Basic principles of fluorescence and energy transfer

The Emerging Role of Raman Spectroscopy as an Omics Approach for Metabolic Profiling and Biomarker Detection toward Precision Medicine

Omics technologies have rapidly evolved with the unprecedented potential to shape precision medicine. Novel omics approaches are imperative toallow rapid and accurate data collection and integration with clinical information and enable a new era of healthcare. In this comprehensive review, we highlight the utility of Raman spectroscopy (RS) as an emerging omics technology for clinically relevant applications using clinically significant samples and models. We discuss the use of RS both as a label-free approach for probing the intrinsic metabolites of biological materials, and as a labeled approach where signal from Raman reporters conjugated to nanoparticles (NPs) serve as an indirect measure for tracking protein biomarkers in vivo and for high throughout proteomics. We summarize the use of machine learning algorithms for processing RS data to allow accurate detection and evaluation of treatment response specifically focusing on cancer, cardiac, gastrointestinal, and neurodegenerative diseases. We also highlight the integration of RS with established omics approaches for holistic diagnostic information. Further, we elaborate on metal-free NPs that leverage the biological Raman-silent region overcoming the challenges of traditional metal NPs. We conclude the review with an outlook on future directions that will ultimately allow the adaptation of RS as a clinical approach and revolutionize precision medicine.

Near-infrared fluorescence imaging of non-Hodgkin's lymphoma CD20 expression using Cy7-conjugated obinutuzumab

PURPOSE

Obinutuzumab is the first fully humanized and glycoengineered monoclonal antibody (mAb) directly targeting CD20 antigen, which is expressed on B cell lymphocytes and the majority of non-Hodgkin's lymphoma (NHL). This study aims to design a diagnostic molecular probe, Cy7-Obinutuzumab (Cy7-Obi), in which Cy7 is a near-infrared fluorescent dye. This probe is used to noninvasively image CD20 antigen expressed in NHL cells.

PROCEDURES

Cy7-Obi probe was synthesized through nucleophilic substitution reaction between NHS-Cy7 and obinutuzumab. After purification, the conjugate was fully characterized by a series of methods. The immunoreactivity and molecular specificity of the probe were confirmed using flow cytometry and in vitro microscopy on Raji (CD20-positive) cells. For in vivo imaging, Cy7-Obi probe (1 nmol) was injected intravenously in severe combined immunodeficiency (SCID) mice bearing Raji tumors which overexpress CD20 (n = 3) and was imaged with near-infrared fluorescence (NIRF) at 6, 9, 12, 24, 60, and 96 h post-probe injection. For pre-block, obinutuzumab (3.25 mg) was injected intravenously in tumor-bearing mice 6 h before the administration of Cy7-Obi probe.

RESULTS

The synthesized Cy7-Obi probe in this paper mimics obinutuzumab in both structure and function. Flow cytometry analysis of the probe and obinutuzumab on Raji cells showed minor difference in binding affinity/specificity with CD20. The probe showed significant fluorescence signal when it was examined on Raji cells using in vitro microscopy. The fluorescence signal can be blocked by pretreatment with obinutuzumab. The probe Cy7-Obi also showed high tumor uptake when it was examined by in vivo optical imaging on Raji tumor-bearing mice. The tumor uptake can be blocked by pretreatment with obinutuzumab (n = 3, p < 0.05). The in vivo imaging results were also confirmed by ex vivo imaging of dissected organs. Finally, the probe Cy7-Obi has shown excellent tumor targeting and specificity through immunofluorescence analysis.

CONCLUSIONS

We have shown that humanized Cy7-Obi probe can be used for NIRF imaging successfully. The probe may be an effective and noninvasive diagnostic molecular probe capable of tracking CD20 overexpression in NHL.

Cyclodextrin-promoted energy transfer for broadly applicable small-molecule detection

Reported herein is the development of non-covalent, proximity-induced energy transfer from small-molecule toxicants to organic fluorophores bound in the cavity of γ-cyclodextrin. This energy transfer occurs with exceptional efficiency for a broad range of toxicants in complex biological media, and is largely independent of the spectral overlap between the donor and acceptor. This generally applicable phenomenon has significant potential in the development of new turn-on detection schemes.

Computational tools for designing smart libraries

Traditional directed evolution experiments are often time-, labor- and cost-intensive because they involve repeated rounds of random mutagenesis and the selection or screening of large mutant libraries. The efficiency of directed evolution experiments can be significantly improved by targeting mutagenesis to a limited number of hot-spot positions and/or selecting a limited set of substitutions. The design of such "smart" libraries can be greatly facilitated by in silico analyses and predictions. Here we provide an overview of computational tools applicable for (a) the identification of hot-spots for engineering enzyme properties, and (b) the evaluation of predicted hot-spots and selection of suitable amino acids for substitutions. The selected tools do not require any specific expertise and can easily be implemented by the wider scientific community.

Effects of lipid-probe interactions in biochemical fluorometric methods that assess HDL redox activity

Background

Fluorescence-based cell-free assays offer an attractive alternative to current cell-based assays for measuring the redox activity of High-Density Lipoprotein (HDL). We have recently developed a biochemical assay that assesses the effect of HDL on the oxidation rate of dihydrorhodamine 123 (DHR), reflected by increasing fluorescence over time. However, an immediate reduction in the fluorescence signal is observed after addition of HDL to DHR, due to fluorescence quenching from lipid-probe interactions. Understanding this process is important for interpretation of the results of all fluorescence-based cell-free assays that measure oxidative properties of lipids.

Methods

We determined the effect of quenchers (proteins or lipids) on the fluorescence signal of two fluorescence-based cell-free assays: the rhodamine 123 (RHD)-based assay, and a previously described assay based on dichlorodihydrofluorescein (DCF) in patients with systemic inflammation or atherosclerosis versus healthy subjects.

Results

We found lipid-probe interactions between the non-fluorescent substrate and the lipid, which affect the observed rate of change of fluorescence after addition of lipids to DHR and DCFH. These interactions depended on: sample collection and storage, types and concentrations of lipid and fluorescent probe, method of HDL isolation, diluents and matrices, and pH. The RHD-based assay yielded reproducible measurements despite fluorescence quenching, while the DCF-based assay displayed more experimental variability. Furthermore, the lipid-probe interactions varied according to the setting of systemic inflammation when using apolipoprotein (apo) B-depleted plasma. However, under fixed conditions the rhodamine assay could reliably detect similar mean relative differences in the redox activity of HDL samples between different groups of patients using either purified HDL or apo-B depleted plasma.

Conclusions

Lipid-probe interactions should be considered when interpreting the results of fluorescence assays for measuring lipid oxidative state. Ideally, samples should be freshly obtained and purified HDL should be utilized rather than Apo B-depleted serum. Assay variability can be reduced by strict standardization of conditions (particularly sample collection, storage, lipid isolation method). Data comparisons between different studies similarly require strict standardization of conditions between studies and this caveat must be considered when using these assays to study the role of HDL function in the development of atherosclerosis in vivo.