Distinct spectral signatures unfold ECM stiffness-triggered biochemical changes in breast cancer cells

Cancer progression often accompanies the stiffening of extracellular matrix (ECM) in and around the tumor, owing to extra deposition and cross-linking of collagen. Stiff ECM has been linked with poor prognosis and is known to fuel invasion and metastasis, notably in breast cancer. However, the underlying biochemical or metabolic changes and the cognate molecular signatures remain elusive. Here, we explored Raman spectroscopy to unveil the spectral fingerprints of breast cancer cells in response to extracellular mechanical cues. Using stiffness-tuneable hydrogels, we showed that cells grown on stiff ECM displayed morphological changes with high proliferation. We further demonstrated that Raman Spectroscopy, a label-free and non-invasive technique, could provide comprehensive information about the biochemical environment of breast cancer cells in response to varying ECM stiffness. Raman spectroscopic analysis classified the cells into distinct clusters based on principal component-based linear discriminant analysis (PC-LDA). Multivariate curve resolution-alternating least squares (MCR-ALS) analysis indicated that cells cultured on stiff ECM exhibited elevated nucleic acid content and lesser lipids. Interestingly, increased intensity of Raman bands corresponding to cytochrome-c was also observed in stiff ECM conditions, suggesting mitochondrial modulation. The key findings harboured by spectral profiles were also corroborated by transmission electron microscopy, confirming altered metabolic status as reflected by increased mitochondria number and decreased lipid droplets in response to ECM stiffening. Collectively, these findings not only give the spectral signatures for mechanoresponse but also provide the landscape of biochemical changes in response to ECM stiffening.

Serum Raman spectroscopy: Evaluation of tumour load variations in experimental carcinogenesis

Several serum Raman spectroscopy (RS) studies have demonstrated its potential as an oral cancer screening tool. This study investigates influence of low tumour load (LTL) and high tumour load (HTL) on serum RS using hamster buccal pouch model of experimental oral carcinogenesis. Sera of untreated control, LTL, and HTL groups at week intervals during malignant transformation were employed. Serum Raman spectra were subjected to multivariate analyses-principal component analysis, principal component-based linear discriminant analysis (for stratification of study groups), and multivariate curve resolution-alternating least squares (MCR-ALS) (to comprehend biomolecular differences). Multivariate analysis revealed misclassifications between LTL and HTL at all week intervals. MCR-ALS components showed statistically significant abundances between control versus LTL and control versus HTL, but could not discern LTL and HTL. MCR-ALS components exhibited spectral mixtures of proteins, lipids, heme and nucleic acids. Thus, these findings support use of serum RS as a screening tool as varying tumour load is not a confounding factor influencing the technique.

Porous materials as effective chemiresistive gas sensors

Chemiresistive gas sensors (CGSs) have revolutionized the field of gas sensing by providing a low-power, low-cost, and highly sensitive means of detecting harmful gases. This technology works by measuring changes in the conductivity of materials when they interact with a testing gas. While semiconducting metal oxides and two-dimensional (2D) materials have been used for CGSs, they suffer from poor selectivity to specific analytes in the presence of interfering gases and require high operating temperatures, resulting in high signal-to-noise ratios. However, nanoporous materials have emerged as a promising alternative for CGSs due to their high specific surface area, unsaturated metal actives, and density of three-dimensional inter-connected conductive and pendant functional groups. Porous materials have demonstrated excellent response and recovery times, remarkable selectivity, and the ability to detect gases at extremely low concentrations. Herein, our central emphasis is on all aspects of CGSs, with a primary focus on the use of porous materials. Further, we discuss the basic sensing mechanisms and parameters, different types of popular sensing materials, and the critical explanations of various mechanisms involved throughout the sensing process. We have provided examples of remarkable performance demonstrated by sensors using these materials. In addition to this, we compare the performance of porous materials with traditional metal-oxide semiconductors (MOSs) and 2D materials. Finally, we discussed future aspects, shortcomings, and scope for improvement in sensing performance, including the use of metal-organic frameworks (MOFs), covalent-organic frameworks (COFs), and porous organic polymers (POPs), as well as their hybrid counterparts. Overall, CGSs using porous materials have the potential to address a wide range of applications, including monitoring water quality, detecting harmful chemicals, improving surveillance, preventing natural disasters, and improving healthcare.

Differences in microplastic degradation in the atmosphere and coastal water environment from two island nations: Japan and New Zealand

Microplastics are subject to environmental forces that can change polymer organization on a molecular scale. However, it is not clear to what extent these changes occur in the environment and whether microplastics in the atmospheric and water environment differ. Here we identify structural differences between microplastics in the atmosphere and water environment from Japan and New Zealand, representing two archipelagos differing in their proximity to nearby countries and highly populated areas. We first highlight the propensity for smaller microplastics to arrive via air masses from the Asian continent to the Japan Sea coastal area, while New Zealand received larger, locally derived microplastics. Analyses of polyethylene in the Japanese atmosphere indicate that microplastics transported to the Japanese coastal areas were more crystalline than polyethylene particles in the water, suggesting that the plastics arriving by air were relatively more aged and brittle. By contrast, polypropylene particles in New Zealand waters were more degraded than the microplastic particles in the air. Due to the lack of abundance, both polyethylene and polypropylene could not be analyzed for both countries. Nevertheless, these findings show the structural variation in microplastics between environments in markedly different real-world locations, with implications for the toxic potential of these particles.

Direct Visualization of Structurally Similar Polysaccharides in Single Yeast Cells in Vivo by Multivariate Analysis Assisted Raman Microspectroscopy

The demand for functional food ingredients like β-glucan has risen enormously in recent times owing to its use in many fields including the food and beverage, cosmetics, pharmaceuticals, and biotechnology industries. Among the many natural sources of glucans such as oats, barley, mushrooms, and seaweeds, yeast has a special advantage in the industrial production of glucans. However, characterizing glucans is not straightforward as there are many different structural variations such as α- or β-glucans with various configurations which vary in their physical and chemical properties. Currently, microscopy, chemical or genetic approaches are followed to study glucan synthesis and accumulation in single yeast cells. However, they are time-consuming, lack molecular specificity, or are practically not feasible for real applications. Therefore, we developed a Raman microspectroscopy based method to identify, distinguish, and visualize structurally similar glucan polysaccharides. By employing multivariate curve resolution analysis, we successfully separated Raman spectra of α- and β-glucans from mixtures with high specificity and visualized heterogeneous molecular distributions during the sporulation of yeasts at the single-cell level in a label-free manner. We believe such an approach when combined with a flow cell can achieve the sorting of yeast cells based on the accumulation of glucans for various applications. Further, such an approach can also be extended to various other biological systems to investigate structurally similar carbohydrate polymers in a fast and reliable manner.

Development of in-situ Raman diagnosis technique of eosinophil esophagitis

The spectra of the live tissue with blood flow measured with 785 nm-excitation light showed a very weak signal due to hemoglobin (Hb). It suggested the possibility to detect eosinophil accumulation in the tissue with the 785 nm-excitation light. The excitation wavelength of 633 nm induced strong fluorescence of sapphire glass that is a material of the ball lens of BHRP (Ball lens top hollow optical fiber Raman probe). On the other hand, the previous study suggested that eosinophil including eosinophil peroxidase (EPO) that showed a strong resonance Raman effect with 633 nm-excitation light. The purpose of the present study is to collect basic information and to evaluate the viability of Raman spectroscopic analysis for the detection of eosinophil accumulation in the live esophagus. BHRP with a sapphire ball lens with 500 µm diameter was applied for measurement of live esophagus tissue of a mouse. In this study, Raman spectra of eosinophil were measured with 633 and 785 nm-excitation. The Raman spectra of eosinophil showed a strong contribution of EPO, suggested that a heme chromophore in EPO had pre-resonance enhancement via Q band with the 785 nm-excitation light. Principal component analysis (PCA) is applied for the analysis of Raman spectra of eosinophil, erythrocyte and other granulocytes. Eosinophil was successfully discriminated from other blood cells in the PCA score plots built for the datasets of the spectra measured with 633 and 785 nm-excitation wavelengths. Consequently, our study demonstrates that Raman spectroscopy with 785 nm-excitation had high viability for in situ analysis of eosinophilic esophagitis (EoE).

Microfluidics and surface-enhanced Raman spectroscopy, a win-win combination?

With the continuous development in nanoscience and nanotechnology, analytical techniques like surface-enhanced Raman spectroscopy (SERS) render structural and chemical information of a variety of analyte molecules in ultra-low concentration. Although this technique is making significant progress in various fields, the reproducibility of SERS measurements and sensitivity towards small molecules are still daunting challenges. In this regard, microfluidic surface-enhanced Raman spectroscopy (MF-SERS) is well on its way to join the toolbox of analytical chemists. This review article explains how MF-SERS is becoming a powerful tool in analytical chemistry. We critically present the developments in SERS substrates for microfluidic devices and how these substrates in microfluidic channels can improve the SERS sensitivity, reproducibility, and detection limit. We then introduce the building materials for microfluidic platforms and their types such as droplet, centrifugal, and digital microfluidics. Finally, we enumerate some challenges and future directions in microfluidic SERS. Overall, this article showcases the potential and versatility of microfluidic SERS in overcoming the inherent issues in the SERS technique and also discusses the advantage of adding SERS to the arsenal of microfluidics.

DNA Fingerprint Analysis of Raman Spectra Captures Global Genomic Alterations in Imatinib-Resistant Chronic Myeloid Leukemia: A Potential Single Assay for Screening Imatinib Resistance

Monitoring the development of resistance to the tyrosine kinase inhibitor (TKI) imatinib in chronic myeloid leukemia (CML) patients in the initial chronic phase (CP) is crucial for limiting the progression of unresponsive patients to terminal phase of blast crisis (BC). This study for the first time demonstrates the potential of Raman spectroscopy to sense the resistant phenotype. Currently recommended resistance screening strategy include detection of BCR-ABL1 transcripts, kinase domain mutations, complex chromosomal abnormalities and BCR-ABL1 gene amplification. The techniques used for these tests are expensive, technologically demanding and have limited availability in resource-poor countries. In India, this could be a reason for more patients reporting to clinics with advanced disease. A single method which can identify resistant cells irrespective of the underlying mechanism would be a practical screening strategy. During our analysis of imatinib-sensitive and -resistant K562 cells, by array comparative genomic hybridization (aCGH), copy number variations specific to resistant cells were detected. aCGH is technologically demanding, expensive and therefore not suitable to serve as a single economic test. We therefore explored whether DNA finger-print analysis of Raman hyperspectral data could capture these alterations in the genome, and demonstrated that it could indeed segregate imatinib-sensitive and -resistant cells. Raman spectroscopy, due to availability of portable instruments, ease of spectrum acquisition and possibility of centralized analysis of transmitted data, qualifies as a preliminary screening tool in resource-poor countries for imatinib resistance in CML. This study provides a proof of principle for a single assay for monitoring resistance to imatinib, available for scrutiny in clinics.

Non-invasive diagnosis of colorectal cancer by Raman spectroscopy: Recent developments in liquid biopsy and endoscopy approaches

Colorectal cancer (CRC) is the third most common cancer diagnosed globally and is also one of the leading causes of cancer deaths in both men and women. The progression of CRC is slow and is often contained in colon but the risk increases with age. Based on the high certainty that the net benefit of screening in an age group is substantial, screening for CRC is recommended beginning at the age of 50. Currently, most of the incidence is concentrated in developed countries but the rate is increasing rapidly in developing geographies. Detecting CRC at an early stage is critical to reduce morbidity and mortality. Colonoscopy is the most preferred screening method but not very widely implemented due to practical considerations such as cost involved, lack of personnel and facility. To address these concerns, Raman spectroscopy (RS) has been suggested as a viable alternative due to its potential as a rapid non-invasive diagnostic tool. Recently, several studies have been reported but many variations of RS applications in CRC exists and are not well understood by non-specialists. This review focuses particularly on developments of Raman based liquid biopsy and endoscopic studies in order to throw light on each of their significance and limitations. Necessary developments in the future to translate RS into a clinical tool for screening and diagnosis of CRC are also briefly presented.

Visualizing wax ester fermentation in single Euglena gracilis cells by Raman microspectroscopy and multivariate curve resolution analysis

BACKGROUND

Global demand for energy is on the rise at a time when limited natural resources are fast depleting. To address this issue, microalgal biofuels are being recommended as a renewable and eco-friendly substitute for fossil fuels. Euglena gracilis is one such candidate that has received special interest due to their ability to synthesize wax esters that serve as precursors for production of drop-in jet fuel. However, to realize economic viability and achieve industrial-scale production, development of novel methods to characterize algal cells, evaluate its culture conditions, and construct appropriate genetically modified strains is necessary. Here, we report a Raman microspectroscopy-based method to visualize important metabolites such as paramylon and ester during wax ester fermentation in single Euglena gracilis cells in a label-free manner.

RESULTS

We measured Raman spectra to obtain intracellular biomolecular information in Euglena under anaerobic condition. First, by univariate approach, we identified Raman markers corresponding to paramylon/esters and constructed their time-lapse chemical images. However, univariate analysis is severely limited in its ability to obtain detailed information as several molecules can contribute to a Raman band. Therefore, we further employed multivariate curve resolution analysis to obtain chain length-specific information and their abundance images of the produced esters. Accumulated esters in Euglena were particularly identified to be myristyl myristate (C28), a wax ester candidate suitable to prepare drop-in jet fuel. Interestingly, we found accumulation of two different forms of myristyl myristate for the first time in Euglena through our exploratory multivariate analysis.

CONCLUSIONS

We succeeded in visualizing molecular-specific information in Euglena during wax ester fermentation by Raman microspectroscopy. It is obvious from our results that simple univariate approach is insufficient and that multivariate curve resolution analysis is crucial to extract hidden information from Raman spectra. Even though we have not measured any mutants in this study, our approach is directly applicable to other systems and is expected to deepen the knowledge on lipid metabolism in microalgae, which eventually leads to new strategies that will help to enhance biofuel production efficiency in the future.

Fibril formation and therapeutic targeting of amyloid-like structures in a yeast model of adenine accumulation

The extension of the amyloid hypothesis to include non-protein metabolite assemblies invokes a paradigm for the pathology of inborn error of metabolism disorders. However, a direct demonstration of the assembly of metabolite amyloid-like structures has so far been provided only in vitro. Here, we established an in vivo model of adenine self-assembly in yeast, in which toxicity is associated with intracellular accumulation of the metabolite. Using a strain blocked in the enzymatic pathway downstream to adenine, we observed a non-linear dose-dependent growth inhibition. Both the staining with an indicative amyloid dye and anti-adenine assemblies antibodies demonstrated the accumulation of adenine amyloid-like structures, which were eliminated by lowering the supplied adenine levels. Treatment with a polyphenol inhibitor reduced the occurrence of amyloid-like structures while not affecting the dramatic increase in intracellular adenine concentration, resulting in inhibition of cytotoxicity, further supporting the notion that toxicity is triggered by adenine assemblies.

Small molecule metabolites like phenylalanine can form amyloid-like structures but so far this has only been demonstrated in vitro. Here the authors generate a yeast in vivo model of adenine self-assembly and characterize the adenine assemblies in cells by indicative amyloid dye and anti-adenine assemblies antibodies.

Biological and Medical Applications of Multivariate Curve Resolution Assisted Raman Spectroscopy

Biological specimens such as cells, tissues and biofluids (urine, blood) contain mixtures of many different biomolecules, all of which contribute to a Raman spectrum at any given point. The separation and identification of pure biochemical components remains one of the biggest challenges in Raman spectroscopy. Multivariate curve resolution, a matrix factorization method, is a powerful, yet flexible, method that can be used with constraints, such as non-negativity, to decompose a complex spectroscopic data matrix into a small number of physically meaningful pure spectral components along with their relative abundances. This paper reviews recent applications of multivariate curve resolution by alternating least squares analysis to Raman spectroscopic and imaging data obtained either in vivo or in vitro from biological and medical samples.

Studying anti-oxidative properties of inclusion complexes of α-lipoic acid with γ-cyclodextrin in single living fission yeast by confocal Raman microspectroscopy

α-lipoic acid (ALA) is an essential cofactor for many enzyme complexes in aerobic metabolism, especially in mitochondria of eukaryotic cells where respiration takes place. It also has excellent anti-oxidative properties. The acid has two stereo-isomers, R- and S- lipoic acid (R-LA and S-LA), but only the R-LA has biological significance and is exclusively produced in our body. A mutant strain of fission yeast, Δdps1, cannot synthesize coenzyme Q10, which is essential during yeast respiration, leading to oxidative stress. Therefore, it shows growth delay in the minimal medium. We studied anti-oxidant properties of ALA in its free form and their inclusion complexes with γ-cyclodextrin using this mutant yeast model. Both free forms R- and S-LA as well as 1:1 inclusion complexes with γ-cyclodextrin recovered growth of Δdps1 depending on the concentration and form. However, it has no effect on the growth of wild type fission yeast strain at all. Raman microspectroscopy was employed to understand the anti-oxidant property at the molecular level. A sensitive Raman band at 1602cm^-1 was monitored with and without addition of ALAs. It was found that 0.5mM and 1.0mM concentrations of ALAs had similar effect in both free and inclusion forms. At 2.5mM ALAs, free forms inhibited the growth while inclusion complexes helped in recovered. 5.0mM ALA showed inhibitory effect irrespective of form. Our results suggest that the Raman band at 1602cm^-1 is a good measure of oxidative stress in fission yeast.

Evidence of C--F-P and aromatic π--F-P weak interactions in imidazolium ionic liquids and its consequences

A simple change from alkyl group to alkene in side chain of imidazolium cation with same anion resulted in a drastic impact on physical properties (e.g., melting point) from bmimPF₆ IL to cmimPF₆ IL. The underlying reasons have been elucidated by structural and interaction studies with the help of DSC, SCXRD, vibrational and multi-nuclear NMR spectroscopic techniques. Experiments reveal existence of new weak interactions involving the carbon and π cloud of the imidazolium aromatic ring with fluoride of PF₆ anion (i.e., C₂--F-P and π--F-P) in cmimPF₆ but are absent in structurally similar prototype IL, bmimPF₆. Though weak, these interactions helped to form ladder type supramolecular arrangement, resulting in quite high melting point for cmimPF₆ IL compared to bmimPF₆ IL. These findings emphasize that an IL system can behave uniquely because of the existence of uncommon weak interactions.

Imaging phospholipid conformational disorder and packing in giant multilamellar liposome by confocal Raman microspectroscopy

Liposomes are closed phospholipid bilayer systems that have profound applications in fundamental cell biology, pharmaceutics and medicine. Depending on the composition (pure or mixture of phospholipids, presence of cholesterol) and preparation protocol, intra- and inter-chain molecular interactions vary leading to changes in the quality (order and packing) of liposomes. So far it is not possible to image conformational disorders and packing densities within a liposome in a straightforward manner. In this study, we utilized confocal Raman microspectroscopy to visualize structural disorders and packing efficiency within a giant multilamellar liposome model by focusing mainly on three regions in the vibrational spectrum (CC stretching, CH deformation and CH stretching). We estimated properties such as trans/gauche isomers and lateral packing probability. Interestingly, our Raman imaging studies revealed gel phase rich domains and heterogeneous lateral packing within the giant multilamellar liposome.

Significance of weak interactions in imidazolium picrate ionic liquids: spectroscopic and theoretical studies for molecular level understanding

The effects of interionic hydrogen bonding and π-π stacking interactions on the physical properties of a new series of picrate anion based ionic liquids (ILs) have been investigated experimentally and theoretically. The existence of aromatic (C2-HO) and aliphatic (C7-HO-N22 and C6-HO-N20) hydrogen bonding and π-π stacking interactions in these ILs has been observed using various spectroscopic techniques. The aromatic and aliphatic C-HO hydrogen bonding interactions are found to have a crucial role in binding the imidazolium cation and picrate anion together. However, the π-π stacking interactions between two successive layers are found to play a decisive role in tight packing in ILs leading to differences in physical properties. The drastic difference in the melting points of the methyl and propyl derivatives (mmimPic and pmimPic respectively) have been found to be primarily due to the difference in the strength and varieties of π-π stacking interactions. While in mmimPic, several different types of π-π stacking interactions between the aromatic rings (such as picrate-picrate, picrate-imidazole and imidazolium-imidazolium cation rings) are observed, only one type of π-π stacking interaction (picrate-picrate rings) is found to exist in the pmimPic IL. NMR spectroscopic studies reveal that the interaction of these ILs with solvent molecules is different and depends on the dielectric constant of the solvent. While an ion solvation model explains the solvation in high dielectric solvents, an ion-pair solvation model is found to be more appropriate for low dielectric constant solvents. The enhanced stability of these investigated picrate ILs compared with that of inorganic picrate salts under high doses of γ radiation clearly indicates the importance of weak interionic interactions in ILs, and also opens up the possibility of the application of picrate ILs as prospective diluents in nuclear separation for advanced fuel cycling process.

Exploring metabolic pathways in vivo by a combined approach of mixed stable isotope-labeled Raman microspectroscopy and multivariate curve resolution analysis

Understanding cellular metabolism is a major challenge in current systems biology and has triggered extensive metabolomics research, which in most cases involves destructive analysis. However, the information obtainable only in a nondestructive manner will be required for accurately mapping the global structure of the organism's metabolic network at a given instant. Here we report that metabolic pathways can be explored in vivo by mixed stable isotope-labeled Raman microspectroscopy in conjunction with multivariate curve resolution analysis. As a model system, we studied ergosterol biosynthesis in single living fission yeast cells grown in mixtures of normal and (13)C-labeled glucose as the sole carbon source. The multivariate spectral data analysis of space-resolved Raman spectra revealed the intrinsic spectra and relative abundances of all isotopomers of ergosterol whose carbon atoms in the 5,7-diene moiety of the sterol skeleton are either partly or fully substituted with (13)C. Our approach is applicable to other metabolites and will earn a place in the toolbox of metabolomic analysis.