Label-Free Quantitative Proteomics Analysis of Adriamycin Selected Multidrug Resistant Human Lung Cancer Cells.

The development of drug resistance in lung cancer is a major clinical challenge, leading to a 5-year survival rate of only 18%. Therefore, unravelling the mechanisms of drug resistance and developing novel therapeutic strategies is of crucial importance. This study systematically explores the novel biomarkers of drug resistance using a lung cancer model (DLKP) with a series of drug-resistant variants. In-depth label-free quantitative mass spectrometry-based proteomics and gene ontology analysis shows that parental DLKP cells significantly differ from drug-resistant variants, and the cellular proteome changes even among the drug-resistant subpopulations. Overall, ABC transporter proteins and lipid metabolism were determined to play a significant role in the formation of drug resistance in DKLP cells. A series of membrane-related proteins such as HMOX1, TMB1, EPHX2 and NEU1 were identified to be correlated with levels of drug resistance in the DLKP subpopulations. The study also showed enrichment in biological processes and molecular functions such as drug metabolism, cellular response to the drug and drug binding. In gene ontology analysis, 18 proteins were determined to be positively or negatively correlated with resistance levels. Overall, 34 proteins which potentially have a therapeutic and diagnostic value were identified.

Monitoring stem cell differentiation using Raman microspectroscopy: chondrogenic differentiation, towards cartilage formation.

Mesenchymal Stem Cells (MSCs) have the ability to differentiate into chondrocytes, the only cellular components of cartilage and are therefore ideal candidates for cartilage and tissue repair technologies. Chondrocytes are surrounded by cartilage-like extracellular matrix (ECM), a complex network rich in glycosaminoglycans, proteoglycans, and collagen, which, together with a multitude of intracellular signalling molecules, trigger the chondrogenesis and allow the chondroprogenitor to acquire the spherical morphology of the chondrocytes. However, although the mechanisms of the differentiation of MSCs have been extensively explored, it has been difficult to provide a holistic picture of the process, in situ. Raman Micro Spectroscopy (RMS) has been demonstrated to be a powerful analytical tool, which provides detailed label free biochemical fingerprint information in a non-invasive way, for analysis of cells, tissues and body fluids. In this work, RMS is explored to monitor the process of Mesenchymal Stem Cell (MSC) differentiation into chondrocytes in vitro, providing a holistic molecular picture of cellular events governing the differentiation. Spectral signatures of the subcellular compartments, nucleolus, nucleus and cytoplasm were initially probed and characteristic molecular changes between differentiated and undifferentiated were identified. Moreover, high density cell micromasses were cultured over a period of three weeks, and a systematic monitoring of cellular molecular components and the progress of the ECM formation, associated with the chondrogenic differentiation, was performed. This study shows the potential applicability of RMS as a powerful tool to monitor and better understand the differentiation pathways and process.

Vibrational Spectroscopy for In Vitro Monitoring Stem Cell Differentiation.

Stem cell technology has attracted considerable attention over recent decades due to its enormous potential in regenerative medicine and disease therapeutics. Studying the underlying mechanisms of stem cell differentiation and tissue generation is critical, and robust methodologies and different technologies are required. Towards establishing improved understanding and optimised triggering and control of differentiation processes, analytical techniques such as flow cytometry, immunohistochemistry, reverse transcription polymerase chain reaction, RNA in situ hybridisation analysis, and fluorescence-activated cell sorting have contributed much. However, progress in the field remains limited because such techniques provide only limited information, as they are only able to address specific, selected aspects of the process, and/or cannot visualise the process at the subcellular level. Additionally, many current analytical techniques involve the disruption of the investigation process (tissue sectioning, immunostaining) and cannot monitor the cellular differentiation process in situ, in real-time. Vibrational spectroscopy, as a label-free, non-invasive and non-destructive analytical technique, appears to be a promising candidate to potentially overcome many of these limitations as it can provide detailed biochemical fingerprint information for analysis of cells, tissues, and body fluids. The technique has been widely used in disease diagnosis and increasingly in stem cell technology. In this work, the efforts regarding the use of vibrational spectroscopy to identify mechanisms of stem cell differentiation at a single cell and tissue level are summarised. Both infrared absorption and Raman spectroscopic investigations are explored, and the relative merits, and future perspectives of the techniques are discussed.

In vitro Label Free Raman Microspectroscopic Analysis to Monitor the Uptake, Fate and Impacts of Nanoparticle Based Materials.

The continued emergence of nanoscale materials for nanoparticle-based therapy, sensing and imaging, as well as their more general adoption in a broad range of industrial applications, has placed increasing demands on the ability to assess their interactions and impacts at a cellular and subcellular level, both in terms of potentially beneficial and detrimental effects. Notably, however, many such materials have been shown to interfere with conventional in vitro cellular assays that record only a single colorimetric end-point, challenging the ability to rapidly screen cytological responses. As an alternative, Raman microspectroscopy can spatially profile the biochemical content of cells, and any changes to it as a result of exogenous agents, such as toxicants or therapeutic agents, in a label free manner. In the confocal mode, analysis can be performed at a subcellular level. The technique has been employed to confirm the cellular uptake and subcellular localization of polystyrene nanoparticles (PSNPs), graphene and molybdenum disulfide micro/nano plates (MoS2), based on their respective characteristic spectroscopic signatures. In the case of PSNPs it was further employed to identify their local subcellular environment in endosomes, lysosomes and endoplasmic reticulum, while for MoS2 particles, it was employed to monitor subcellular degradation as a function of time. For amine functionalized PSNPs, the potential of Raman microspectroscopy to quantitatively characterize the dose and time dependent toxic responses has been explored, in a number of cell lines. Comparing the responses to those of poly (amidoamine) nanoscale polymeric dendrimers, differentiation of apoptotic and necrotic pathways based on the cellular spectroscopic responses was demonstrated. Drawing in particular from the experience of the authors, this paper details the progress to date in the development of applications of Raman microspectroscopy for in vitro, label free analysis of the uptake, fate and impacts of nanoparticle based materials, in vitro, and the prospects for the development of a routine, label free high content spectroscopic analysis technique.

Exploring subcellular responses of prostate cancer cells to X-ray exposure by Raman mapping.

Understanding the response of cancer cells to ionising radiation is a crucial step in modern radiotherapy. Raman microspectroscopy, together with Partial Least Squares Regression (PLSR) analysis has been shown to be a powerful tool for monitoring biochemical changes of irradiated cells on the subcellular level. However, to date, the majority of Raman studies have been performed using a single spectrum per cell, giving a limited view of the total biochemical response of the cell. In the current study, Raman mapping of the whole cell area was undertaken to ensure a more comprehensive understanding of the changes induced by X-ray radiation. On the basis of the collected Raman spectral maps, PLSR models were constructed to elucidate the time-dependent evolution of chemical changes induced in cells by irradiation, and the performance of PLSR models based on whole cell averages as compared to those based on average Raman spectra of cytoplasm and nuclear region. On the other hand, prediction of X-ray doses for individual cellular components showed that cytoplasmic and nuclear regions should be analysed separately. Finally, the advantage of the mapping technique over single point measurements was verified by a comparison of the corresponding PLSR models.

Graphene Nanoflake Uptake Mediated by Scavenger Receptors.

The biological interactions of graphene have been extensively investigated over the last 10 years. However, very little is known about graphene interactions with the cell surface and how the graphene internalization process is driven and mediated by specific recognition sites at the interface with the cell. In this work, we propose a methodology to investigate direct molecular correlations between the biomolecular corona of graphene and specific cell receptors, showing that key protein recognition motifs, presented on the nanomaterial surface, can engage selectively with specific cell receptors. We consider the case of apolipoprotein A-I, found to be very abundant in the graphene protein corona, and observe that the uptake of graphene nanoflakes is somewhat increased in cells with greatly elevated expression of scavenger receptors B1, suggesting a possible mechanism of endogenous interaction. The uptake results, obtained by flow cytometry, have been confirmed using Raman microspectroscopic mapping, exploiting the strong Raman signature of graphene.

Raman spectroscopy detects biochemical changes due to different cell culture environments in live cells in vitro.

The in vitro cell culture environment can impact on cell biochemistry and cell cycle. The manifestation of such substrate-induced changes in cell cycle in the Raman microspectroscopic profiles of cell cultures is investigated at the level of nucleolus, nucleus and cytoplasm. HeLa immortalised human cervical cells and HaCaT dermal cells were cultured on three different substrates, conventional polystyrene cell culture dishes, CaF2 slides as a commonly used Raman substrate, and glass slides coated with collagen rat tail, as a mimic of the extra-cellular matrix (ECM) environment. A cell cycle study, based on percentage DNA content, as determined using propidium iodide staining and monitored by flow cytometry, was performed on cells of both types, grown on the different substrates, confirming that the in vitro cell culture environment impacts significantly on the cell cycle. Live cell in vitro Raman spectroscopic analysis of cells on the 2D CaF2 and 3D collagen substrates was performed and data was analysed using principal component analysis (PCA). The spectroscopic analysis revealed differences in profiles which reflect the differences in cell cycle for both in vitro culture environments. In particular, the Raman spectra of cells grown on CaF2 show indicators of cell stress, which are also associated with cell cycle arrest at the G0/G1 phase. This work contributes to the field of Raman spectroscopic analysis by providing a fresh look at the significance of the effect of in vitro culture environment to cell cycle and the sensitivity of Raman spectroscopy to such differences in cell metabolism.

Advancing Raman microspectroscopy for cellular and subcellular analysis: towards in vitro high-content spectralomic analysis.

In the confocal mode, Raman microspectroscopy can profile the biochemical content of biological cells at a subcellular level, and any changes to it by exogenous agents, such as therapeutic drugs or toxicants. As an exploration of the potential of the technique as a high-content, label-free analysis technique, this report reviews work to monitor the spectroscopic signatures associated with the uptake and response pathways of commercial chemotherapeutic agents and polymeric nanoparticles by human lung cells. It is demonstrated that the signatures are reproducible and characteristic of the cellular event, and can be used, for example, to identify the mode of action of the agent as well as the subsequent cell death pathway, and even mechanisms of cellular resistance. Data mining approaches are discussed and a spectralomics approach is proposed.

Toxicological assessment of nanomaterials: the role of in vitro Raman microspectroscopic analysis.

The acceleration of nanomaterials research has brought about increased demands for rapid analysis of their bioactivity, in a multi-parametric fashion, to minimize the gap between potential applications and knowledge of their toxicological properties. The potential of Raman microspectroscopy for the analysis of biological systems with the aid of multivariate analysis techniques has been demonstrated. In this study, an overview of recent efforts towards establishing a 'label-free high content nanotoxicological assessment technique' using Raman microspectroscopy is presented. The current state of the art for cellular toxicity assessment and the potential of Raman microspectroscopy are discussed, and the spectral markers of the cellular toxic responses upon exposure to nanoparticles, changes on the identified spectral markers upon exposure to different nanoparticles, cell death mechanisms, and the effects of nanoparticles on different cell lines are summarized. Moreover, 3D toxicity plots of spectral markers, as a function of time and dose, are introduced as new methodology for toxicological analysis based on the intrinsic properties of the biomolecular changes, such as cytoplasmic RNA aberrations, protein and lipid damage associated with the toxic response. The 3D evolution of the spectral markers are correlated with the results obtained by commonly used cytotoxicity assays, and significant similarities are observed between band intensity and percentage viability obtained by the Alamar Blue assay, as an example. Therefore, the developed 3D plots can be used to identify toxicological properties of a nanomaterial and can potentially be used to predict toxicity, which can provide rapid advances in nanomedicine. Graphical Abstract Spectral markers of cytotoxicity as a function of time and dose.

Determination of spectral markers of cytotoxicity and genotoxicity using in vitro Raman microspectroscopy: cellular responses to polyamidoamine dendrimer exposure.

Although consumer exposure to nanomaterials is ever increasing, with potential increased applications in areas such as drug and/or gene delivery, contrast agents and diagnosis, the determination of the cyto- and geno-toxic effects of nanomaterials on human health and the environment still remains challenging. Although many techniques have been established and adapted to determine the cytotoxicity and genotoxicity of nano-sized materials, these techniques remain limited by the number of assays required, total cost, and use of labels and they struggle to explain the underlying interaction mechanisms. In this study, Raman microspectroscopy is employed as an in vitro label-free, high content screening technique to observe toxicological changes within the cell in a multi-parametric fashion. The evolution of spectral markers as a function of time and applied dose has been used to elucidate the mechanism of action of polyamidoamine (PAMAM) dendrimers associated with cytotoxicity and their impact on nuclear biochemistry. PAMAM dendrimers are chosen as a model nanomaterial due to their widely studied cytotoxic and genotoxic properties and commercial availability. Point spectra were acquired from the cytoplasm to monitor the cascade of toxic events occurring in the cytoplasm upon nanoparticle exposure, whereas the spectra acquired from the nucleus and the nucleolus were used to explore PAMAM-nuclear material interaction as well as genotoxic responses.

Label-free, high content screening using Raman microspectroscopy: the toxicological response of different cell lines to amine-modified polystyrene nanoparticles (PS-NH2).

Nanotoxicology has become an established area of science due to growing concerns over the production and potential use of nanomaterials in a wide-range of areas from pharmaceutics to nanomedicine. Although different cytotoxicity assays have been developed and are widely used to determine the toxicity of nanomaterials, the production of multi-parametric information in a rapid and non-invasive way is still challenging, when the amount and diversity of physicochemical properties of nanomaterials are considered. High content screening can provide such analysis, but is often prohibitive in terms of capital and recurrent costs in academic environments. As a label-free technique, the applicability of Raman microspectroscopy for the analysis of cells, tissues and bodily fluids has been extensively demonstrated. The multi-parametric information in the fingerprint region has also been used for the determination of nanoparticle localisation and toxicity. In this study, the applicability of Raman microspectroscopy as a 'high content nanotoxicological screening technique' is demonstrated, with the aid of multivariate analysis, on non-cancerous (immortalized human bronchial epithelium) and cancerous cell-lines (human lung carcinoma and human lung epidermoid cells). Aminated polystyrene nanoparticles are chosen as model nanoparticles due to their well-established toxic properties and cells were exposed to the nanoparticles for periods from 24-72 hours. Spectral markers of cellular responses such as oxidative stress, cytoplasmic RNA aberrations and liposomal rupture are identified and cell-line dependent systematic variations in these spectral markers, as a function of the exposure time, are observed using Raman microspectroscopy, and are correlated with cellular assays and imaging techniques.

In vitro monitoring of time and dose dependent cytotoxicity of aminated nanoparticles using Raman spectroscopy.

Investigation of possible adverse health effects of nanomaterials, in a rapid multi-parametric fashion, has become increasingly important, due to their increased production and potential uses in a wide range of application areas, from cosmetics to pharmaceutics. Although conventional in vitro cytotoxicological techniques provide valuable information about the particle toxicity, the importance of gaining high content information in a single assay with the analysis of multiple parameters in a non-invasive and label-free way is still one of the biggest challenges in nanotoxicology. As a vibrational spectroscopic technique, the power of Raman spectroscopy for the analysis of cells, tissues and also nanoparticle localization within cells has been shown previously. In this study, the ability of Raman spectroscopy to fingerprint the dose and time dependent cellular responses and effect of cytotoxic events on biochemical constituents of the cells is monitored. A549 human lung carcinoma cells and aminated polystyrene nanoparticles (PS-NH2) are used as a model cell line and nanoparticle, respectively. Following the determination of cellular responses in the presence of toxic PS-NH2 by using conventional cellular assays, Alamar Blue (AB) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromid (MTT), and calculation of EC50 values for both assays, Raman spectroscopy was employed at response related doses and time points. Multiple point spectra from the cytoplasm, nucleus and nucleolus of 20 cells were acquired using Raman spectroscopy for each exposure dose and timepoint. Unsupervised principle components analysis (PCA) was applied to the Raman data sets for the comparison of exposed and unexposed cells as well as different exposure doses and times. The study shows the ability of Raman spectroscopy to provide information about cellular responses at different particle concentrations and exposure times with the aid of multivariate analysis. In the chosen range of concentrations, the most significant changes were observed in the cytoplasm for both time dependent and dose dependent cases due to the route of endocytosis. The Raman spectral markers for lipidosis, ROS formation and oxidative stress related biochemical damage are determined and correlated with exposure dose and time, and the responses are correlated with conventional cytotoxicity assays.

Evaluation of cytotoxicity profile and intracellular localisation of doxorubicin-loaded chitosan nanoparticles.

In the emerging field of nanomedicine, targeted delivery of nanoparticle encapsulated active pharmaceutical ingredients (API) is seen as a potential significant development, promising improved pharmacokinetics and reduced side effects. In this context, understanding the cellular uptake of the nanoparticles and subsequent subcellular distribution of the API is of critical importance. Doxorubicin (DOX) was encapsulated within chitosan nanoparticles to investigate its intracellular delivery in A549 cells in vitro. Unloaded (CS-TPP) and doxorubicin-loaded (DOX-CS-TPP) chitosan nanoparticles were characterised for size (473 ± 41 nm), polydispersity index (0.3 ± 0.2), zeta potential (34 ± 4 mV), drug content (76 ± 7 µM) and encapsulation efficiency (95 ± 1 %). The cytotoxic response to DOX-CS-TPP was substantially stronger than to CS-TPP, although weaker than that of the equivalent free DOX. Fluorescence microscopy showed a dissimilar pattern of distribution of DOX within the cell, being predominantly localised in the nucleus for free form and in cytoplasm for DOX-CS-TPP. Confocal microscopy demonstrated endosomal localisation of DOX-CS-TPP. Numerical simulations, based on a rate equation model to describe the uptake and distribution of the free DOX, nanoparticles and DOX-loaded nanoparticles within the cells and the subsequent dose- and time-dependent cytotoxic responses, were used to further elucidate the API distribution processes. The study demonstrates that encapsulation of the API in nanoparticles results in a delayed release of the drug to the cell, resulting in a delayed cellular response. This work further demonstrates the potential of mathematical modelling in combination with intracellular imaging techniques to visualise and further understand the intracellular mechanisms of action of external agents, both APIs and nanoparticles in cells.

In situ-monitoring of biofilm formation by using surface-enhanced Raman scattering.

A biofilm is a complex biochemical structure composed of microorganisms and extracellular polymeric substances used by microorganisms to adhere to each other and to surfaces. The monitoring of molecular changes during biofilm formation in situ can provide valuable insights in medicine, microbiology, and industrial processes. In this study, we investigated the characterization of biofilm produced by two model bacteria by using surface-enhanced Raman scattering (SERS) with the use of core silver (AgNPs)-shell chitosan nanoparticles (c-AgNPs), which are prepared by coating citrate-reduced AgNPs with a thin layer of chitosan averaging 10 nm. The chitosan thin film acts as porous layer and prevents the excess interactions of biological media secreted by bacteria. The two model bacteria, Escherichia coli and Staphylococcus cohnii, gram positive and gram negative, respectively, were chosen for the study. The SERS spectra were acquired directly from the growth culture by simply placing c-AgNPs substrate on the biofilm formed during the growth of the bacteria for in situ monitoring. It was found that c-AgNPs are effective SERS substrates to monitor molecular changes in the biofilm during the biofilm formation.

Label-free detection of proteins in ternary mixtures using surface-enhanced Raman scattering and protein melting profiles.

ABSTRACT. The multiplex detection of biologically important molecules such as proteins in complex mixtures has critical importance not only in disease diagnosis but also in other fields such as proteomics and biotechnology. Surface-enhanced Raman scattering (SERS) is a powerful technique for multiplex identification of molecular components in a mixture. We combined the multiplexing power of SERS and heat denaturation of proteins to identify proteins in ternary protein mixtures. The heat denaturation profiles of four model blood proteins, transferrin, human serum albumin, fibrinogen, and hemoglobin, were studied with SERS. Then, two ternary mixtures of these four proteins were used to test the feasibility of the approach. It was demonstrated that unique denaturation profiles of each protein could be used for their identification in the mixture.