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Zhu M, Hwang J, Xu C. Meta-analysis identifies key genes and pathways implicated in Benzo[a]pyrene exposure response. CHEMOSPHERE 2024; 364:143121. [PMID: 39154768 PMCID: PMC11424241 DOI: 10.1016/j.chemosphere.2024.143121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/30/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
INTRODUCTION Benzo[a]pyrene (B[a]P) is a carcinogenic polycyclic aromatic hydrocarbon that poses significant risks to human health. B[a]P influences cellular processes via intricate interactions; however, a comprehensive understanding of B[a]P's effects on the transcriptome remains elusive. This study aimed to conduct a comprehensive analysis focused on identifying relevant genes and signaling pathways affected by B[a]P exposure and their impact on human gene expression. METHODS We searched the Gene Expression Omnibus database and identified four studies involving B[a]P exposure in human cells (T lymphocytes, hepatocellular carcinoma cells, and C3A cells). We utilized two approaches for differential expression analysis: the LIMMA package and linear regression. A meta-analysis was utilized to combine log fold changes (FC) and p-values from the identified studies using a random effects model. We identified significant genes at a Bonferroni-adjusted significance level of 0.05 and determined overlapping genes across datasets. Pathway enrichment analysis elucidated key cellular processes modulated by B[a]P exposure. RESULTS The meta-analysis revealed significant upregulation of CYP1B1 (log FC = 1.15, 95% CI: 0.51-1.79, P < 0.05, I2 = 82%) and ASB2 (log FC = 0.44, 95% CI: 0.20-0.67, P < 0.05, I2 = 40%) in response to B[a]P exposure. Pathway analyses identified 26 significantly regulated pathways, with the top including Aryl Hydrocarbon Receptor Signaling (P = 0.00214) and Xenobiotic Metabolism Signaling (P = 0.00550). Key genes CYP1A1, CYP1B1, and CDKN1A were implicated in multiple pathways, highlighting their roles in xenobiotic metabolism, oxidative stress response, and cell cycle regulation. CONCLUSION The results provided insights into the mechanisms of B[a]P toxicity, highlighting CYP1B1's key role in B[a]P bioactivation. The findings underscored the complexity of B[a]P's mechanisms of action and their potential implications for human health. The identified genes and pathways provided a foundation for further exploration and enhanced our understanding of the multifaceted biological activities associated with B[a]P exposure.
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Affiliation(s)
- Mingze Zhu
- Department of Occupational and Environmental Health, Hudson College of Public Health, University of Oklahoma Health Sciences, Oklahoma City, OK, 73104, USA
| | - Jooyeon Hwang
- Department of Occupational and Environmental Health, Hudson College of Public Health, University of Oklahoma Health Sciences, Oklahoma City, OK, 73104, USA; Department of Environmental & Occupational Health Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, 77030, USA; Southwest Center for Occupational and Environmental Health, University of Texas Health Science Center, Houston, TX, 77030, USA.
| | - Chao Xu
- Department of Biostatistics and Epidemiology, Hudson College of Public Health, University of Oklahoma Health Sciences, Oklahoma City, OK, 73104, USA.
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Zheng X, Tang J, Song A, Zhou Y, Miao J, Li Z, Pan L. Study on reproductive endocrine disturbance and DNA damage mechanism of female Ruditapes philippinarum under Benzo[a]pyrene stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122844. [PMID: 37918772 DOI: 10.1016/j.envpol.2023.122844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/22/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
The reproductive toxicity of polycyclic aromatic hydrocarbons (PAHs) in aquatic organisms has attracted increasing attention from scholars. Currently, research in this field primarily focuses on vertebrates such as zebrafish and other model species. However, there is still a significant knowledge gap in the toxicity of PAHs to invertebrates and its potential mechanisms. Benzo[a]pyrene (B[a]P) is one of the most representative PAHs. In this study, female Ruditapes philippinarum (R. philippinarum) was treated with B[a]P concentrations of 0, 0.8, 4, and 20 μg/L to investigate reproductive indicators in the proliferative, growth, mature, and spawn stages. Transcriptomics was used to investigate the expression of genes associated with the reproductive endocrine system, DNA repair, autophagy, apoptosis, and ovarian development at different reproductive stages. Our results suggested that B[a]P disrupted the endocrine system by interfering with the production of steroid hormones and the transmission of estrogen signals in female R. philippinarum. The structure of the ovarian DNA duplex is severely damaged under the stress of B[a]P, and a series of cellular responses caused by DNA damage are also interfered. Additionally, we observed a reduction in the gonadosomatic index (GSI) and mature oocytes numbers after B[a]P exposed. Tissue section indicated that severe damage to the ovarian structure at mature and spawn stages. In conclusion, this study combined transcriptomic and toxicological to explore the negative effects on ovarian development induced by B[a]P, focusing on reproductive endocrine disturbance and DNA damage.
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Affiliation(s)
- Xin Zheng
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jian Tang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Aimin Song
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yueyao Zhou
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jingjing Miao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Zeyuan Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) is an elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2D-GE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The use of an internal pooled standard makes 2D-DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. Technical limitations of this technique (i.e., underrating of low abundant, high molecular mass and integral membrane proteins) are counterbalanced by the incomparable separation power which allows proteoforms and unknown PTM (posttranslational modification) identification. Moreover, the image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.
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Affiliation(s)
- Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, Segrate, Italy
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, Segrate, Italy.
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4
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Wang Z, Karkossa I, Großkopf H, Rolle-Kampczyk U, Hackermüller J, von Bergen M, Schubert K. Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP. Toxicology 2020; 448:152652. [PMID: 33278487 DOI: 10.1016/j.tox.2020.152652] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/19/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
The application of quantitative proteomics provides a new and promising tool for standardized toxicological research. However, choosing a suitable quantitative method still puzzles many researchers because the optimal method needs to be determined. In this study, we investigated the advantages and limitations of two of the most commonly used global quantitative proteomics methods, namely label-free quantitation (LFQ) and tandem mass tags (TMT). As a case study, we exposed hepatocytes (HepG2) to the environmental contaminant benzo[a]pyrene (BaP) using a concentration of 2 μM. Our results revealed that both methods yield a similar proteome coverage, in which for LFQ a wider range of fold changes was observed but with less significant p-values compared to TMT. We detected 37 and 47 significantly enriched pathways by LFQ and TMT, respectively, with 17 overlapping pathways. To define the minimally required effort in proteomics as a benchmark, we artificially reduced the LFQ, and TMT data sets stepwise and compared the pathway enrichment. Thereby, we found that fewer proteins are necessary for detecting significant enrichment of pathways in TMT compared to LFQ, which might be explained by the higher reproducibility of the TMT data that was observed. In summary, we showed that the TMT approach is the preferable one when investigating toxicological questions because it offers a high reproducibility and sufficient proteome coverage in a comparably short time.
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Affiliation(s)
- Zhipeng Wang
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jörg Hackermüller
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Leipzig University, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
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5
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Abstract
Two-dimensional difference gel electrophoresis (2-D DIGE) is an advanced and elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2-DE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The two-dye or three-dye systems can be adopted and their choice depends on specific applications. Furthermore, the use of an internal pooled standard makes 2-D DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. The image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.
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Affiliation(s)
- Cecilia Gelfi
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, via f.lli Cervi, 93, 20090, Segrate, Milan, Italy.
- U.O. Proteomica clinica, IRCCS Policlinico San Donato, 20097, San Donato, Milan, Italy.
- Istituto di Bioimmagini e Fisiologia Molecolare, CNR, 20090, Segrate, Milan, Italy.
| | - Daniele Capitanio
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, via f.lli Cervi, 93, 20090, Segrate, Milan, Italy
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6
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Wang Y, Jia Y, Yan L, Fu J, Hao M, Chen W, Yao B, Zhao P, Zhou Z. Clusterin and neuropilin-2 as potential biomarkers of tumor progression in benzo[a]pyrene-transformed 16HBE cells xenografted nude mouse model. Chem Biol Interact 2017; 275:145-151. [PMID: 28784314 DOI: 10.1016/j.cbi.2017.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/24/2017] [Accepted: 08/02/2017] [Indexed: 01/01/2023]
Abstract
Benzo[a]pyrene (BaP) is a ubiquitous environment contaminant and its exposure could increase incidence of human lung cancer. In order to confirm and compare potential biomarkers of BaP-induce carcinogenesis and tumor progression, time-dependent changes of clusterin (CLU) and neuropilin-2 (NRP2) levels were evaluated in sera of BaP-transformed 16HBE cell line T-16HBE-C1 cells xenografted nude mice. Performance of CLU and NRP2 on tissue classification and tumor progression forecast was also calculated. Levels of CLU and NRP2 were significant elevated in both culture supernatant of T-16HBE-C1 cells and sera of T-16HBE-C1 cells xenografted nude mice compared with control. CLU and NRP2 were both found positively stained in tumor tissue. CLU and NRP2 alone could well predicate tumor progression in nude mice and CLU appeared to be more sensitive than NRP2. When both of them combined, performance of predication would improve. In conclusion, CLU and NRP2 could serve as potential biomarkers of tumor progression in nude mice xenografted with T-16HBE-C1 cells.
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Affiliation(s)
- Yu Wang
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China
| | - Yongrui Jia
- Medical and Healthy Analytical Center, Peking University Health Science Center, Beijing 100191, PR China
| | - Lailai Yan
- Central Laboratory, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China
| | - Juanling Fu
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China
| | - Mingmei Hao
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China
| | - Wen Chen
- Department of Toxicology, Faculty of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Biyun Yao
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China
| | - Peng Zhao
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China; Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China.
| | - Zongcan Zhou
- Department of Toxicology, School of Public Health, Peking University Health Science Center, Beijing 100191, PR China.
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7
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Kalkhof S, Dautel F, Loguercio S, Baumann S, Trump S, Jungnickel H, Otto W, Rudzok S, Potratz S, Luch A, Lehmann I, Beyer A, von Bergen M. Pathway and time-resolved benzo[a]pyrene toxicity on Hepa1c1c7 cells at toxic and subtoxic exposure. J Proteome Res 2014; 14:164-82. [PMID: 25362887 DOI: 10.1021/pr500957t] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Benzo[a]pyrene (B[a]P) is an environmental contaminant mainly studied for its toxic/carcinogenic effects. For a comprehensive and pathway orientated mechanistic understanding of the effects directly triggered by a toxic (5 μM) or a subtoxic (50 nM) concentration of B[a]P or indirectly by its metabolites, we conducted time series experiments for up to 24 h to study the effects in murine hepatocytes. These cells rapidly take up and actively metabolize B[a]P, which was followed by quantitative analysis of the concentration of intracellular B[a]P and seven representative degradation products. Exposure with 5 μM B[a]P led to a maximal intracellular concentration of 1604 pmol/5 × 10(4) cells, leveling at 55 pmol/5 × 10(4) cells by the end of the time course. Changes in the global proteome (>1000 protein profiles) and metabolome (163 metabolites) were assessed in combination with B[a]P degradation. Abundance profiles of 236 (both concentrations), 190 (only 5 μM), and 150 (only 50 nM) proteins were found to be regulated in response to B[a]P in a time-dependent manner. At the endogenous metabolite level amino acids, acylcarnitines and glycerophospholipids were particularly affected by B[a]P. The comprehensive chemical, proteome and metabolomic data enabled the identification of effects on the pathway level in a time-resolved manner. So in addition to known alterations, also protein synthesis, lipid metabolism, and membrane dysfunction were identified as B[a]P specific effects.
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Affiliation(s)
- Stefan Kalkhof
- Department of Proteomics, UFZ, Helmholtz-Centre for Environmental Research , Permoserstr. 15, 04318 Leipzig, Germany
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8
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Bond JJ, Pernthaner A, Zhang K, Rosanowski SM, Clerens S, Bisset SA, Sutherland IAS, Koolaard JP, Hein WR. Efferent intestinal lymph protein responses in nematode-resistant, -resilient and -susceptible lambs under challenge with Trichostrongylus colubriformis. J Proteomics 2014; 109:356-67. [PMID: 25072800 DOI: 10.1016/j.jprot.2014.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/17/2022]
Abstract
UNLABELLED The mechanisms underlying resistance to challenge by gastrointestinal nematode parasites in sheep are complex. Using DIGE, we profiled ovine lymph proteins in lambs with host resistance (R), resilience (Ri) or susceptibility (S) to a daily trickle challenge with the nematode Trichostrongylus colubriformis. Efferent intestinal lymph was collected prior to infection (day 1) and on days 5 and 10 post-infection. Eight proteins identified by LC-MS/MS, showed differences relating to host genotype. Of these, Serpin A3-3 and Serpin A3-7 have not been reported previously in the lymph proteome. Three acute phase proteins showed significant differences relating to interactions between breeding line and parasite challenge, including complement C3β, C3α and haptoglobin (Hp) β. In the R lambs C3α was significantly up regulated (P<0.05) on day 10, while in the Ri lambs Hp β was significantly down regulated (P<0.05). In the S lambs, levels of C3β were up regulated and levels of Hp β down regulated (both P<0.05) on day 10. Hence we demonstrate that acute phase inflammation proteins contribute to differences in the innate immune response of sheep to challenge by T. colubriformis. The findings may lead to the development of new approaches to combat nematode infestations in sheep production systems. BIOLOGICAL SIGNIFICANCE Breeding lines of sheep with resistance (R), resilience (Ri) or susceptibility (S) to nematode infections provide an experimental model to examine the biological mechanisms underlying the ability of some sheep to expel worms and remain healthy without the use of an anthelmintic. Using proteomics we identified differences in the expression of acute phase lymph proteins in the R, Ri and S lambs. The results will assist the development of alternative control strategies to manage nematode infections in livestock.
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Affiliation(s)
- J J Bond
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
| | - A Pernthaner
- AgResearch Ltd, The Hopkirk Research Institute, Palmerston North, New Zealand
| | - K Zhang
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - S M Rosanowski
- AgResearch Ltd, The Hopkirk Research Institute, Palmerston North, New Zealand
| | - S Clerens
- AgResearch Ltd, Lincoln Research Centre, Christchurch, New Zealand
| | - S A Bisset
- AgResearch Ltd, The Hopkirk Research Institute, Palmerston North, New Zealand
| | - I A S Sutherland
- AgResearch Ltd, The Hopkirk Research Institute, Palmerston North, New Zealand
| | - J P Koolaard
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - W R Hein
- AgResearch Ltd, The Hopkirk Research Institute, Palmerston North, New Zealand
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9
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Madureira DJ, Weiss FT, Van Midwoud P, Helbling DE, Sturla SJ, Schirmer K. Systems toxicology approach to understand the kinetics of benzo(a)pyrene uptake, biotransformation, and DNA adduct formation in a liver cell model. Chem Res Toxicol 2014; 27:443-53. [PMID: 24446834 DOI: 10.1021/tx400446q] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cell-based models are important for deriving mechanistic information about stress response pathways that have evolved to protect cells from toxic insult, such as exposure to environmental pollutants. One determinant of the stress response is the amount of chemical entering the cell and the cell's ability to detoxify and remove the chemical. If the stress response is overwhelmed, an adverse outcome will ensue. It was the goal of our study to quantify uptake and elimination rates of benzo(a)pyrene (BaP), a ubiquitous environmental pollutant, in a murine liver cell line. We evaluated the kinetic behavior in the context of BaP uptake, biotransformation, DNA adduct formation and repair along with the transcriptional and cell proliferation response. A low (50 nM) and a high (5 μM) BaP concentration were chosen in order to differentiate the role of exposure concentration in the time-resolved interaction of BaP with cells. While rates of uptake and the initial transcriptional response were similar for both BaP concentrations, cells exposed to 50 nM BaP completely recovered from exposure within 24 h, whereas cells exposed to 5 μM BaP did not. Biotransformation proceeded faster on 50 nM BaP, and the few DNA adducts formed were completely repaired after transient cell cycle arrest. In contrast, DNA adducts greatly accumulated in cells exposed to 5 μM BaP, despite significant biotransformation; complete cell cycle arrest and toxicity evolved. On the basis of the kinetic rate constants and cellular response, we conclude that at least short-term, pulsed exposures to 50 nM BaP, which we consider environmentally relevant, can be handled by cells without adverse outcome. Further studies are needed to determine the ability of cells to recover from repeated exposure. Our study emphasizes the importance of quantifying chemical uptake and fate in cell models to differentiate a stress response from an adverse outcome for better risk assessment.
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Affiliation(s)
- Danielle J Madureira
- Eawag, Swiss Federal Institute of Aquatic Science and Technology , Dübendorf, Switzerland
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10
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Murugaiyan J, Rockstroh M, Wagner J, Baumann S, Schorsch K, Trump S, Lehmann I, Bergen MV, Tomm JM. Benzo[a]pyrene affects Jurkat T cells in the activated state via the antioxidant response element dependent Nrf2 pathway leading to decreased IL-2 secretion and redirecting glutamine metabolism. Toxicol Appl Pharmacol 2013; 269:307-16. [DOI: 10.1016/j.taap.2013.03.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 02/01/2023]
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Kliemt S, Lange C, Otto W, Hintze V, Möller S, von Bergen M, Hempel U, Kalkhof S. Sulfated Hyaluronan Containing Collagen Matrices Enhance Cell-Matrix-Interaction, Endocytosis, and Osteogenic Differentiation of Human Mesenchymal Stromal Cells. J Proteome Res 2012; 12:378-89. [DOI: 10.1021/pr300640h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Stefanie Kliemt
- Department
of Proteomics, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse
15, 04318 Leipzig, Germany
| | - Claudia Lange
- Institute of Physiological Chemistry, TU Dresden, Fiedlerstrasse 42, Dresden 01307, Germany
| | - Wolfgang Otto
- Department
of Proteomics, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse
15, 04318 Leipzig, Germany
| | - Vera Hintze
- Institute of Material Science,
Max-Bergmann-Centre of Biomaterials, TU Dresden, 01069 Dresden, Germany
| | | | - Martin von Bergen
- Department
of Proteomics, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse
15, 04318 Leipzig, Germany
- Department of Metabolomics, Helmholtz-Centre for Environmental Research-UFZ, 04318
Leipzig, Germany
- Department of
Biotechnology, Chemistry
and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49,DK-9000 Aalborg, Denmark
| | - Ute Hempel
- Institute of Physiological Chemistry, TU Dresden, Fiedlerstrasse 42, Dresden 01307, Germany
| | - Stefan Kalkhof
- Department
of Proteomics, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse
15, 04318 Leipzig, Germany
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12
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Lichtenfels R, Mougiakakos D, Johansson CC, Dressler SP, Recktenwald CV, Kiessling R, Seliger B. Comparative expression profiling of distinct T cell subsets undergoing oxidative stress. PLoS One 2012; 7:e41345. [PMID: 22911781 PMCID: PMC3401147 DOI: 10.1371/journal.pone.0041345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 06/20/2012] [Indexed: 12/28/2022] Open
Abstract
The clinical outcome of adoptive T cell transfer-based immunotherapies is often limited due to different escape mechanisms established by tumors in order to evade the hosts' immune system. The establishment of an immunosuppressive micromilieu by tumor cells along with distinct subsets of tumor-infiltrating lymphocytes is often associated with oxidative stress that can affect antigen-specific memory/effector cytotoxic T cells thereby substantially reducing their frequency and functional activation. Therefore, protection of tumor-reactive cytotoxic T lymphocytes from oxidative stress may enhance the anti-tumor-directed immune response. In order to better define the key pathways/proteins involved in the response to oxidative stress a comparative 2-DE-based proteome analysis of naïve CD45RA+ and their memory/effector CD45RO+ T cell counterparts in the presence and absence of low dose hydrogen peroxide (H2O2) was performed in this pilot study. Based on the profiling data of these T cell subpopulations under the various conditions, a series of differentially expressed spots were defined, members thereof identified by mass spectrometry and subsequently classified according to their cellular function and localization. Representative targets responding to oxidative stress including proteins involved in signaling pathways, in regulating the cellular redox status as well as in shaping/maintaining the structural cell integrity were independently verified at the transcript and protein level under the same conditions in both T cell subsets. In conclusion the resulting profiling data describe complex, oxidative stress-induced, but not strictly concordant changes within the respective expression profiles of CD45RA+ and CD45RO+ T cells. Some of the differentially expressed genes/proteins might be further exploited as potential targets toward modulating the redox capacity of the distinct lymphocyte subsets thereby providing the basis for further studies aiming at rendering them more resistant to tumor micromilieu-induced oxidative stress.
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Affiliation(s)
- Rudolf Lichtenfels
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dimitrios Mougiakakos
- Department of Oncology and Pathology, Cancer Center Karolinska, Stockholm, Sweden
- Department of Internal Medicine 5, Hematology and Oncology, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Sven P. Dressler
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | | | - Rolf Kiessling
- Department of Oncology and Pathology, Cancer Center Karolinska, Stockholm, Sweden
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
- * E-mail:
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Verma N, Pink M, Rettenmeier AW, Schmitz-Spanke S. Review on proteomic analyses of benzo[a]pyrene toxicity. Proteomics 2012; 12:1731-55. [DOI: 10.1002/pmic.201100466] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nisha Verma
- Institute of Hygiene and Occupational Medicine; University Hospital Essen; Essen Germany
| | - Mario Pink
- Institute of Hygiene and Occupational Medicine; University Hospital Essen; Essen Germany
| | - Albert W. Rettenmeier
- Institute of Hygiene and Occupational Medicine; University Hospital Essen; Essen Germany
| | - Simone Schmitz-Spanke
- Institute of Hygiene and Occupational Medicine; University Hospital Essen; Essen Germany
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Gündel U, Kalkhof S, Zitzkat D, von Bergen M, Altenburger R, Küster E. Concentration-response concept in ecotoxicoproteomics: effects of different phenanthrene concentrations to the zebrafish (Danio rerio) embryo proteome. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 76:11-22. [PMID: 22062151 DOI: 10.1016/j.ecoenv.2011.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 08/16/2011] [Accepted: 10/08/2011] [Indexed: 05/31/2023]
Abstract
Concentration-response experiments, based on the testing of less replicates in favour of more exposure concentrations, represent the typical design of choice applied in toxicological and ecotoxicological effect assessment studies using traditional endpoints such as lethality. However, to our knowledge this concept has not found implementation in the increasingly applied OMICS techniques studying thousands of molecular endpoints at the same time. The present study is among the first applying the concentration-response concept for an ecotoxicoproteomics study. The effects of six different concentrations in the low effect range (<LC₂₀) of the PAH phenanthrene to the proteome of the ecotoxicological vertebrate model zebrafish (Danio rerio) embryo were investigated (two replicates per concentration) after 5 days exposure. Proteomics analyses were performed on organism extracts using 2-DE DIGE. Protein abundance profiles of around 713 protein spots were studied. About one-third of the protein signals could be detected to show robust reactions correlating with stressor concentration. Within this group, 65 protein signals showed significant changes compared to controls already at 1% lethal concentration (LC₀₁). Interestingly, 28 proteins significantly reacted at very low concentrations (<LC₀₁) and showed an exposure concentration dependent regulation status. Characteristic protein spots were identified by mass spectrometry. With the results of the present study the utility and several benefits using a concentration-response approach in proteomics studies could be shown. These included (i) knowledge about and the ability to model concentration dependent dynamics of molecular endpoints, (ii) to gain information about sensitivity of the molecular response in comparison to traditional endpoints and (iii) to help selecting the most promising protein spots for further investigations such as protein identification and biomarker studies. Using this experimental design based on testing of several exposure concentrations and less replicates might provide a step forward in getting increased output from toxicoproteomics studies.
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Affiliation(s)
- Ulrike Gündel
- Department Bioanalytical Ecotoxicology, UFZ Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318 Leipzig, Germany.
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Michaelson JJ, Trump S, Rudzok S, Gräbsch C, Madureira DJ, Dautel F, Mai J, Attinger S, Schirmer K, von Bergen M, Lehmann I, Beyer A. Transcriptional signatures of regulatory and toxic responses to benzo-[a]-pyrene exposure. BMC Genomics 2011; 12:502. [PMID: 21995607 PMCID: PMC3215681 DOI: 10.1186/1471-2164-12-502] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 10/13/2011] [Indexed: 01/01/2023] Open
Abstract
Background Small molecule ligands often have multiple effects on the transcriptional program of a cell: they trigger a receptor specific response and additional, indirect responses ("side effects"). Distinguishing those responses is important for understanding side effects of drugs and for elucidating molecular mechanisms of toxic chemicals. Results We explored this problem by exposing cells to the environmental contaminant benzo-[a]-pyrene (B[a]P). B[a]P exposure activates the aryl hydrocarbon receptor (Ahr) and causes toxic stress resulting in transcriptional changes that are not regulated through Ahr. We sought to distinguish these two types of responses based on a time course of expression changes measured after B[a]P exposure. Using Random Forest machine learning we classified 81 primary Ahr responders and 1,308 genes regulated as side effects. Subsequent weighted clustering gave further insight into the connection between expression pattern, mode of regulation, and biological function. Finally, the accuracy of the predictions was supported through extensive experimental validation. Conclusion Using a combination of machine learning followed by extensive experimental validation, we have further expanded the known catalog of genes regulated by the environmentally sensitive transcription factor Ahr. More broadly, this study presents a strategy for distinguishing receptor-dependent responses and side effects based on expression time courses.
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Affiliation(s)
- Jacob J Michaelson
- Cellular Networks and Systems Biology, Biotechnology Center, TU Dresden, Dresden, Germany
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