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1.
Opt Express ; 29(15): 24068-24082, 2021 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-34614659

RESUMEN

Fundamental bounds on the performance of monochromatic scattering-cancellation and field-zeroing cloaks made of prescribed linear passive materials occupying a predefined design region are formulated by projecting field quantities onto a sub-sectional basis and applying quadratically constrained quadratic programming. Formulations are numerically tested revealing key physical trends as well as advantages and disadvantages between the two classes of cloaks. Results show that the use of low-loss materials with high dielectric contrast affords the highest potential for effective cloaking.

2.
Sci Total Environ ; 774: 145503, 2021 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-33609838

RESUMEN

In urban environments, particularly areas under reconstruction, metals, organic pollutants (OP), and microplastics (MP), are released in large amounts due to heavy traffic. Road runoff, a major transport route for urban pollutants, contributes significantly to a deteriorated water quality in receiving waters. This study was conducted in Gothenburg, Sweden, and is unique because it simultaneously investigates the occurrence of OP, metals, and MP on roads and in stormwater from an urban area under reconstruction. Correlations between the various pollutants were also explored. The study was carried out by collecting washwater and sweepsand generated from street sweeping, road surface sampling, and flow-proportional stormwater sampling on several occasions. The liquid and solid samples were analyzed for metals, polycyclic aromatic hydrocarbons (PAH), oxy-PAH, aliphatics, aromatics, phthalates, and MP. The occurrence of OP was also analyzed with a non-target screening method of selected samples. Microplastics, i.e. plastic fragments/fibers, paint fragments, tire wear particles (TWP) and bitumen, were analyzed with a method based on density separation with sodium iodide and identification with a stereo microscope, melt-tests, and tactile identification. MP concentrations amounted to 1500 particles/L in stormwater, 51,000 particles/L in washwater, and 2.6 × 106 particles/kg dw in sweepsand. In stormwater, washwater and sweepsand, MP ≥20 µm were found to be dominated by TWP (38%, 83% and 78%, respectively). The results confirm traffic as an important source to MP, OP, and metal emissions. Concentrations exceeding water and sediment quality guidelines for metals (e.g. Cu and Zn), PAH, phthalates, and aliphatic hydrocarbons in the C16-C35 fraction were found in most samples. The results show that the street sweeper collects large amounts of polluted materials and thereby prevents further spread of the pollutants to the receiving stormwater.

3.
Opt Express ; 28(24): 36584-36599, 2020 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-33379749

RESUMEN

Trade-offs between absorption and scattering cross sections of lossy obstacles confined to an arbitrarily shaped volume are formulated as a multi-objective optimization problem solvable by Lagrangian-dual methods. Solutions to this optimization problem yield a Pareto-optimal set, the shape of which reveals the feasibility of achieving simultaneously extremal absorption and scattering. Two forms of the trade-off problems are considered involving both pre-assigned loss and reactive material parameters. Numerical comparisons between the derived multi-objective bounds and several classes of realized structures are made. Additionally, low-frequency (electrically small, long wavelength) limits are examined for certain special cases.

4.
Sci Total Environ ; 729: 138950, 2020 Aug 10.
Artículo en Inglés | MEDLINE | ID: mdl-32371211

RESUMEN

Tire and road wear particles have been identified as a potential major source of microplastics in the environment. However, more knowledge of the emissions and their further fate in the environment is needed, and the effectiveness and benefits of potential measures must be investigated to support future risk management efforts. Here the concentrations of tire and bitumen microplastic particles (TBMP) on roads and in nearby in stormwater, sweepsand and washwater were measured for the first time within the same area and time period. The analysis also included plastic, paint and fiber particles. Road dust was sampled on the road surface using a wet dust sampler, before and after street sweeping on two occasions. On each of these occasions, and several occasions during a four-month period with frequent street sweeping, sweepsand and washwater, as well as flow-weighted sampling of stormwater, were collected. TBMP concentrations were operationally defined, using density separation for some samples, followed by analysis by stereo microscopy. Sodium iodide (NaI) was found to be effective for density separation of TBMP. The largest proportion of anthropogenic microplastics detected consisted of tire tread wear and bitumen. The number of TBMP ≥100 µm in the WDS samples was up to 2561 particles/L. Sweepsand and washwater contained high amounts of TBMP ≥100 µm, up to 2170 particles/kg dw and 4500 particles/L, respectively. The results show that the sweeper collects considerable amounts of TBMP, and thus weekly sweeping might prevent further transport of TBMP to the receiving stormwater. In stormwater the number of particles ≥100 µm was up to 3 particles/L and ≥ 20 µm was up to 5900 particles/L showing the importance of analysing smaller microparticle sizes than 100 µm in all samples in future studies. This study also confirms that there is a substantial volume of TBMP generated from traffic that enters the environment.

5.
PLoS One ; 15(5): e0232989, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32407402

RESUMEN

Multi drug treatments are increasingly used in the clinic to combat complex and co-occurring diseases. However, most drug combination discovery efforts today are mainly focused on anticancer therapy and rarely examine the potential of using more than two drugs simultaneously. Moreover, there is currently no reported methodology for performing second- and higher-order drug combination analysis of secretomic patterns, meaning protein concentration profiles released by the cells. Here, we introduce COMBSecretomics (https://github.com/EffieChantzi/COMBSecretomics.git), the first pragmatic methodological framework designed to search exhaustively for second- and higher-order mixtures of candidate treatments that can modify, or even reverse malfunctioning secretomic patterns of human cells. This framework comes with two novel model-free combination analysis methods; a tailor-made generalization of the highest single agent principle and a data mining approach based on top-down hierarchical clustering. Quality control procedures to eliminate outliers and non-parametric statistics to quantify uncertainty in the results obtained are also included. COMBSecretomics is based on a standardized reproducible format and could be employed with any experimental platform that provides the required protein release data. Its practical use and functionality are demonstrated by means of a proof-of-principle pharmacological study related to cartilage degradation. COMBSecretomics is the first methodological framework reported to enable secretome-related second- and higher-order drug combination analysis. It could be used in drug discovery and development projects, clinical practice, as well as basic biological understanding of the largely unexplored changes in cell-cell communication that occurs due to disease and/or associated pharmacological treatment conditions.


Asunto(s)
Combinación de Medicamentos , Descubrimiento de Drogas/métodos , Metabolómica/métodos , Cartílago/efectos de los fármacos , Cartílago/metabolismo , Simulación por Computador , Descubrimiento de Drogas/estadística & datos numéricos , Evaluación Preclínica de Medicamentos/métodos , Evaluación Preclínica de Medicamentos/estadística & datos numéricos , Humanos , Técnicas In Vitro , Metabolómica/estadística & datos numéricos , Modelos Biológicos , Osteoartritis/tratamiento farmacológico , Osteoartritis/metabolismo , Proteómica/métodos , Proteómica/estadística & datos numéricos , Programas Informáticos
6.
Ann Biomed Eng ; 48(10): 2438-2448, 2020 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-32472364

RESUMEN

Osteoarthritis (OA) is characterized by irreversible cartilage degradation with very limited therapeutic interventions. Drug candidates targeted at prototypic players had limited success until now and systems based approaches might be necessary. Consequently, drug evaluation platforms should consider the biological complexity looking beyond well-known contributors of OA. In this study an ex vivo model of cartilage degradation, combined with measuring releases of 27 proteins, was utilized to study 9 drug candidates. After an initial single drug evaluation step the 3 most promising compounds were selected and employed in an exhaustive combinatorial experiment. The resulting most and least promising treatment candidates were selected and validated in an independent study. This included estimation of mechanical properties via finite element modelling (FEM) and quantification of cartilage degradation as glycosaminoglycan (GAG) release. The most promising candidate showed increase of Young's modulus, decrease of hydraulic permeability and decrease of GAG release. The least promising candidate exhibited the opposite behaviour. The study shows the potential of a novel drug evaluation platform in identifying treatments that might reduce cartilage degradation. It also demonstrates the promise of exhaustive combination experiments and a connection between chondrocyte responses at the molecular level with changes of biomechanical properties at the tissue level.


Asunto(s)
Antiinflamatorios/farmacología , Cartílago Articular/efectos de los fármacos , Evaluación Preclínica de Medicamentos/métodos , Modelos Biológicos , Osteoartritis/tratamiento farmacológico , Anciano , Fenómenos Biomecánicos , Cartílago Articular/metabolismo , Cartílago Articular/fisiología , Supervivencia Celular , Femenino , Cabeza Femoral , Glicosaminoglicanos/metabolismo , Humanos , Proteínas/metabolismo
7.
Environ Int ; 135: 105337, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31794938

RESUMEN

Road areas are pollution hotspots where many metals, organic pollutants (OPs) and nano/microparticles accumulate before being transported to receiving waters. Particles on roads originate from e.g. road, tyre and vehicle wear, winter road maintenance, soil erosion, and deposition. Street sweeping has the potential to be an effective and affordable practice to reduce the occurrence of road dust, and thereby the subsequent spreading of pollutants, but there is currently little knowledge regarding its effectiveness. In this paper we investigate the potential of street sweeping to reduce the amounts of OPs and nano/microparticles reaching stormwater, in a case study sampling road dust and washwater from a street sweeping machine, road dust before and after sweeping, and stormwater. The compound groups generally found in the highest concentrations in all matrices were aliphatics C5-C35 > phthalates > aromatics C8-C35 > PAH-16. The concentrations of aliphatics C16-C35 and PAHs in washwater were extremely high at ≤ 53,000 µg/L and ≤ 120 µg/L, respectively, and the highest concentrations were found after a 3-month winter break in sweeping. In general, fewer aliphatic and aromatic petroleum hydrocarbons and PAHs were detected in road dust samples than in washwater. The relative composition of the specific PAH-16 suggests tyre wear, vehicle exhausts, brake linings, motor oils and road surface wear as possible sources. The study indicates that many of the hydrophobic compounds quantified in washwater are attached to small particles or truly dissolved. The washwater contains a wide range of small particles, including nanoparticles in sizes from just below 1 nm up to 300 nm, with nanoparticles in the size range 25-300 nm present in the highest concentrations. The results also indicated agglomeration of nanoparticles in the washwater. The street sweeping collected a large amount of fine particles and associated pollutants, leading to the conclusion that washwater from street sweeping needs to be treated before disposal.


Asunto(s)
Contaminantes Atmosféricos , Contaminantes Ambientales , Hidrocarburos Policíclicos Aromáticos , Emisiones de Vehículos , Polvo , Monitoreo del Ambiente , Contaminación Ambiental
8.
Opt Express ; 27(23): 34323-34342, 2019 Nov 11.
Artículo en Inglés | MEDLINE | ID: mdl-31878482

RESUMEN

Two different versions of an optical theorem for a scattering body embedded inside a lossy background medium are derived in this paper. The corresponding fundamental upper bounds on absorption are then obtained in closed form by elementary optimization techniques. The first version is formulated in terms of polarization currents (or equivalent currents) inside the scatterer and generalizes previous results given for a lossless medium. The corresponding bound is referred to here as a variational bound and is valid for an arbitrary geometry with a given material property. The second version is formulated in terms of the T-matrix parameters of an arbitrary linear scatterer circumscribed by a spherical volume and gives a new fundamental upper bound on the total absorption of an inclusion with an arbitrary material property (including general bianisotropic materials). The two bounds are fundamentally different as they are based on different assumptions regarding the structure and the material property. Numerical examples including homogeneous and layered (core-shell) spheres are given to demonstrate that the two bounds provide complimentary information in a given scattering problem.

9.
PLoS One ; 14(10): e0224231, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31634377

RESUMEN

The pathophysiology of osteoarthritis (OA) involves dysregulation of anabolic and catabolic processes associated with a broad panel of proteins that ultimately lead to cartilage degradation. An increased understanding about these protein interactions with systematic in vitro analyses may give new ideas regarding candidates for treatment of OA related cartilage degradation. Therefore, an ex vivo tissue model of cartilage degradation was established by culturing tissue explants with bacterial collagenase II. Responses of healthy and degrading cartilage were analyzed through protein abundance in tissue supernatant with a 26-multiplex protein profiling assay, after exposing the samples to a panel of 55 protein stimulations present in synovial joints of OA patients. Multivariate data analysis including exhaustive pairwise variable subset selection identified the most outstanding changes in measured protein secretions. MMP9 response to stimulation was outstandingly low in degrading cartilage and there were several protein pairs like IFNG and MMP9 that can be used for successful discrimination between degrading and healthy samples. The discovered changes in protein responses seem promising for accurate detection of degrading cartilage. The ex vivo model seems interesting for drug discovery projects related to cartilage degradation, for example when trying to uncover the unknown interactions between secreted proteins in healthy and degrading tissues.


Asunto(s)
Cartílago Articular/patología , Condrocitos/patología , Interferón gamma/metabolismo , Metaloproteinasa 9 de la Matriz/metabolismo , Osteoartritis/patología , Anciano , Anciano de 80 o más Años , Cartílago Articular/efectos de los fármacos , Cartílago Articular/metabolismo , Estudios de Casos y Controles , Condrocitos/efectos de los fármacos , Condrocitos/metabolismo , Colagenasas/farmacología , Femenino , Humanos , Masculino , Osteoartritis/tratamiento farmacológico , Osteoartritis/metabolismo
10.
BMC Bioinformatics ; 20(1): 304, 2019 Jun 04.
Artículo en Inglés | MEDLINE | ID: mdl-31164078

RESUMEN

BACKGROUND: Pharmacological treatment of complex diseases using more than two drugs is commonplace in the clinic due to better efficacy, decreased toxicity and reduced risk for developing resistance. However, many of these higher-order treatments have not undergone any detailed preceding in vitro evaluation that could support their therapeutic potential and reveal disease related insights. Despite the increased medical need for discovery and development of higher-order drug combinations, very few reports from systematic large-scale studies along this direction exist. A major reason is lack of computational tools that enable automated design and analysis of exhaustive drug combination experiments, where all possible subsets among a panel of pre-selected drugs have to be evaluated. RESULTS: Motivated by this, we developed COMBImage2, a parallel computational framework for higher-order drug combination analysis. COMBImage2 goes far beyond its predecessor COMBImage in many different ways. In particular, it offers automated 384-well plate design, as well as quality control that involves resampling statistics and inter-plate analyses. Moreover, it is equipped with a generic matched filter based object counting method that is currently designed for apoptotic-like cells. Furthermore, apart from higher-order synergy analyses, COMBImage2 introduces a novel data mining approach for identifying interesting temporal response patterns and disentangling higher- from lower- and single-drug effects. COMBImage2 was employed in the context of a small pilot study focused on the CUSP9v4 protocol, which is currently used in the clinic for treatment of recurrent glioblastoma. For the first time, all 246 possible combinations of order 4 or lower of the 9 single drugs consisting the CUSP9v4 cocktail, were evaluated on an in vitro clonal culture of glioma initiating cells. CONCLUSIONS: COMBImage2 is able to automatically design and robustly analyze exhaustive and in general higher-order drug combination experiments. Such a versatile video microscopy oriented framework is likely to enable, guide and accelerate systematic large-scale drug combination studies not only for cancer but also other diseases.


Asunto(s)
Antineoplásicos/uso terapéutico , Minería de Datos/métodos , Combinación de Medicamentos , Glioblastoma/tratamiento farmacológico , Algoritmos , Apoptosis , Humanos , Microscopía por Video , Recurrencia Local de Neoplasia/tratamiento farmacológico , Proyectos Piloto
11.
BMC Bioinformatics ; 19(1): 453, 2018 Nov 26.
Artículo en Inglés | MEDLINE | ID: mdl-30477419

RESUMEN

BACKGROUND: Large-scale pairwise drug combination analysis has lately gained momentum in drug discovery and development projects, mainly due to the employment of advanced experimental-computational pipelines. This is fortunate as drug combinations are often required for successful treatment of complex diseases. Furthermore, most new drugs cannot totally replace the current standard-of-care medication, but rather have to enter clinical use as add-on treatment. However, there is a clear deficiency of computational tools for label-free and temporal image-based drug combination analysis that go beyond the conventional but relatively uninformative end point measurements. RESULTS: COMBImage is a fast, modular and instrument independent computational framework for in vitro pairwise drug combination analysis that quantifies temporal changes in label-free video microscopy movies. Jointly with automated analyses of temporal changes in cell morphology and confluence, it performs and displays conventional cell viability and synergy end point analyses. The image processing algorithms are parallelized using Google's MapReduce programming model and optimized with respect to method-specific tuning parameters. COMBImage is shown to process time-lapse microscopy movies from 384-well plates within minutes on a single quad core personal computer. This framework was employed in the context of an ongoing drug discovery and development project focused on glioblastoma multiforme; the most deadly form of brain cancer. Interesting add-on effects of two investigational cytotoxic compounds when combined with vorinostat were revealed on recently established clonal cultures of glioma-initiating cells from patient tumor samples. Therapeutic synergies, when normal astrocytes were used as a toxicity cell model, reinforced the pharmacological interest regarding their potential clinical use. CONCLUSIONS: COMBImage enables, for the first time, fast and optimized pairwise drug combination analyses of temporal changes in label-free video microscopy movies. Providing this jointly with conventional cell viability based end point analyses, it could help accelerating and guiding any drug discovery and development project, without use of cell labeling and the need to employ a particular live cell imaging instrument.


Asunto(s)
Quimioterapia Combinada , Procesamiento de Imagen Asistido por Computador , Microscopía por Video/métodos , Algoritmos , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Neoplasias Encefálicas/tratamiento farmacológico , Supervivencia Celular/efectos de los fármacos , Descubrimiento de Drogas , Glioblastoma/tratamiento farmacológico , Humanos , Películas Cinematográficas
12.
Oncotarget ; 8(61): 103952-103967, 2017 Nov 28.
Artículo en Inglés | MEDLINE | ID: mdl-29262612

RESUMEN

We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequently, concentration dependent but mutation independent joint Bliss and Loewe synergy/antagonism was found statistically significant. Four combinations were found synergistic/antagonistic specifically to the parental (harboring KRAS or BRAF mutation) cell line of the corresponding iso-genic cell lines pair. COMBIA offers considerable improvements over established software for synergy analysis such as MacSynergy™ II as it includes both Bliss (independence) and Loewe (additivity) analyses, together with a tailored non-parametric statistical analysis employing heteroscedasticity, controlled resampling, and global (omnibus) testing. In many cases Loewe analyses found significant synergistic as well as antagonistic effects in a cell line at different concentrations of a tested drug combination. By contrast, Bliss analysis found only one type of significant effect per cell line. In conclusion, the integrated Bliss and Loewe interaction analysis based on non-parametric statistics may provide more robust interaction analyses and reveal complex patterns of synergy and antagonism.

13.
Leuk Res ; 63: 41-46, 2017 12.
Artículo en Inglés | MEDLINE | ID: mdl-29100024

RESUMEN

We previously reported that the anti-malarial drug quinacrine has potential to be repositioned for treatment of acute myeloid leukemia (AML). As a next step towards clinical use, we assessed the efficacy of quinacrine in an AML-PS mouse model and investigated possible synergistic effects when combining quinacrine with nine other antileukemic compounds in two AML cell lines. Furthermore, we explored the in vivo activity of quinacrine in combination with the widely used AML agent cytarabine. The in vivo use of quinacrine (100mg/kg three times per week for two consecutive weeks) significantly suppressed circulating blast cells at days 30/31 and increased the median survival time (MST). The in vitro drug combination analysis yielded promising synergistic interactions when combining quinacrine with cytarabine, azacitidine and geldanamycin. Finally, combining quinacrine with cytarabine in vivo showed a significant decrease in circulating leukemic blast cells and increased MST compared to the effect of either drug used alone, thus supporting the findings from the in vitro combination experiments. Taken together, the repositioning potential of quinacrine for treatment of AML is reinforced by demonstrating significant in vivo activity and promising synergies when quinacrine is combined with different agents, including cytarabine, the hypomethylating agent azacitidine and HSP-90 inhibitor geldanamycin.


Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica/farmacología , Reposicionamiento de Medicamentos , Sinergismo Farmacológico , Leucemia Mieloide Aguda/tratamiento farmacológico , Animales , Apoptosis/efectos de los fármacos , Proliferación Celular/efectos de los fármacos , Citarabina/administración & dosificación , Femenino , Humanos , Leucemia Mieloide Aguda/patología , Masculino , Ratones , Ratones SCID , Persona de Mediana Edad , Quinacrina/administración & dosificación , Células Tumorales Cultivadas , Ensayos Antitumor por Modelo de Xenoinjerto
14.
Exp Cell Res ; 361(2): 308-315, 2017 12 15.
Artículo en Inglés | MEDLINE | ID: mdl-29107068

RESUMEN

We and others have previously reported a correlation between high phosphodiesterase 3A (PDE3A) expression and selective sensitivity to phosphodiesterase (PDE) inhibitors. This indicates that PDE3A could serve both as a drug target and a biomarker of sensitivity to PDE3 inhibition. In this report, we explored publicly available mRNA gene expression data to identify cell lines with different PDE3A expression. Cell lines with high PDE3A expression showed marked in vitro sensitivity to PDE inhibitors zardaverine and quazinone, when compared with those having low PDE3A expression. Immunofluorescence and immunohistochemical stainings were in agreement with PDE3A mRNA expression, providing suitable alternatives for biomarker analysis of clinical tissue specimens. Moreover, we here demonstrate that tumor cells from patients with ovarian carcinoma show great variability in PDE3A protein expression and that level of PDE3A expression is correlated with sensitivity to PDE inhibition. Finally, we demonstrate that PDE3A is highly expressed in subsets of patient tumor cell samples from different solid cancer diagnoses and expressed at exceptional levels in gastrointestinal stromal tumor (GIST) specimens. Importantly, vulnerability to PDE3 inhibitors has recently been associated with co-expression of PDE3A and Schlafen family member 12 (SLFN12). We here demonstrate that high expression of PDE3A in clinical specimens, at least on the mRNA level, seems to be frequently associated with high SLFN12 expression. In conclusion, PDE3A seems to be both a promising biomarker and drug target for individualized drug treatment of various cancers.


Asunto(s)
Biomarcadores de Tumor/genética , Fosfodiesterasas de Nucleótidos Cíclicos Tipo 3/genética , Proteínas de Neoplasias/genética , Inhibidores de Fosfodiesterasa/farmacología , ARN Mensajero/genética , Adulto , Anciano , Antineoplásicos/farmacología , Biomarcadores de Tumor/metabolismo , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Línea Celular Tumoral , Neoplasias del Colon/tratamiento farmacológico , Neoplasias del Colon/genética , Neoplasias del Colon/metabolismo , Neoplasias del Colon/patología , Fosfodiesterasas de Nucleótidos Cíclicos Tipo 3/metabolismo , Femenino , Tumores del Estroma Gastrointestinal/tratamiento farmacológico , Tumores del Estroma Gastrointestinal/genética , Tumores del Estroma Gastrointestinal/metabolismo , Tumores del Estroma Gastrointestinal/patología , Expresión Génica , Humanos , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patología , Masculino , Melanoma/tratamiento farmacológico , Melanoma/genética , Melanoma/metabolismo , Melanoma/patología , Persona de Mediana Edad , Terapia Molecular Dirigida , Proteínas de Neoplasias/antagonistas & inhibidores , Proteínas de Neoplasias/metabolismo , Especificidad de Órganos , Compuestos Organoplatinos/farmacología , Oxaliplatino , Piridazinas/farmacología , Quinazolinas/farmacología , ARN Mensajero/antagonistas & inhibidores , ARN Mensajero/metabolismo , Neoplasias Cutáneas/tratamiento farmacológico , Neoplasias Cutáneas/genética , Neoplasias Cutáneas/metabolismo , Neoplasias Cutáneas/patología
15.
Metabolomics ; 13(7): 79, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28596718

RESUMEN

INTRODUCTION: Mass spectrometry based metabolomics has become a promising complement and alternative to transcriptomics and proteomics in many fields including in vitro systems pharmacology. Despite several merits, metabolomics based on liquid chromatography mass spectrometry (LC-MS) is a developing area that is yet attached to several pitfalls and challenges. To reach a level of high reliability and robustness, these issues need to be tackled by implementation of refined experimental and computational protocols. OBJECTIVES: This study illustrates some key pitfalls in LC-MS based metabolomics and introduces an automated computational procedure to compensate for them. METHOD: Non-cancerous mammary gland derived cells were exposed to 27 chemicals from four pharmacological classes plus a set of six pesticides. Changes in the metabolome of cell lysates were assessed after 24 h using LC-MS. A data processing pipeline was established and evaluated to handle issues including contaminants, carry over effects, intensity decay and inherent methodology variability and biases. A key component in this pipeline is a latent variable method called OOS-DA (optimal orthonormal system for discriminant analysis), being theoretically more easily motivated than PLS-DA in this context, as it is rooted in pattern classification rather than regression modeling. RESULT: The pipeline is shown to reduce experimental variability/biases and is used to confirm that LC-MS spectra hold drug class specific information. CONCLUSION: LC-MS based metabolomics is a promising methodology, but comes with pitfalls and challenges. Key difficulties can be largely overcome by means of a computational procedure of the kind introduced and demonstrated here. The pipeline is freely available on www.github.com/stephanieherman/MS-data-processing.

16.
Cell Chem Biol ; 23(11): 1428-1438, 2016 Nov 17.
Artículo en Inglés | MEDLINE | ID: mdl-27984028

RESUMEN

Cancer cell lines grown as two-dimensional (2D) cultures have been an essential model for studying cancer biology and anticancer drug discovery. However, 2D cancer cell cultures have major limitations, as they do not closely mimic the heterogeneity and tissue context of in vivo tumors. Developing three-dimensional (3D) cell cultures, such as multicellular tumor spheroids, has the potential to address some of these limitations. Here, we combined a high-throughput gene expression profiling method with a tumor spheroid-based drug-screening assay to identify context-dependent treatment responses. As a proof of concept, we examined drug responses of quiescent cancer cells to oxidative phosphorylation (OXPHOS) inhibitors. Use of multicellular tumor spheroids led to discovery that the mevalonate pathway is upregulated in quiescent cells during OXPHOS inhibition, and that OXPHOS inhibitors and mevalonate pathway inhibitors were synergistically toxic to quiescent spheroids. This work illustrates how 3D cellular models yield functional and mechanistic insights not accessible via 2D cultures.


Asunto(s)
Antineoplásicos/farmacología , Técnicas de Cultivo de Célula/métodos , Ensayos de Selección de Medicamentos Antitumorales/métodos , Neoplasias/tratamiento farmacológico , Fosforilación Oxidativa/efectos de los fármacos , Esferoides Celulares/efectos de los fármacos , Línea Celular Tumoral , Perfilación de la Expresión Génica/métodos , Ensayos Analíticos de Alto Rendimiento/métodos , Humanos , Ácido Mevalónico/metabolismo , Neoplasias/genética , Neoplasias/metabolismo , Transducción de Señal/efectos de los fármacos , Esferoides Celulares/metabolismo , Transcriptoma/efectos de los fármacos , Células Tumorales Cultivadas
17.
Cell Rep ; 17(11): 2994-3009, 2016 12 13.
Artículo en Inglés | MEDLINE | ID: mdl-27974212

RESUMEN

Intratumoral heterogeneity is a hallmark of glioblastoma multiforme and thought to negatively affect treatment efficacy. Here, we establish libraries of glioma-initiating cell (GIC) clones from patient samples and find extensive molecular and phenotypic variability among clones, including a range of responses to radiation and drugs. This widespread variability was observed as a continuum of multitherapy resistance phenotypes linked to a proneural-mesenchymal shift in the transcriptome. Multitherapy resistance was associated with a semi-stable cell state that was characterized by an altered DNA methylation pattern at promoter regions of mesenchymal master regulators and enhancers. The gradient of cell states within the GIC compartment constitutes a distinct form of heterogeneity. Our findings may open an avenue toward the development of new therapeutic rationales designed to reverse resistant cell states.


Asunto(s)
Metilación de ADN/genética , Glioblastoma/genética , Proteínas de Neoplasias/genética , Células Madre Neoplásicas/metabolismo , Línea Celular Tumoral , Metilación de ADN/efectos de los fármacos , Metilación de ADN/efectos de la radiación , Transición Epitelial-Mesenquimal/efectos de los fármacos , Transición Epitelial-Mesenquimal/efectos de la radiación , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Regulación Neoplásica de la Expresión Génica/efectos de la radiación , Glioblastoma/tratamiento farmacológico , Glioblastoma/patología , Glioblastoma/radioterapia , Humanos , Células Madre Neoplásicas/patología , Regiones Promotoras Genéticas
18.
PLoS One ; 11(2): e0149821, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-26914813

RESUMEN

The objective of this study was to develop and apply a novel multiplex panel of solid-phase proximity ligation assays (SP-PLA) requiring only 20 µL of samples, as a tool for discovering protein biomarkers for neurological disease and treatment thereof in cerebrospinal fluid (CSF). We applied the SP-PLA to samples from two sets of patients with poorly understood nervous system pathologies amyotrophic lateral sclerosis (ALS) and neuropathic pain, where patients were treated with spinal cord stimulation (SCS). Forty-seven inflammatory and neurotrophic proteins were measured in samples from 20 ALS patients and 15 neuropathic pain patients, and compared to normal concentrations in CSF from control individuals. Nineteen of the 47 proteins were detectable in more than 95% of the 72 controls. None of the 21 proteins detectable in CSF from neuropathic pain patients were significantly altered by SCS. The levels of the three proteins, follistatin, interleukin-1 alpha, and kallikrein-5 were all significantly reduced in the ALS group compared to age-matched controls. These results demonstrate the utility of purpose designed multiplex SP-PLA panels in CSF biomarker research for understanding neuropathological and neurotherapeutic mechanisms. The protein changes found in the CSF of ALS patients may be of diagnostic interest.


Asunto(s)
Esclerosis Amiotrófica Lateral/líquido cefalorraquídeo , Proteínas del Líquido Cefalorraquídeo/líquido cefalorraquídeo , Neuralgia/líquido cefalorraquídeo , Adulto , Anciano , Anciano de 80 o más Años , Biomarcadores/líquido cefalorraquídeo , Estudios de Casos y Controles , Femenino , Humanos , Masculino , Persona de Mediana Edad , Adulto Joven
19.
Mol Cancer Ther ; 14(6): 1504-16, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25911689

RESUMEN

Because dormant cancer cells in hypoxic and nutrient-deprived regions of solid tumors provide a major obstacle to treatment, compounds targeting those cells might have clinical benefits. Here, we describe a high-throughput drug screening approach, using glucose-deprived multicellular tumor spheroids (MCTS) with inner hypoxia, to identify compounds that specifically target this cell population. We used a concept of drug repositioning-using known molecules for new indications. This is a promising strategy to identify molecules for rapid clinical advancement. By screening 1,600 compounds with documented clinical history, we aimed to identify candidates with unforeseen potential for repositioning as anticancer drugs. Our screen identified five molecules with pronounced MCTS-selective activity: nitazoxanide, niclosamide, closantel, pyrvinium pamoate, and salinomycin. Herein, we show that all five compounds inhibit mitochondrial respiration. This suggests that cancer cells in low glucose concentrations depend on oxidative phosphorylation rather than solely glycolysis. Importantly, continuous exposure to the compounds was required to achieve effective treatment. Nitazoxanide, an FDA-approved antiprotozoal drug with excellent pharmacokinetic and safety profile, is the only molecule among the screening hits that reaches high plasma concentrations persisting for up to a few hours after single oral dose. Nitazoxanide activated the AMPK pathway and downregulated c-Myc, mTOR, and Wnt signaling at clinically achievable concentrations. Nitazoxanide combined with the cytotoxic drug irinotecan showed anticancer activity in vivo. We here report that the FDA-approved anthelmintic drug nitazoxanide could be a potential candidate for advancement into cancer clinical trials.


Asunto(s)
Técnicas de Cultivo de Célula/métodos , Neoplasias Colorrectales/tratamiento farmacológico , Tiazoles/farmacología , Ensayos Antitumor por Modelo de Xenoinjerto , Administración Oral , Animales , Antihelmínticos/administración & dosificación , Antihelmínticos/farmacocinética , Antihelmínticos/farmacología , Antineoplásicos/administración & dosificación , Antineoplásicos/farmacocinética , Antineoplásicos/farmacología , Hipoxia de la Célula , Supervivencia Celular/efectos de los fármacos , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Relación Dosis-Respuesta a Droga , Reposicionamiento de Medicamentos/métodos , Ensayos de Selección de Medicamentos Antitumorales/métodos , Femenino , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Células HCT116 , Células HT29 , Humanos , Ratones Endogámicos , Ratones Desnudos , Microscopía Fluorescente , Nitrocompuestos , Fosforilación Oxidativa/efectos de los fármacos , Transducción de Señal/efectos de los fármacos , Esferoides Celulares/efectos de los fármacos , Esferoides Celulares/metabolismo , Tiazoles/administración & dosificación , Tiazoles/farmacocinética
20.
Clin Epigenetics ; 7: 11, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25729447

RESUMEN

BACKGROUND: We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL. RESULTS: We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived that consisted of only 246 CpG sites. The mean sensitivity and specificity of the classifier across the known subtypes was 0.90 and 0.99, respectively. We then used DNA methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations ('other' subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative polymerase chain reaction (PCR) and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5. CONCLUSIONS: Our findings indicate that DNA methylation profiling contributes to the clarification of the heterogeneity in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant biological characteristics in otherwise unclassified ALL patients.

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