Highly sensitive and specific protein detection via combined capillary isoelectric focusing and proximity ligation

Emergence of infectious diseases and role of advanced nanomaterials in point-of-care diagnostics: a review

Infectious outbreaks are the foremost global public health concern, challenging the current healthcare system, which claims millions of lives annually. The most crucial way to control an infectious outbreak is by early detection through point-of-care (POC) diagnostics. POC diagnostics are highly advantageous owing to the prompt diagnosis, which is economical, simple and highly efficient with remote access capabilities. In particular, utilization of nanomaterials to architect POC devices has enabled highly integrated and portable (compact) devices with enhanced efficiency. As such, this review will detail the factors influencing the emergence of infectious diseases and methods for fast and accurate detection, thus elucidating the underlying factors of these infections. Furthermore, it comprehensively highlights the importance of different nanomaterials in POCs to detect nucleic acid, whole pathogens, proteins and antibody detection systems. Finally, we summarize findings reported on nanomaterials based on advanced POCs such as lab-on-chip, lab-on-disc-devices, point-of-action and hospital-on-chip. To this end, we discuss the challenges, potential solutions, prospects of integrating internet-of-things, artificial intelligence, 5G communications and data clouding to achieve intelligent POCs.

How does DNA 'meet' capillary-based microsystems?

DNA possesses various chemical and physical properties which make it important in biological analysis. The opportunity for DNA to 'meet' capillary-based microsystems is rapidly increasing owing to the expanding development of miniaturization. Novel capillary-based methods can provide favourable platforms for DNA-ligand interaction assay, DNA translocation study, DNA separation, DNA aptamer selection, DNA amplification assay, and DNA digestion. Meanwhile, DNA exhibits great potential in the fabrication of new capillary-based biosensors and enzymatic bioreactors. Moreover, DNA has received significant research interest in improving capillary electrophoresis (CE) performance. We focus on highlighting the advantages of combining DNA and capillary-based microsystems. The general trend presented in this review suggests that the 'meeting' has offered a stepping stone for the application of DNA and capillary-based microsystems in the field of analytical chemistry.

Proximity Ligation Assay as a Tool for Antibody Validation in Human Tissues

Immunohistochemistry (IHC) is the accepted standard for spatial analysis of protein expression in tissues. IHC is widely used for cancer diagnostics and in basic research. The development of new antibodies to proteins with unknown expression patterns has created a demand for thorough validation. We have applied resources from the Human Protein Atlas project and the Antibody Portal at National Cancer Institute to generate protein expression data for 12 proteins across 39 cancer cell lines and 37 normal human tissue types. The outcome of IHC on consecutive sections from both cell and tissue microarrays using two independent antibodies for each protein was compared with in situ proximity ligation (isPLA), where binding by both antibodies is required to generate detection signals. Semi-quantitative scores from IHC and isPLA were compared with expression of the corresponding 12 transcripts across all cell lines and tissue types. Our results show a more consistent correlation between mRNA levels and isPLA as compared to IHC. The main benefits of isPLA include increased detection specificity and decreased unspecific staining compared to IHC. We conclude that implementing isPLA as a complement to IHC for analysis of protein expression and in antibody validation pipelines can lead to more accurate localization of proteins in tissue.

A simple and highly sensitive masking fluorescence detection system for capillary array electrophoresis and its application to food and medicine analysis

A high sampling rate, good stability, high throughput masking fluorescence detection system with easy positioning of each channel for capillary array electrophoresis was prepared and studied. A special mask combined with convex lenses was designed to modulate signals, without using any extra device to position each channel. The signal of each channel was detected by a photomultiplier tube, classified and saved by software. The design was used to evidently reduce the rotational vibration of optical components and to stabilize the system, so a high sampling rate was obtained by increasing the DC motor speed. To improve the optical system, optical fibers instead of conventional bulky optical components were used to transmit optical signal and to collect fluorescences in multiple directions, which greatly raised the sensitivity. Other important parameters including sampling rate, rotating speed and driven voltage laser diode (LDs) have also been investigated. Under optimal conditions, the performance of the detection system was evaluated. This novel system had a well-designed structure, and allowed independent multiple capillary operations and easy microanalysis. Its limit of detection for rhodamine 6G was 2.0 × 10^-2 µg/mL.

Rapid Ultrasensitive Gel-Free Immunoblotting with Magnetic Labels

Immunoblotting is widely used for the detection of proteins using specific antibodies. We present here a new immunoblotting method, which is characterized by exceptional sensitivity, rapidness, and low consumption of antibodies. A thin conductive layer between touching hydrophilic cellulose membranes instead of polyacrylamide gel is used for the electrophoretic separation of proteins. Contrary to common Western blotting, the separation occurs in nondenaturing conditions. The membrane surface is smoothed by deposition of the cellulose layer and modified with azidophenyl groups, allowing for the photochemical in situ immobilization of proteins, which are carried out after the electrophoresis. Thus, the additional step of transferring the protein from the gel onto the membrane is eliminated. Specific protein bands are then visualized by decoration with magnetic beads. The limit of detection of interleukin IL-1β reaches 0.3 fg or ∼10⁴ molecules, whereas the total blotting time is about 5 min. The application of the technique is demonstrated by the detection of IL-1β, total IgA, and IgA specific to Mycobacterium tuberculosis antigen in the exhaled breath samples, obtained from healthy subjects and tuberculosis patients.

Potency Assessment of CBD Oils by Their Effects on Cell Signaling Pathways

This study used nanofluidic protein posttranslational modification (PTM) profiling to measure the effects of six cannabidiol (CBD) oils and isolated CBD on the signaling pathways of a cultured SH-SY5Y neuronal cell line. Chemical composition analysis revealed that all CBD oils met the label claims and legal regulatory limit regarding the CBD and tetrahydrocannabinol (THC) contents, respectively. Isolated CBD was cytotoxic, with an effective concentration (EC₅₀) of 40 µM. In contrast, the CBD oils had no effect on cell viability at CBD concentrations exceeding 1.2 mM. Interestingly, only an unadulterated CBD oil had strong and statistically significant suppressive effects on the pI3K/Akt/mTOR signaling pathway with an EC₅₀ value of 143 µM and a slow-acting timescale requiring hours. Systematic profiling of twenty-six proteins, which served as biomarkers for nine signaling pathways, revealed that the unadulterated CBD oil downregulated seven signaling pathways but had no measurable effect on the other two signaling pathways. The remaining CBD oils, which were adulterated, and isolated CBD had weak, variable, or undetectable effects on neuronal signaling pathways. Our data clearly showed that adulteration diminished the biological activities of CBD oils. In addition, nanofluidic protein PTM profiling provided a robust means for potency assessment of CBD oils.

Differentiation of Essential Oils Using Nanofluidic Protein Post-Translational Modification Profiling

Current methods for the authentication of essential oils focus on analyzing their chemical composition. This study describes the use of nanofluidic protein post-translational modification (PTM) profiling to differentiate essential oils by analyzing their biochemical effects. Protein PTM profiling was used to measure the effects of four essential oils, copaiba, mandarin, Melissa, and turmeric, on the phosphorylation of MEK1, MEK2, and ERK1/2 in the MAPK signaling pathway; Akt and 4EBP1 in the pI3K/Akt/mTOR signaling pathway; and STAT3 in the JAK/STAT signaling pathway in cultured HepG2 cells. The gain or loss of the phosphorylation of these proteins served as direct read-outs for the positive or negative regulatory effects of essential oils on their respective signaling pathways. Furthermore, protein PTM profiling and GC-MS were employed side-by-side to assess the quality of the essential oils. In general, protein PTM profiling data concurred with GC-MS data on the identification of adulterated mandarin, Melissa, and turmeric essential oils. Most interestingly, protein PTM profiling data identified the differences in biochemical effects between copaiba essential oils, which were indistinguishable with GC-MS data on their chemical composition. Taken together, nanofluidic protein PTM profiling represents a robust method for the assessment of the quality and therapeutic potential of essential oils.

Chaperome heterogeneity and its implications for cancer study and treatment

The chaperome is the collection of proteins in the cell that carry out molecular chaperoning functions. Changes in the interaction strength between chaperome proteins lead to an assembly that is functionally and structurally distinct from each constituent member. In this review, we discuss the epichaperome, the cellular network that forms when the chaperome components of distinct chaperome machineries come together as stable, functionally integrated, multimeric complexes. In tumors, maintenance of the epichaperome network is vital for tumor survival, rendering them vulnerable to therapeutic interventions that target critical epichaperome network components. We discuss how the epichaperome empowers an approach for precision medicine cancer trials where a new target, biomarker, and relevant drug candidates can be correlated and integrated. We introduce chemical biology methods to investigate the heterogeneity of the chaperome in a given cellular context. Lastly, we discuss how ligand-protein binding kinetics are more appropriate than equilibrium binding parameters to characterize and unravel chaperome targeting in cancer and to gauge the selectivity of ligands for specific tumor-associated chaperome pools.

Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer

BACKGROUND: Due to difficulties in predicting recurrences in colorectal cancer stages II and III, reliable prognostic biomarkers could be a breakthrough for individualized treatment and follow-up. OBJECTIVE: To find potential prognostic protein biomarkers in colorectal cancer, using the proximity extension assays. METHODS: A panel of 92 oncology-related proteins was analyzed with proximity extension assays, in plasma from a cohort of 261 colorectal cancer patients with stage II-IV. The survival analyses were corrected for disease stage and age, and the recurrence analyses were corrected for disease stage. The significance threshold was adjusted for multiple comparisons. RESULTS: The plasma proteins expression levels had a greater prognostic relevance in disease stage III colorectal cancer than in disease stage II, and for overall survival than for time to recurrence. Osteoprotegerin was the only biomarker candidate in the protein panel that had a statistical significant association with overall survival (P = .00029). None of the proteins were statistically significantly associated with time to recurrence. CONCLUSIONS: Of the 92 analyzed plasma proteins, osteoprotegerin showed the strongest prognostic impact in patients with colorectal cancer, and therefore osteoprotegerin is a potential predictive marker, and it also could be a target for treatments.

Detection of the Cell Cycle-Regulated Negative Feedback Phosphorylation of Mitogen-Activated Protein Kinases in Breast Carcinoma using Nanofluidic Proteomics

Mitogen-activated protein kinases (MAPKs) play an important role in the regulation of cell proliferation, oncogenic transformation, and drug resistance. This study examined the capability of nanofluidic proteomics to identify aberrations in the MAPK signaling cascade, monitor its drug response, and guide the rational design of intervention strategies. Specifically, the protein post-translational modification (PTM) profiles of MEK1, MEK2, and ERK1/2 were measured in breast carcinoma and breast cancer cell lines. Nanofluidic proteomics revealed hyper-phosphorylation of MAPKs in breast carcinoma and breast cancer cells treated with kinase inhibitors that interfere with cell cycle regulation, such as dinaciclib, an inhibitor of cyclin-dependent kinases, and rigosertib, an inhibitor of polo-like kinase 1. A pMEK1 (Thr286) phosphor-isoform, which serves as a biomarker of cell cycle-regulated negative feedback phosphorylation in breast cancer cells, was detected in breast carcinoma. Inhibition of the MAPK pathway with dabrafenib, a B-Raf inhibitor, or trametinib, a MEK1/2 inhibitor, suppressed both the positively regulated phosphorylation of MAPKs and the negatively regulated phosphorylation of MEK1. Interestingly, the combinations of dabrafenib and rigosertib or trametinib and rigosertib permitted the suppression of positively regulated MAPK phosphorylation together with the promotion of negatively regulated MEK1 phosphorylation. The effectiveness of protein PTM-guided drug combinations for inhibition of the MAPK pathway remains to be experimentally tested. Via protein PTM profiling, nanofluidic proteomics provides a robust means to detect anomalies in the MAPK signaling cascade, monitor its drug response, and guide the possible design of drug combinations for MAPK pathway-focused targeting.

Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes

We have redesigned probes for in situ proximity ligation assay (PLA), resulting in more efficient localized detection of target proteins. In situ PLA depends on recognition of target proteins by pairs of antibody-oligonucleotide conjugates (PLA probes), which jointly give rise to DNA circles that template localized rolling circle amplification reactions. The requirement for dual recognition of the target proteins improves selectivity by ignoring any cross-reactivity not shared by the antibodies, and it allows detection of protein-protein interactions and post-translational modifications. We herein describe an improved design of the PLA probes –UnFold probes – where all elements required for formation of circular DNA strands are incorporated in the probes. Premature interactions between the UnFold probes are prevented by including an enzymatic “unfolding” step in the detection reactions. This allows DNA circles to form by pairs of reagents only after excess reagents have been removed. We demonstrate the performance of UnFold probes for detection of protein-protein interactions and post-translational modifications in fixed cells and tissues, revealing considerably more efficient signal generation. We also apply the UnFold probes to detect IL-6 in solution phase after capture on solid supports, demonstrating increased sensitivity over both normal sandwich enzyme-linked immunosorbent assays and conventional PLA assays.