM, Reamon-Buettner SM, Ritter D, Knebel J, Niehof M, Escher SE. A comparison of the TempO-Seq and Affymetrix microarray platform using RTqPCR validation. BMC Genomics 2024; 25:669. [PMID: 38961363 PMCID: PMC11223392 DOI: 10.1186/s12864-024-10586-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
Next-generation risk assessment relies on mechanistic data from new approach methods, including transcriptome data. Various technologies, such as high-throughput targeted sequencing methods and microarray technologies based on hybridization with complementary probes, are used to determine differentially expressed genes (DEGs). The integration of data from different technologies requires a good understanding of the differences arising from the use of various technologies.To better understand the differences between the TempO-Seq platform and Affymetrix chip technology, whole-genome data for the volatile compound dimethylamine were compared. Selected DEGs were also confirmed using RTqPCR validation. Although the overlap of DEGs between TempO-Seq and Affymetrix was no higher than 37%, a comparison of the gene regulation in terms of log2fold changes revealed a very high concordance. RTqPCR confirmed the majority of DEGs from either platform in the examined dataset. Only a few conflicts were found (11%), while 22% were not confirmed, and 3% were not detected.Despite the observed differences between the two platforms, both can be validated using RTqPCR. Here we highlight some of the differences between the two platforms and discuss their applications in toxicology.
Collapse
Affiliation(s)
- Matthias M Wehr
- Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany.
| | | | - Detlef Ritter
- Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
| | - Jan Knebel
- Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
| | - Monika Niehof
- Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
| | - Sylvia E Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
| |
Collapse
|
2
|
Ritter D, Knebel J, Hansen T, Zifle A, Fuchs A, Fautz R, Schwarz K. Development of a non-target strategy for evaluation of potential biological effects of inhalable aerosols generated during purposeful room conditioning using an in vitro inhalation model. Inhal Toxicol 2023; 35:271-284. [PMID: 37853720 DOI: 10.1080/08958378.2023.2267618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/29/2023] [Indexed: 10/20/2023]
Abstract
OBJECTIVES An integrated in vitro inhalation approach was outlined to estimate potential adverse acute inhalation effects of aerosols from commercial nebulizer applications used for purposeful room conditioning such as disinfection, scenting or others. Aerosol characterization, exposure estimation and evaluation of acute biological effects by in vitro inhalation were included to generate dose-response data, allowing for determination of in vitro lowest observable adverse effect levels (LOAELs). Correlation of these to estimates of human lung deposition was included for quantitative in vitro to in vivo extrapolation approach (QIVIVE) for acute effects during human exposure. METHODS To test the proposed approach, a case study was undertaken using two realistic test materials. An acute in vitro inhalation setup with air-liquid interface A549-cells in an optimized exposure situation (P.R.I.T.® ExpoCube®) was used to expose cells and analysis of relevant biological effects (viability, mitochondrial membrane potential, stress, IL-8 release) was carried out. RESULTS The observed dose-responsive effects in a sub-toxic dose-range could be attributed to the main component of one test material and its presence in the aerosol phase of the nebulized material. QIVIVE resulted in a factor of at least 256 between the in vitro LOAEL and the estimated acute human lung exposure for this test material. CONCLUSIONS The case-study shows the value of the non-target in vitro inhalation testing approach especially in case of a lack of knowledge on complex product composition. It is expected that approaches like this will be of high value for product safety and environmental health in the future.
Collapse
Affiliation(s)
- Detlef Ritter
- Respiratory Pharmacology, Fraunhofer ITEM, Hannover, Germany
| | - Jan Knebel
- Respiratory Pharmacology, Fraunhofer ITEM, Hannover, Germany
| | - Tanja Hansen
- Respiratory Pharmacology, Fraunhofer ITEM, Hannover, Germany
| | | | | | | | | |
Collapse
|
3
|
Primavessy D, Metz J, Schnur S, Schneider M, Lehr CM, Hittinger M. Pulmonary in vitro instruments for the replacement of animal experiments. Eur J Pharm Biopharm 2021; 168:62-75. [PMID: 34438019 DOI: 10.1016/j.ejpb.2021.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/19/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
Advanced in vitro systems often combine a mechanical-physical instrument with a biological component e.g. cell culture models. For testing of aerosols, it is of advantage to consider aerosol behavior, particle deposition and lung region specific cell lines. Although there are many good reviews on the selection of cell cultures, articles on instruments are rare. This article focuses on the development of in vitro instruments targeting the exposure of aerosols on cell cultures. In this context, guidelines for toxicity investigation are taken into account as the aim of new methods must be the prediction of human relevant data and the replacement of existing animal experiments. We provide an overview on development history of research-based instruments from a pharmaceutical point of view. The standardized commercial devices resulting from the research-based instruments are presented and the future perspectives on pulmonary in vitro devices are discussed.
Collapse
Affiliation(s)
- Daniel Primavessy
- Department of Drug Delivery, PharmBioTec Research and Development GmbH, Saarbrücken, Germany.
| | - Julia Metz
- Department of Drug Delivery, PharmBioTec Research and Development GmbH, Saarbrücken, Germany
| | - Sabrina Schnur
- Department of Drug Delivery, PharmBioTec Research and Development GmbH, Saarbrücken, Germany; Department of Pharmacy, Biopharmaceutics and Pharmaceutical Technology, Saarland University, Saarbrücken, Germany
| | - Marc Schneider
- Department of Pharmacy, Biopharmaceutics and Pharmaceutical Technology, Saarland University, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Department of Drug Delivery, PharmBioTec Research and Development GmbH, Saarbrücken, Germany; Department of Pharmacy, Biopharmaceutics and Pharmaceutical Technology, Saarland University, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
| | - Marius Hittinger
- Department of Drug Delivery, PharmBioTec Research and Development GmbH, Saarbrücken, Germany; 3RProducts Marius Hittinger, Blieskastel, Germany
| |
Collapse
|
4
|
Welch J, Wallace J, Lansley AB, Roper C. Evaluation of the toxicity of sodium dodecyl sulphate (SDS) in the MucilAir™ human airway model in vitro. Regul Toxicol Pharmacol 2021; 125:105022. [PMID: 34333067 DOI: 10.1016/j.yrtph.2021.105022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/21/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
The aim of the study was to use multiple in vitro assays to assess the effects of a model irritant, sodium dodecyl sulphate (SDS) (≤10 mM (0.29 %, w/v)), on an in vitro model of the airway, MucilAir™. The use of MucilAir™ in recovery studies was also explored. A 24 h exposure increased IL-8 release at an SDS concentration ≥0.63 mM (0.018 %, w/v). Mucin secretion increased and transepithelial electrical resistance (TEER) decreased at SDS concentrations ≥1.25 mM (0.04 %, w/v). Cytotoxicity (lactate dehydrogenase (LDH) release into basolateral chamber) was observed at SDS concentrations of ≥2.5 mM (0.07 %, w/v). The sensitivity of the assays was IL-8 release > TEER = mucin secretion > LDH release. After 7 days, full or partial recovery was observed for intermediate concentrations of SDS using all assays but not at 5 and 10 mM SDS. Morphologically, erosion and cell loss were observed at these concentrations. Resazurin metabolism at 7 days tended to decrease in a dose-dependent manner at SDS concentrations above 2.5 mM (0.07 %, w/v). Together, these data support a No Observable Effect Level of 0.31 mM (0.009 % w/v) SDS and the use of MucilAir™ as a relevant model for airway toxicity studies.
Collapse
Affiliation(s)
- Jonathan Welch
- Department of In Vitro Toxicology, Charles River Laboratories, Tranent, Edinburgh, EH33 2NE, UK.
| | - Joanne Wallace
- Department of In Vitro Toxicology, Charles River Laboratories, Tranent, Edinburgh, EH33 2NE, UK.
| | - Alison B Lansley
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 1GJ, UK.
| | - Clive Roper
- Department of In Vitro Toxicology, Charles River Laboratories, Tranent, Edinburgh, EH33 2NE, UK.
| |
Collapse
|
5
|
Mülhopt S, Schlager C, Berger M, Murugadoss S, Hoet PH, Krebs T, Paur HR, Stapf D. A novel TEM grid sampler for airborne particles to measure the cell culture surface dose. Sci Rep 2020; 10:8401. [PMID: 32439902 PMCID: PMC7242374 DOI: 10.1038/s41598-020-65427-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 01/17/2023] Open
Abstract
The applied surface dose is a key parameter for the measurement of toxic effects of airborne particles by air liquid interface exposure of human lung cells. Besides online measurement of the deposited particle mass by quartz crystal microbalance frequently other dose metrics such as particle size distribution, surface and agglomeration state are required. These particle properties and their spatial distribution can be determined by digital processing of micrographs obtained by transmission electron microscopy (TEM). Here, we report the development and characterization of a novel holder for film coated TEM copper grids, which allows for sampling under identical geometric and ambient conditions as in a cell culture chamber. The sample holder avoids artefacts by reliable grounding of the grids and improves handling of the grids to prevent damage of the sensitive film. This sample holder is applied during exposure experiments with titanium dioxide nanoparticles. The measured dose of 0.2 µg/cm² corresponds well to the mass loading signal of the quartz crystal microbalance. Additionally, the spatial distribution of particles on the sampling surface shows a good homogeneity of deposition. This novel sampling method allows verifying other dosimetry methods and gives additional information about particle properties and homogeneity of the dose.
Collapse
Affiliation(s)
- Sonja Mülhopt
- Karlsruhe Institute of Technology (KIT), Institute for Technical Chemistry, Eggenstein-Leopoldshafen, 76344, Germany.
| | | | | | | | - Peter H Hoet
- KU Leuven, Environment and Health, Leuven, 3000, Belgium
| | - Tobias Krebs
- Vitrocell Systems GmbH, Waldkirch, 79183, Germany
| | - Hanns-Rudolf Paur
- Karlsruhe Institute of Technology (KIT), Institute for Technical Chemistry, Eggenstein-Leopoldshafen, 76344, Germany
| | - Dieter Stapf
- Karlsruhe Institute of Technology (KIT), Institute for Technical Chemistry, Eggenstein-Leopoldshafen, 76344, Germany
| |
Collapse
|
6
|
Intermittent exposure to whole cigarette smoke alters the differentiation of primary small airway epithelial cells in the air-liquid interface culture. Sci Rep 2020; 10:6257. [PMID: 32277131 PMCID: PMC7148343 DOI: 10.1038/s41598-020-63345-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Cigarette smoke (CS) is the leading risk factor to develop COPD. Therefore, the pathologic effects of whole CS on the differentiation of primary small airway epithelial cells (SAEC) were investigated, using cells from three healthy donors and three COPD patients, cultured under ALI (air-liquid interface) conditions. The analysis of the epithelial physiology demonstrated that CS impaired barrier formation and reduced cilia beat activity. Although, COPD-derived ALI cultures preserved some features known from COPD patients, CS-induced effects were similarly pronounced in ALI cultures from patients compared to healthy controls. RNA sequencing analyses revealed the deregulation of marker genes for basal and secretory cells upon CS exposure. The comparison between gene signatures obtained from the in vitro model (CS vs. air) with a published data set from human epithelial brushes (smoker vs. non-smoker) revealed a high degree of similarity between deregulated genes and pathways induced by CS. Taken together, whole cigarette smoke alters the differentiation of small airway basal cells in vitro. The established model showed a good translatability to the situation in vivo. Thus, the model can help to identify and test novel therapeutic approaches to restore the impaired epithelial repair mechanisms in COPD, which is still a high medical need.
Collapse
|
7
|
Ritter D, Knebel J, Niehof M, Loinaz I, Marradi M, Gracia R, te Welscher Y, van Nostrum CF, Falciani C, Pini A, Strandh M, Hansen T. In vitro inhalation cytotoxicity testing of therapeutic nanosystems for pulmonary infection. Toxicol In Vitro 2020; 63:104714. [DOI: 10.1016/j.tiv.2019.104714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/30/2022]
|