| 1. |
- Farnebo, Lovisa, et al.
(författare)
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Combining factors on protein and gene level to predict radioresponse in head and neck cancer cell lines
- 2011
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Ingår i: Journal of Oral Pathology & Medicine. - : John Wiley and sons. - 0904-2512 .- 1600-0714. ; 40:10, s. 739-746
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Radiotherapy is the main therapy for head and neck squamous cell carcinoma (HNSCC); however, treatment resistance and local recurrence are significant problems, highlighting the need for predictive markers. In this study, we evaluated selected proteins, mutations, and single nucleotide polymorphisms (SNPs) involved in apoptosis, cell proliferation, and DNA repair alone or combined as predictive markers for radioresponse in 42 HNSCC cell lines. METHODS: The expression of epidermal growth factor receptor, survivin, Bax, Bcl-2, Bcl-XL, cyclooxygenase-2, and heat shock protein 70 was analyzed by ELISA. Furthermore, mutations and SNPs in the p53 gene as well as SNPs in the MDM2, XRCC1, and XRCC3 genes were analyzed for their relation to radioresponse. To enable the evaluation of the predictive value of several factors combined, each cell line was allocated points based on the number of negative points (NNP) system, and the NNP sum was correlated with radioresponse. RESULTS: Survivin was the only factor that alone was significantly correlated with the intrinsic radiosensitivity (r=0.36, p=0.02). The combination of survivin, Bax, Bcl-2, Bcl-XL, cyclooxygenase-2, and the p53 Arg72Pro polymorphism was found to most strongly correlate with radioresponse (r=0.553, p<0.001). CONCLUSION: These data indicate that the intrinsic radiosensitivity of 42 HNSCC cell lines can be predicted by a panel of factors on both the protein and gene levels. Moreover, among the investigated factors, survivin was the most promising biomarker of radioresponse.
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| 2. |
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| 3. |
- Jerhammar, Fredrik, 1979-
(författare)
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Predictive Markers of Treatment Resistance in Head and Neck Squamous Cell Carcinoma
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Head and neck cancer is a common malignancy with approximately 600 000 new cases yearly. Disappointingly, the overall survival has not increased over the last decades. The concept of personalized medicine, i.e. to treat every patient with an individually planned treatment regime has gathered increased interest, but requires the establishment of novel biomarkers that can predict treatment response.The aim of this thesis is to propose novel predictive single markers or combinations of markers of response to radiation, cisplatin and cetuximab. The general methodology is to evaluate common differences of cell lines resistant to radiation, cisplatin or cetuximab compared to sensitive counterparts.In paper I, we analysed the expression of 14 proteins involved in growth control and/or apoptosis by western blot and related them to intrinsic radiosensitivity (IR) in nine cell lines. No factor had a significant correlation to IR on its own. A combination of EGFR, survivin, Bak, Smad4, and Hsp70 had the best correlation to IR (R=0.886, p=0.001). Additionally, we analysed the presence of p53 mutations in the cell lines. All cell lines had at least one missense, splice site or loss of transcript mutation. To be able to combine protein expression and presence of p53 mutations we created a system designated the number of negative points (NNP). With this system we could extract that expression of EGFR, survivin, and p53 missense or splice site mutations had the best correlation to IR (R=0.990, p<0.001).In paper II we conducted a gene expression microarray analysis of three cell lines, from which common deregulations in two cisplatin resistant cell lines was compared to a cisplatin sensitive cell line. From a bioinformatic approach of gene ontology and molecular network analysis, we defined a transcriptional profile of 20 genes. Finally, key findings were analysed in a larger panel of cell lines, where high MMP-7 expression correlated with higher cisplatin resistance.Paper III compared 4 cell lines with high IR to a radiosensitive equivalent. Using a similar bioinformatic approach as paper II, we established a transcriptional profile of 14 genes. Analysis in a larger panel of cell lines revealed that FN1 expression predicts higher IR.Paper IV establishes the cetuximab sensitivity of 35 cell lines of which 12 were resistant and five were sensitive to cetuximab. After whole genome gene copy number analysis of five cetuximab resistant and five cetuximab sensitive cell lines, and verification of key findings in a larger cell line panel, the results show that the amplification of the YAP1 gene is coupled to cetuximab resistance.In summary, this thesis proposes a number of novel markers of resistance to radiation, cisplatin, and cetuximab which could influence treatment choice in the future, following verifications in primary tumor material.
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| 4. |
- Kohonen, Pekka, et al.
(författare)
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Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand
- 2014
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Ingår i: Basic & Clinical Pharmacology & Toxicology. - : Wiley. - 1742-7835 .- 1742-7843. ; 115:1, s. 50-58
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Forskningsöversikt (refereegranskat)abstract
- Toxicological research faces the challenge of integrating knowledge from diverse fields and novel technological developments generally in the biological and medical sciences. We discuss herein the fact that the multiple facets of cancer research, including discovery related to mechanisms, treatment and diagnosis, overlap many up and coming interest areas in toxicology, including the need for improved methods and analysis tools. Common to both disciplines, in vitro and in silico methods serve as alternative investigation routes to animal studies. Knowledge on cancer development helps in understanding the relevance of chemical toxicity studies in cell models, and many bioinformatics-based cancer biomarker discovery tools are also applicable to computational toxicology. Robotics-aided cell-based high throughput screening, microscale immunostaining techniques, and gene expression profiling analyses are common tools in cancer research, and when sequentially combined, form a tiered approach to structured safety evaluation of thousands of environmental agents, novel chemicals or engineered nanomaterials. Comprehensive tumour data collections in databases have been translated into clinically useful data, and this concept serves as template for computer-driven evaluation of toxicity data into meaningful results. Future “cancer research-inspired knowledge management” of toxicological data will aid the translation of basic discovery results and chemicals- and materials-testing data to information relevant to human health and environmental safety.
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| 5. |
- Nilsson, Cathrine, 1978-, et al.
(författare)
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Intrinsic differences in cisplatin sensitivity of head and neck cancer celllines correlates to lysosomal pH
- 2010
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Ingår i: Head and Neck. - : John Wiley & Sons. - 1043-3074 .- 1097-0347. ; 32:9, s. 1185-1194
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Tidskriftsartikel (refereegranskat)abstract
- Cisplatin is part of the treatment regime of head and neck squamous cell carcinomas (HNSCC). In order to predict the clinical outcome of the treatment, markers for evaluation of the intrinsic cisplatin sensitivity are inquired. In this study we characterize the lysosomal compartment and compare cisplatin sensitivity in five HNSCC lines and normal oral keratinocytes (NOKs). Cisplatin sensitivity differed 3-fold between the least and most sensitive cell lines, and the cisplatin LD50 correlated significantly to lysosomal pH, which varied from 4.3 in NOKs to 4.9 in the most resistant HNSCC line. Lysosomes are acidified by the V0V1-ATPase complex located in the lysosomal membrane. Interestingly, in cell lines exhibiting high lysosomal pH, we found decreased expression of the V0V1-ATPase B2 subunit, possibly explaining the defective acidification. In all cell lines, exposure to cisplatin caused activation of caspase-3. Cisplatin exposure was accompanied by lysosomal membrane permeabilization and inhibition of the llysosomal cathepsins B, D and L partly prevented cell death. No correlation between cisplatin sensitivity and expression of cathepsins B, D and L or secretion of their respective proforms into the culture medium was found in the cell lines studied. We conclude that lysosomal pH and expression of V0V1-ATPase subunits are possible future markers of intrinsic cisplatin sensitivity.
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| 6. |
- Spjuth, Ola, 1977-, et al.
(författare)
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A novel infrastructure for chemical safety predictions with focus on human health
- 2012
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Ingår i: Toxicology Letters. - : Elsevier BV. - 0378-4274 .- 1879-3169. ; 211:Supplm, s. S59-
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Tidskriftsartikel (refereegranskat)abstract
- A major objective of Computational Toxicology is to provide reliable and useful estimates in silico of (potentially) harmful actions of chemicals in humans. Predictive models are commonly based on in vitro and in vivo data, and aims at supporting risk assessment in various areas, including the environmental protection, food, and pharmaceutical sectors. The field is however hampered by the lack of standards, access to high quality data, validated predictive models, as well as means to connect toxicity data to genomics data.We present a framework and roadmap for a novel public infrastructure for predictive computational toxicology and chemical safety assessment, consisting of: (1) a repository capable of aggregating high quality toxicity data with gene expression data, (2) a repository where scientists can share and download predictive models for chemical safety, and (3) a user-friendly platform which makes the services and resources accessible for the scientific community. Databases under the framework will adhere to open standards and use standardized open exchange formats in order to interoperate with emerging international initiatives, such as the FP7-funded OpenTox and ToxBank projects.The infrastructure will strengthen and facilitate already ongoing activities within in silico toxicology, open up new possibilities for incorporating genomics data in chemicals safety modeling (toxicogenomics), as well as deepen the exploitation of signal transduction networks. The initiative will lay the foundation needed to boost decision support in risk assessment in a wide range of fields, including drug discovery, food safety, as well as agricultural and ecological safety assessment.
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| 7. |
- Willighagen, Egon, et al.
(författare)
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Computational toxicology using OpenTox & Bioclipse
- 2012
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Ingår i: Toxicology Letters. - : Elsevier BV. - 0378-4274 .- 1879-3169. ; 211, s. S60-S60
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Computational methods, e.g., OECD QSAR Toolbox and ToxPredict, are increasingly used to support chemicals toxicity assessment in academic settings, industry and governments. The in silico-based assessments complement experimental approaches and have potential to fill the knowledge gaps needed to broadly assess chemical hazards. We present here the interoperable Bioclipse–OpenTox platform as a novel alternative made freely and openly available.The interactive Bioclipse software is combined with remote computational toxicity prediction provided by services in the OpenTox network from various European institutes and SMEs. These online services apply machine learning methods for integration of a number of end points, e.g., Ames mutagenicity test in salmonella, Caco-2 cell model permeability and micronucleus assay in rodents. Coupling of such data to chemical structure assessments lead to prediction of site(s) for metabolism (using SMARTCyp), biodegradation (START), and toxicity mode prediction (Verhaar scheme). The OpenTox platform thus unifies how the services are accessed whereas the Bioclipse software provides the easy-to-use interface for interactively studying the toxic part of molecules. Additional predictive methods that are made accessible via the OpenTox network are automatically discovered by Bioclipse and models can be improved over time without any need to reinstall Bioclipse itself.
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| 8. |
- Willighagen, Egon, et al.
(författare)
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Computational toxicology using the OpenTox application programming interface and Bioclipse
- 2011
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Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 4:1, s. 487-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings: This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions: A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers.
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