Spectral cross-correlation as a supervised approach for the analysis of complex Raman datasets: the case of nanoparticles in biological cells

Monitoring and modelling the glutamine metabolic pathway: a review and future perspectives

BACKGROUND

Analysis of the glutamine metabolic pathway has taken a special place in metabolomics research in recent years, given its important role in cell biosynthesis and bioenergetics across several disorders, especially in cancer cell survival. The science of metabolomics addresses the intricate intracellular metabolic network by exploring and understanding how cells function and respond to external or internal perturbations to identify potential therapeutic targets. However, despite recent advances in metabolomics, monitoring the kinetics of a metabolic pathway in a living cell in situ, real-time and holistically remains a significant challenge.

AIM

This review paper explores the range of analytical approaches for monitoring metabolic pathways, as well as physicochemical modeling techniques, with a focus on glutamine metabolism. We discuss the advantages and disadvantages of each method and explore the potential of label-free Raman microspectroscopy, in conjunction with kinetic modeling, to enable real-time and in situ monitoring of the cellular kinetics of the glutamine metabolic pathway.

KEY SCIENTIFIC CONCEPTS

Given its important role in cell metabolism, the ability to monitor and model the glutamine metabolic pathways are highlighted. Novel, label free approaches have the potential to revolutionise metabolic biosensing, laying the foundation for a new paradigm in metabolomics research and addressing the challenges in monitoring metabolic pathways in living cells.

Microfluidic SERS devices: brightening the future of bioanalysis

A new avenue has opened up for applications of surface-enhanced Raman spectroscopy (SERS) in the biomedical field, mainly due to the striking advantages offered by SERS tags. SERS tags provide indirect identification of analytes with rich and highly specific spectral fingerprint information, high sensitivity, and outstanding multiplexing potential, making them very useful in in vitro and in vivo assays. The recent and innovative advances in nanomaterial science, novel Raman reporters, and emerging bioconjugation protocols have helped develop ultra-bright SERS tags as powerful tools for multiplex SERS-based detection and diagnosis applications. Nevertheless, to translate SERS platforms to real-world problems, some challenges, especially for clinical applications, must be addressed. This review presents the current understanding of the factors influencing the quality of SERS tags and the strategies commonly employed to improve not only spectral quality but the specificity and reproducibility of the interaction of the analyte with the target ligand. It further explores some of the most common approaches which have emerged for coupling SERS with microfluidic technologies, for biomedical applications. The importance of understanding microfluidic production and characterisation to yield excellent device quality while ensuring high throughput production are emphasised and explored, after which, the challenges and approaches developed to fulfil the potential that SERS-based microfluidics have to offer are described.

Reusable and highly sensitive SERS immunoassay utilizing gold nanostars and a cellulose hydrogel-based platform

The development of robust and sensitive point-of-care testing platforms is necessary to improve patient care and outcomes. Surface-enhanced Raman scattering (SERS)-based immunosensors are especially suited for this purpose. Here, we present a highly sensitive and selective SERS immunoassay, demonstrating for example the detection of horseradish peroxidase (HRP), in a sandwich format. The strength of our biosensor lies in merging: (i) SERS-immunotags based on gold nanostars, allowing exceptional intense SERS from attached Raman probes, covalent attachment of anti-HRP antibodies by a simple chemical method providing exceptional antigen binding activity; (ii) the ease of preparation of the capture platform from a regenerated cellulose-based hydrogel, a transparent material, ideal for microfluidics applications, with low background fluorescence and Raman signal, particularly suited for preserving high activity of the covalently bound anti-HRP antibodies. The sandwich complexes formed were characterised by atomic force microscopy, and by scanning electron microscopy coupled with electron diffraction spectroscopy; and (iii) the robustness of the simple Classical Least Squares method for SERS data analysis, resulting in superior discrimination of SERS signals from the background and much better data fitting, compared to the commonly used peak integral method. Our SERS immunoassay greatly improves the detection limits of traditional enzyme-linked immunosorbent assay approaches, and its performance is better or comparable to those of existing SERS-based immunosensors. Our approach successfully overcomes the main challenges of application at point-of-care, including increasing reproducibility, sensitivity, and specificity, associated with an environmentally friendly and robust design. Also, the proposed design withstands several cycles of regeneration, a feature absent in paper-SERS immunoassays and this opens the way for sensitive multiplexing applications on a microfluidic platform.

Label-free screening of biochemical changes in macrophage-like cells following MoS2 exposure using Raman micro-spectroscopy

The emergence of large scale production techniques for 2D particulate materials has dramatically increased their applications potential. Understanding the interactions of biological cells with such particulate material is therefore of paramount importance, both for toxicological assessment and potential biomedical applications. Conventional in-vitro cytological assays commonly record only a single colorimetric end-point, and do not provide an in-depth analysis of how such materials are uptaken and processed within cells. To demonstrate its potential as an alternative, label free approach, confocal Raman micro-spectroscopy has been used to profile the cellular response of macrophage-like immune cells as a result of exposure to a sub-lethal dose of particulate MoS₂, as an example novel 2D material. Particles were seen to be uptaken and trafficked in sub-cellular vesicles, and this sensitive technique allows differences in the biochemical composition of the vesicles to be assessed and monitored as a function of time. Untreated macrophage-like cells contain lipidic vesicles which are found to be relatively rich in the membrane lipid sphingomyelin, key to the process of cell membrane regeneration. After exposure to MoS₂, the particulate material is seen to be invaginated in similar vesicles, the most prominent of which now, however, have spectroscopic signatures which are dominated by those of phosphatidyl family lipids, consistent with the phagocytotic pathway. The lipidic content of cells is seen to increase at all time-points (4, 24 and 72 h). although vesicles composed of sphingomyelin become more prominent again following a prolonged incubation of 72 h to a sub-lethal dose of MoS₂, as the immune cell has processed the particulate material and initiates recovery to a normal/untreated state. This study reveals Raman micro-spectroscopy is an effective method for monitoring cellular responses and evolution of organelle compositions in response to MoS₂ exposure. The additional benefit of using this technique is that cells can be monitored as a function of time, while it can also be used for screening other micro/nano materials for toxicology and/or establishing cell responses.

Comprehensive phenotyping and multi-omic profiling in the toxicity assessment of nanopolystyrene with different surface properties

There is a growing concern regarding the toxic effects of terrestrial nanoplastic contaminants. However, an all-encompassing phenotyping- and omics-based strategy for the toxicity assessment of nanoplastics with different surface properties on soil living organisms remains to be established. Herein, we devised a comprehensive phenotyping and multi-omic profiling method to examine the molecular disturbance of nanopolystyrene (PS)-exposed Caenorhabditis elegans. The exposure time was 24 h with either 1 μg/mL or 10 μg/mL of PS. We found that PS considerably affected the reproduction and locomotion, as well as increased the oxidative stress of worms regardless of their surface properties. Nevertheless, each type of PS affected the metabolome and lipidome of the nematodes differently. Uncharged PS (PS-N) triggered significant metabolic disturbances, whereas the metabolic influences from PS-NH₂ and PS-COOH were subtle. The dysregulated transcriptome profiles of PS-N were strongly associated with the metabolic pathways. Besides, the altered expression of several genes associated with autophagy and longevity was observed. Collectively, we demonstrated that comprehensive phenotyping and omics-based profiling establish a practical framework that allows us to gain deeper insights into the maladaptive consequences of PS in nematodes. It can be utilized for the evaluation of other environmental contaminants in the terrestrial ecosystem.

Biomolecular and bioanalytical applications of infrared spectroscopy - A review

Infrared (IR; or mid-infrared, MIR; 4000-400 cm^-1; 2500-25,000 nm) spectroscopy has become one of the most powerful and versatile tools at the disposal of modern bioscience. Because of its high molecular specificity, applicability to wide variety of samples, rapid measurement and non-invasivity, IR spectroscopy forms a potent approach to elucidate qualitative and quantitative information from various kinds of biological material. For these reasons, it became an established bioanalytical technique with diverse applications. This work aims to be a comprehensive and critical review of the recent accomplishments in the field of biomolecular and bioanalytical IR spectroscopy. That progress is presented on a wider background, with fundamental characteristics, the basic principles of the technique outlined, and its scientific capability directly compared with other methods being used in similar fields (e.g. near-infrared, Raman, fluorescence). The article aims to present a complete examination of the topic, as it touches the background phenomena, instrumentation, spectra processing and data analytical methods, spectra interpretation and related information. To suit this goal, the article includes a tutorial information essential to obtain a thorough perspective of bio-related applications of the reviewed methodologies. The importance of the fundamental factors to the final performance and applicability of IR spectroscopy in various areas of bioscience is explained. This information is interpreted in critical way, with aim to gain deep understanding why IR spectroscopy finds extraordinarily intensive use in this remarkably diverse and dynamic field of research and utility. The major focus is placed on the diversity of the applications in which IR biospectroscopy has been established so far and those onto which it is expanding nowadays. This includes qualitative and quantitative analytical spectroscopy, spectral imaging, medical diagnosis, monitoring of biophysical processes, and studies of physicochemical properties and dynamics of biomolecules. The application potential of IR spectroscopy in light of the current accomplishments and the future prospects is critically evaluated and its significance in the progress of bioscience is comprehensively presented.

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.

Confocal Raman spectroscopic imaging for in vitro monitoring of active ingredient penetration and distribution in reconstructed human epidermis model

Topically applied active cosmetic ingredients (ACI) or active pharmaceutical ingredients (API) efficacy is directly related to their efficiency of penetration in the skin. In vitro reconstructed human epidermis surrogate models offer in vivo like skin samples for transdermal studies. Using Delipidol®, an ACI currently used in the cosmetics industry, the capabilities to deliver accurate distribution maps and penetration profiles of this molecule by means of confocal Raman spectroscopic imaging have been demonstrated. Using a non-negative constrained least squares (NCLS) approach, contribution of specific molecules can be estimated at each point of spectral maps in order to deliver semi-quantitative heat maps representing the ACI levels in the different skin layers. The concentration profiles obtained are approximately single exponential for all 3 time points evaluated, with a consistent decay constant, which is independent of the sublayer structure. Notably, however, there is no significant penetration into the lower basal layers until a critical concentration is built up, after 3 hours. Combination of Raman confocal imaging with spectral unmixing methods such as NCLS is demonstrated to be a relevant approach for in vitro biological evaluation of cosmetic and pharmaceutical active ingredients and could easily be implemented as a screening tool for industrial use.

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

Raman microspectroscopy as anin vitrolabel-free, high content screening technique to determine spectral markers of cytogenotoxicity.

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

Raman microspectroscopy as a ‘high content nanotoxicological screening technique’ with the aid of multivariate analysis, on non-cancerous and cancerous cell lines.

Spectral pre and post processing for infrared and Raman spectroscopy of biological tissues and cells

This review presents the current understanding of the factors influencing the quality of spectra recorded and the pre-processing steps commonly employed to improve on spectral quality, as well as some of the most common techniques for classification and analysis of the spectral data for biomedical applications.

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

Monitoring of time and dose dependent molecular changes by using Raman spectroscopy with the aid of multivariate analysis techniques and determination of Raman spectral markers of cellular toxicity.

Spectropathology for the next generation: Quo vadis?

Vibrational spectroscopy for biomedical applications has shown great promise although its translation into clinical practice has, as yet, been relatively slow. This Editorial assesses the challenges facing the field and the potential way forward.

Multivariate statistical methodologies applied in biomedical Raman spectroscopy: assessing the validity of partial least squares regression using simulated model datasets

In the drive towards biomedical applications of Raman spectroscopy, it is critically important to validate the data analysis tools.

Raman spectroscopy in nanomedicine: current status and future perspective

Raman spectroscopy is a branch of vibration spectroscopy that is capable of probing the chemical composition of materials. Recent advances in Raman microscopy have significantly added to the range of applications, which now extend from medical diagnostics to exploring the interfaces between biological organisms and nanomaterials. In this review, Raman is introduced in a general context, highlighting some of the areas in which the technique has been successful in the past, as well as some of the potential benefits it offers over other analytical modalities. The subset of Raman techniques that specifically probe the nanoscale, namely surface- and tip-enhanced Raman spectroscopy, will be described and specific applications relevant to nanomedical applications will be reviewed. Progress in the use of traditional label-free Raman for investigation of nanoscale interactions will be described, and recent developments in coherent anti-Stokes Raman scattering will be explored, particularly its applications to biomedical and nanomedical fields.