Label-Free Human Disease Characterization through Circulating Cell-Free DNA Analysis Using Raman Spectroscopy

Circulating cell-free DNA (ccfDNA) is a liquid biopsy biomaterial attracting significant attention for the implementation of precision medicine diagnostics. Deeper knowledge related to its structure and biology would enable the development of such applications. In this study, we employed Raman spectroscopy to unravel the biomolecular profile of human ccfDNA in health and disease. We established reference Raman spectra of ccfDNA samples from healthy males and females with different conditions, including cancer and diabetes, extracting information about their chemical composition. Comparative observations showed a distinct spectral pattern in ccfDNA from breast cancer patients taking neoadjuvant therapy. Raman analysis of ccfDNA from healthy, prediabetic, and diabetic males uncovered some differences in their biomolecular fingerprints. We also studied ccfDNA released from human benign and cancer cell lines and compared it to their respective gDNA, confirming it mirrors its cellular origin. Overall, we explored for the first time Raman spectroscopy in the study of ccfDNA and provided spectra of samples from different sources. Our findings introduce Raman spectroscopy as a new approach to implementing liquid biopsy diagnostics worthy of further elaboration.

Application of Caenorhabditis elegans in Lipid Metabolism Research

Over the last decade, the development and prevalence of obesity have posed a serious public health risk, which has prompted studies on the regulation of adiposity. With the ease of genetic manipulation, the diversity of the methods for characterizing body fat levels, and the observability of feeding behavior, Caenorhabditis elegans (C. elegans) is considered an excellent model for exploring energy homeostasis and the regulation of the cellular fat storage. In addition, the homology with mammals in the genes related to the lipid metabolism allows many aspects of lipid modulation by the regulators of the central nervous system to be conserved in this ideal model organism. In recent years, as the complex network of genes that maintain an energy balance has been gradually expanded and refined, the regulatory mechanisms of lipid storage have become clearer. Furthermore, the development of methods and devices to assess the lipid levels has become a powerful tool for studies in lipid droplet biology and the regulation of the nematode lipid metabolism. Herein, based on the rapid progress of C. elegans lipid metabolism-related studies, this review outlined the lipid metabolic processes, the major signaling pathways of fat storage regulation, and the primary experimental methods to assess the lipid content in nematodes. Therefore, this model system holds great promise for facilitating the understanding, management, and therapies of human obesity and other metabolism-related diseases.

Innovative fluorescent probes for in vivo visualization of biomolecules in living Caenorhabditis elegans

Caenorhabditis elegans (C. elegans) as a well-established multicellular model organism has been widely used in the biological field for half a century. Its numerous advantages including small body size, rapid life cycle, high-reproductive rate, well-defined anatomy, and conserved genome, has made C. elegans one of the most successful multicellular model organisms. Discoveries obtained from the C. elegans model have made great contributions to research fields such as development, aging, biophysics, immunology, and neuroscience. Because of its transparent body and giant cell size, C. elegans is also an ideal subject for high resolution and high-throughput optical imaging and analysis. During the past decade, great advances have been made to develop biomolecule-targeting techniques for noninvasive optical imaging. These novel technologies expanded the toolbox for qualitative and quantitative analysis of biomolecules in C. elegans. In this review, we summarize recently developed fluorescent probes or labeling techniques for visualizing biomolecules at the cellular, subcellular or molecular scale by using C. elegans as the major model organism or designed specifically for the applications in C. elegans. Combining the technological advantages of the C. elegans model with the novel fluorescent labeling techniques will provide new horizons for high-efficiency quantitative optical analysis in live organisms.

SERS Probing of Proteins in Gold Nanoparticle Agglomerates

The collection of surface-enhanced Raman scattering (SERS) spectra of proteins and other biomolecules in complex biological samples such as animal cells has been achieved with gold nanoparticles that are introduced to the sample. As a model for such a situation, SERS spectra were measured in protein solutions using gold nanoparticles in the absence of aggregating agents, allowing for the free formation of a protein corona. The SERS spectra indicate a varied interaction of the protein molecule with the gold nanoparticles, depending on protein concentration. The concentration-dependent optical properties of the formed agglomerates result in strong variation in SERS enhancement. At protein concentrations that correspond to those inside cells, SERS signals are found to be very low. The results suggest that in living cells the successful collection of SERS spectra must be due to the positioning of the aggregates rather than the crowded biomolecular environment inside the cells. Experiments with DNA suggest the suitability of the applied sample preparation approach for an improved understanding of SERS nanoprobes and nanoparticle-biomolecule interactions in general.

Laser-induced remote release in vivo in C. elegans from novel silver nanoparticles-alginate hydrogel shells

Non-destructive, controllable, remote light-induced release inside cells enables studying time- and space-specific processes in biology. In this work we demonstrate the remote release of tagged proteins in Caenorhabditis elegans (C. elegans) worms using a near-infrared laser light as a trigger from novel hydrogel shells functionalized with silver nanoparticles responsive to laser light. A new type of hydrogel shells was developed capable of withstanding prolonged storage in the lyophilized state to enable the uptake of the shell by worms, which takes place on an agar plate under standard culture conditions. Uptake of the shells by C. elegans was confirmed using confocal laser scanning microscopy, while release from alginate shells in C. elegans and the laser effect on the shells on a substrate in air was followed using fluorescence microscopy. In addition, Raman microscopy was used to track the localization of particles to avoid the influence of autofluorescence. Hierarchical cluster spectral analysis is used to extract information about the biochemical composition of an area of a nematode containing the hydrogel shells, whose Raman signal is enhanced by the SERS (Surface Enhanced Raman Scattering) effect due to hot spots formed by silver nanoparticles present in the shells. The in vivo release demonstrated here can be used to study intestinal microbiota and probiotic compounds as well as a possible future strategy for gene delivery in the worms, other insects and other organisms.

Materials and toxicological approaches to study metal and metal-oxide nanoparticles in the model organism Caenorhabditis elegans

Understanding the in vivo fate and transport of nanoparticles (NPs) is challenging, but critical. We review recent studies of metal and metal oxide NPs using the model organism Caenorhabditis elegans, summarizing major findings to date. In a joint transdisciplinary effort, we highlight underutilized opportunities offered by powerful techniques lying at the intersection of mechanistic toxicology and materials science,. To this end, we firstly summarize the influence of exposure conditions (media, duration, C. elegans lifestage) and NP physicochemical properties (size, coating, composition) on the response of C. elegans to NP treatment. Next, we focus on the techniques employed to study NP entrance route, uptake, biodistribution and fate, emphasizing the potential of extending the toolkit available with novel and powerful techniques. Next, we review findings on several NP-induced biological responses, namely transport routes and altered molecular pathways, and illustrate the molecular biology and genetic strategies applied, critically reviewing their strengths and weaknesses. Finally, we advocate the incorporation of a set of minimal materials and toxicological science experiments that will permit meta-analysis and synthesis of multiple studies in the future. We believe this review will facilitate coordinated integration of both well-established and underutilized approaches in mechanistic toxicology and materials science by the nanomaterials research community.

Imaging and lipidomics methods for lipid analysis in metabolic and cardiovascular disease

Cardiometabolic diseases exhibit changes in lipid biology, which is important as lipids have critical roles in membrane architecture, signalling, hormone synthesis, homoeostasis and metabolism. However, Developmental Origins of Health and Disease studies of cardiometabolic disease rarely include analysis of lipids. This short review highlights some examples of lipid pathology and then explores the technology available for analysing lipids, focussing on the need to develop imaging modalities for intracellular lipids. Analytical methods for studying interactions between the complex endocrine and intracellular signalling pathways that regulate lipid metabolism have been critical in expanding our understanding of how cardiometabolic diseases develop in association with obesity and dietary factors. Biochemical methods can be used to generate detailed lipid profiles to establish links between lifestyle factors and metabolic signalling pathways and determine how changes in specific lipid subtypes in plasma and homogenized tissue are associated with disease progression. New imaging modalities enable the specific visualization of intracellular lipid traffic and distribution in situ. These techniques provide a dynamic picture of the interactions between lipid storage, mobilization and signalling, which operate during normal cell function and are altered in many important diseases. The development of methods for imaging intracellular lipids can provide a dynamic real-time picture of how lipids are involved in complex signalling and other cell biology pathways; and how they ultimately regulate metabolic function/homoeostasis during early development. Some imaging modalities have the potential to be adapted for in vivo applications, and may enable the direct visualization of progression of pathogenesis of cardiometabolic disease after poor growth in early life.

Interrogating Cells, Tissues, and Live Animals with New Generations of Surface-Enhanced Raman Scattering Probes and Labels

Surface-enhanced Raman scattering (SERS) probes and labels exploit surface-enhanced Raman signatures of specifically chosen reporter molecules and intrinsic biomolecules in the plasmonic near field of gold and silver nanostructures. They offer several advantages over other optical labels and sensors with respect to sensitivity and selectivity, mobility, and biocompatibility. Here, the multifunctionality and versatility of SERS labels that come from the vibrational spectroscopic information and their ability to act as nanoprobes of a biological environment are discussed. Surface-enhanced Raman scattering probes have the potential to become the next-generation sensor technology for monitoring cells and tissues. They improve our understanding of cellular function and will play a major role in future theranostic applications.

Detection of residual rifampicin in urine via fluorescence quenching of gold nanoclusters on paper

Background

Rifampicin or rifampin (R) is a common drug used to treat inactive meningitis, cholestatic pruritus and tuberculosis (TB), and it is generally prescribed for long-term administration under regulated dosages. Constant monitoring of rifampicin is important for controlling the side effects and preventing overdose caused by chronic medication. In this study, we present an easy to use, effective and less costly method for detecting residual rifampicin in urine samples using protein (bovine serum albumin, BSA)-stabilized gold nanoclusters (BSA-Au NCs) adsorbed on a paper substrate in which the concentration of rifampicin in urine can be detected via fluorescence quenching. The intensity of the colorimetric assay performed on the paper-based platforms can be easily captured using a digital camera and subsequently analyzed.

Results

The decreased fluorescence intensity of BSA-Au NCs in the presence of rifampicin allows for the sensitive detection of rifampicin in a range from 0.5 to 823 µg/mL. The detection limit for rifampicin was measured as 70 ng/mL. The BSA-Au NCs were immobilized on a wax-printed paper-based platform and used to conduct real-time monitoring of rifampicin in urine.

Conclusion

We have developed a robust, cost-effective, and portable point-of-care medical diagnostic platform for the detection of rifampicin in urine based on the ability of rifampicin to quench the fluorescence of immobilized BSA-Au NCs on wax-printed papers. The paper-based assay can be further used for the detection of other specific analytes via surface modification of the BSA in BSA-Au NCs and offers a useful tool for monitoring other diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12951-015-0105-5) contains supplementary material, which is available to authorized users.

C. elegans as a tool for in vivo nanoparticle assessment

Characterization of the in vivo behavior of nanomaterials aims to optimize their design, to determine their biological effects, and to validate their application. The characteristics of the model organism Caenorhabditis elegans (C. elegans) advocate this 1mm long nematode as an ideal living system for the primary screening of engineered nanoparticles in a standard synthetic laboratory. This review describes some practicalities and advantages of working with C. elegans that will be of interest for chemists and materials scientists who would like to enter the "worm" community, anticipates some drawbacks, and offers relevant examples of nanoparticle assessment by using C. elegans.

Multiplex optical sensing with surface-enhanced Raman scattering: a critical review

Multiplex analysis permits the detection of several analytical targets at the same time. This approach may permit to draw a rapid and accurate diagnostic about the health of an individual or an environment. Among the analytical techniques with potential for multiplexing surface-enhanced Raman scattering (SERS) offer unique advantages such as ultrasensitive detection down low the deconvolution times, a unique signature containing all the vibrational information of the target molecules, and the possibility of performing the experiments even in very demanding environments such as natural or biological fluids. Here we review the late advances in multiplex SERS including the direct methods, those aided by the surface functionalization of the plasmonic nanoparticles and the use of SERS encoded particles.

Distinguishing breast cancer cells using surface-enhanced Raman scattering

The detection and identification of epidermal growth factor receptor 2 (HER2)-positive breast cancer cells is crucial for the clinic therapy of breast cancer. For the aim of the detection, a novel surface-enhanced Raman scattering (SERS) probe for distinguishing breast cancers at different HER2 statuses is reported in this paper. In such a probe, anti-HER2 antibody-conjugated silver nanoparticles have been synthesized for specific targeting of HER2-positive breast cancer cells. More importantly, different from the previously reported SERS probe for targeting cancer cells, p-mercaptobenzoic acid is utilized as both the Raman reporter and the conjugation agent for attaching antibody molecules, which leads to a much simplified structure. For investigating the ability of such a probe to distinguish breast cancer cells, SKBR3 and MCF7 cells were chosen as two model systems, which are HER2-positive- and HER2-negative-expressing cells, respectively. The experimental results reveal that SKBR3 cells exhibit much stronger SERS signals than MCF7 cells, indicating that the probe could be utilized to distinguish breast cancer cells at different HER2 statuses. This kind of SERS probe holds a potential for a direct detection of living breast cancer cells with the advantages of easy fabrication, high SERS sensitivity, and biocompatibility.