Staging of colorectal cancer using lipid biomarkers and machine learning.

INTRODUCTION: Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. Alteration in lipid metabolism and chemokine expression are considered hallmark characteristics of malignant progression and metastasis of CRC. Validated diagnostic and prognostic biomarkers are urgently needed to define molecular heterogeneous CRC clinical stages and subtypes, as liver dominant metastasis has poor survival outcomes. OBJECTIVES: The aim of this study was to integrate lipid changes, concentrations of chemokines, such as platelet factor 4 and interleukin 8, and gene marker status measured in plasma samples, with clinical features from patients at different CRC stages or who had progressed to stage-IV colorectal liver metastasis (CLM). METHODS: High-resolution liquid chromatography-mass spectrometry (HR-LC-MS) was used to determine the levels of candidate lipid biomarkers in each CRC patient's preoperative plasma samples and combined with chemokine, gene and clinical data. Machine learning models were then trained using known clinical outcomes to select biomarker combinations that best classify CRC stage and group. RESULTS: Bayesian neural net and multilinear regression-machine learning identified candidate biomarkers that classify CRC (stages I-III), CLM patients and control subjects (cancer-free or patients with polyps/diverticulitis), showing that integrating specific lipid signatures and chemokines (platelet factor-4 and interluken-8; IL-8) can improve prognostic accuracy. Gene marker status could contribute to disease prediction, but requires ubiquitous testing in clinical cohorts. CONCLUSION: Our findings demonstrate that correlating multiple disease related features with lipid changes could improve CRC prognosis. The identified signatures could be used as reference biomarkers to predict CRC prognosis and classify stages, and monitor therapeutic intervention.

Rapid and selective screening of organic peroxide explosives using acid-hydrolysis induced chemiluminescence.

Organic peroxide explosives (OPEs) are unstable, non-military, contemporary security threats often found in improvised explosive devices. Chemiluminescence (CL) can be used to detect OPEs, via radical formation consisting of peroxide moieties (-O-O-) under acidic conditions. However, selectivity for specific OPEs is hampered by the ubiquitous background of H2O2. Herein, we report the differentiation of hexamethylene triperoxide diamine (HMTD), triacetone triperoxide (TATP), and methyl ethyl ketone peroxide (MEKP) by specific flow injection analysis-CL (FIA-CL) signal profiles, after H2SO4 treatment. The radical degradation pathway of each structure, and its corresponding FIA-CL profile, was explored using mass spectrometry to reveal the rapid loss of -O-O- from TATP and HMTD structures, while MEKP formed CL signal-sustaining oligomers, as opposed to the immediate attenuation of H2O2. The CL response for OPEs in an aqueous media, measured via the described FIA-CL method, enabled ultra-trace limits of detection down to 0.40 µM for MEKP, 0.43 µM for HMTD, and 0.40 µM for TATP (combined linear range 1-83 µM with 95% confidence limit, n = 12). Expanded uncertainties of measurement (UM) of MEKP = ±0.98, HMTD = ±1.03, and TATP = ±1.1 (UM included probabilities of false positive and false negative as well as standard deviations of % recoveries and limit of detections of OPEs). Direct aqueous sample introduction via FIA-CL thus offers the prospect of rapid and selective screening of OPEs in security-heightened settings (e.g., airports), averting false positives from more ubiquitous H2O2.

Clinical Sphingolipids Pathway in Parkinson's Disease: From GCase to Integrated-Biomarker Discovery.

Alterations in the sphingolipid metabolism of Parkinson's Disease (PD) could be a potential diagnostic feature. Only around 10-15% of PD cases can be diagnosed through genetic alterations, while the remaining population, idiopathic PD (iPD), manifest without validated and specific biomarkers either before or after motor symptoms appear. Therefore, clinical diagnosis is reliant on the skills of the clinician, which can lead to misdiagnosis. IPD cases present with a spectrum of non-specific symptoms (e.g., constipation and loss of the sense of smell) that can occur up to 20 years before motor function loss (prodromal stage) and formal clinical diagnosis. Prodromal alterations in metabolites and proteins from the pathways underlying these symptoms could act as biomarkers if they could be differentiated from the broad values seen in a healthy age-matched control population. Additionally, these shifts in metabolites could be integrated with other emerging biomarkers/diagnostic tests to give a PD-specific signature. Here we provide an up-to-date review of the diagnostic value of the alterations in sphingolipids pathway in PD by focusing on the changes in definitive PD (postmortem confirmed brain data) and their representation in "probable PD" cerebrospinal fluid (CSF) and blood. We conclude that the trend of holistic changes in the sphingolipid pathway in the PD brain seems partly consistent in CSF and blood, and could be one of the most promising pathways in differentiating PD cases from healthy controls, with the potential to improve early-stage iPD diagnosis and distinguish iPD from other Parkinsonism when combined with other pathological markers.

Theranostic nanoparticles for the management of thrombosis.

Acute thrombosis and thromboembolisms are one of the leading causes of mortality and morbidity in both developed and developing countries, placing a huge burden on health and economic systems. Early diagnosis is critical but currently limited in accuracy and hampered by a narrow time frame, where the short therapeutic window also severely restricts treatment options. Additionally, clinically used antithrombotics and thrombolytics suffer from severe side effects and are limited in efficacy by a short half-life and susceptibility to degradation. The use of systems containing both diagnostic and therapeutic moieties, known as theranostics, can potentially improve patient outcomes by increasing the precision and efficacy of diagnosis and treatment, enabling personalised and precision medicine. Leveraging nanomedicine may further improve treatment by improving the system's pharmacokinetic properties including controlled drug delivery. This review provides an overview of the development of such theranostic nanoparticle systems, with a focus on approaches that may be utilised to usher this field towards clinical use.

Bacteriophage uptake by mammalian cell layers represents a potential sink that may impact phage therapy.

It is increasingly apparent that bacteriophages, viruses that infect bacteria and more commonly referred to as simply phages, have tropisms outside their bacterial hosts. Using live tissue culture cell imaging, we demonstrate that cell type, phage size, and morphology play a major role in phage internalization. Uptake was validated under physiological conditions using a microfluidic device. Phages adhered to mammalian tissues, with adherent phages being subsequently internalized by macropinocytosis, with functional phages accumulating intracellularly. We incorporated these results into a pharmacokinetic model demonstrating the potential impact of phage accumulation by cell layers, which represents a potential sink for circulating phages in the body. During phage therapy, high doses of phages are directly administered to a patient in order to treat a bacterial infection, thereby facilitating broad interactions between phages and mammalian cells. Understanding these interactions will have important implications on innate immune responses, phage pharmacokinetics, and the efficacy of phage therapy.

Stimulus-cleavable chemistry in the field of controlled drug delivery.

Stimulus-cleavable nanoscale drug delivery systems are receiving significant attention owing to their capability of achieving exquisite control over drug release via the exposure to specific stimuli. Central to the construction of such systems is the integration of cleavable linkers showing susceptibility to one stimulus or several stimuli with drugs, prodrugs or fluorogenic probes on the one hand, and nanocarriers on the other hand. This review summarises recent advances in stimulus-cleavable linkers from various research areas and the corresponding mechanisms of linker cleavage and biological applications. The feasibility of extending their applications to the majority of nanoscale drug carriers including nanomaterials, polymers and antibodies are further highlighted and discussed. This review also provides general design guidelines to incorporate stimulus-cleavable linkers into nanocarrier-based drug delivery systems, which will hopefully spark new ideas and applications.

Risk assessment on-a-chip: a cell-based microfluidic device for immunotoxicity screening.

Nanomaterials are widely used in industrial and clinical settings due to their unique physical and chemical properties. However, public health and environmental concerns have emerged owing to their undesired toxicity and ability to trigger immune responses. This paper presents the development of a microfluidic-based cell biochip device that enables the administration of nanoparticles under laminar flow to cells of the immune system to assess their cytotoxicity. The exposure of human B lymphocytes to 10 nm silver nanoparticles under fluid flow led to a 3-fold increase in toxicity compared to static conditions, possibly indicating enhanced cell-nanoparticle interactions. To investigate whether the administration under flow was the main contributing factor, we compared and validated the cytotoxicity of the same nanoparticles in different platforms, including the conventional well plate format and in-house fabricated microfluidic devices under both static and dynamic flow conditions. Our results suggest that commonly employed static platforms might not be well-suited to perform toxicological screening of nanomaterials and may lead to an underestimation of cytotoxic responses. The simplicity of the developed flow system makes this setup a valuable tool to preliminary screen nanomaterials.

Mapping insoluble indole metabolites in the gastrointestinal environment of a murine colorectal cancer model using desorption/ionisation on porous silicon imaging.

Indole derivatives are a structurally diverse group of compounds found in food, toxins, medicines, and produced by commensal microbiota. On contact with acidic stomach conditions, indoles undergo condensation to generate metabolites that vary in solubility, activity and toxicity as they move through the gut. Here, using halogenated ions, we map promising chemo-preventative indoles, i) 6-bromoisatin (6Br), ii) the mixed indole natural extract (NE) 6Br is found in, and iii) the highly insoluble metabolites formed in vivo using desorption/ionisation on porous silicon-mass spectrometry imaging (DIOS-MSI). The functionalised porous silicon architecture allowed insoluble metabolites to be detected that would otherwise evade most analytical platforms, providing direct evidence for identifying the therapeutic component, 6Br, from the mixed indole NE. As a therapeutic lead, 0.025 mg/g 6Br acts as a chemo-preventative compound in a 12 week genotoxic mouse model; at this dose 6Br significantly reduces epithelial cell proliferation, tumour precursors (aberrant crypt foci; ACF); and tumour numbers while having minimal effects on liver, blood biochemistry and weight parameters compared to controls. The same could not be said for the NE where 6Br originates, which significantly increased liver damage markers. DIOS-MSI revealed a large range of previously unknown insoluble metabolites that could contribute to reduced efficacy and increased toxicity.

Advances in Microfluidic Blood-Brain Barrier (BBB) Models.

Therapeutic options for neurological disorders currently remain limited. The intrinsic complexity of the brain architecture prevents potential therapeutics from reaching their cerebral target, thus limiting their efficacy. Recent advances in microfluidic technology and organ-on-chip systems have enabled the development of a new generation of in vitro platforms that can recapitulate complex in vivo microenvironments and physiological responses. In this context, microfluidic-based in vitro models of the blood-brain barrier (BBB) are of particular interest as they provide an innovative approach for conducting research related to the brain, including modeling of neurodegenerative diseases and high-throughput drug screening. Here, we present the most recent advances in BBB-on-chip devices and examine validation steps that will strengthen their future applications.

Beta-cyclodextrin decorated nanostructured SERS substrates facilitate selective detection of endocrine disruptor chemicals.

We demonstrate the selective detection of endocrine disruptor chemicals (EDCs) from river water using surface enhanced Raman scattering (SERS). By means of nanosphere lithography, the SERS substrate was prepared via the initial deposition of a monolayer of silica nanospheres (with diameter of ∼330 nm) on a silicon substrate as the template. Subsequently, a 180 nm thick layer of silver followed by a 20 nm layer of gold was deposited. This surface was modified with mono-6-deoxy-6-((2-mercaptoethyl)amino)-beta-cyclodextrin (ß-CD) in order to produce a selective capture surface suitable for EDC capture and their detection by means of SERS. We show that EDC model compounds, including 3-amino-2-naphthoic acid (NAPH), potassium hydrogen phthalate (PHTH) and the EDC ß-estradiol (ESTR), were captured by the ß-CD decorated surface. This surface facilitated SERS detection with limits of detection of 3.0 µM (NAPH), 10 µM (PHTH) and 300 nM (ESTR), all 10-100 times lower than that without the surface modification with ß-CD. Individual and simultaneous detection of NAPH and PHTH from their mixture was achieved as evidenced using the bianalyte Raman technique.

Fabrication of self-supporting porous silicon membranes and tuning transport properties by surface functionalization.

This study presents a simple approach to perform selective mass transport through freestanding porous silicon (pSi) membranes. pSi membranes were fabricated by the electrochemical etching of silicon to produce membranes with controlled structure and pore sizes close to molecular dimensions (approximately 12 nm in diameter). While these membranes are capable of size-exclusion based separations, chemically specific filtration remains a great challenge especially in the biomedical field. Herein, we investigate the transport properties of chemically functionalized pSi membranes. The membranes were functionalized using silanes (heptadecafluoro-1,1,2,2-tetrahydrodecyl)dimethylchlorosilane (PFDS) and N-(triethoxysilylpropyl)-o-polyethylene oxide urethane (PEGS) to give membranes hydrophobic (PFDS) and hydrophilic (PEGS) properties. The transport of probe dyes tris(2,2'-bipyridyl)dichlororuthenium(ii) hexahydrate (Rubpy) and Rose Bengal (RB) through these functionalized membranes was examined to determine the effect surface functionalization has on the selectivity and separation ability of pSi membranes. This study provides the basis for further investigation into more sophisticated surface functionalization and coupled with the biocompatibility of pSi will lead to new advances in membrane based bio-separations.

Recent developments in PDMS surface modification for microfluidic devices.

PDMS is enjoying continued and ever increasing popularity as the material of choice for microfluidic devices due to its low cost, ease of fabrication, oxygen permeability and optical transparency. However, PDMS's hydrophobicity and fast hydrophobic recovery after surface hydrophilization, attributed to its low glass transition temperature of less than -120 degrees C, negatively impacts on the performance of PDMS-based microfluidic device components. This issue has spawned a flurry of research to devise longer lasting surface modifications of PDMS, with particular emphasis on microfluidic applications. This review will present recent research on surface modifications of PDMS using techniques ranging from metal layer coatings and layer-by-layer depositions to dynamic surfactant treatments and the adsorption of amphipathic proteins. We will also discuss significant advances that have been made with a broad palette of gas-phase processing methods including plasma processing, sol-gel coatings and chemical vapor deposition. Finally, we will present examples of applications and future prospects of modified PDMS surfaces in microfluidics, in areas such as molecular separations, cell culture in microchannels and biomolecular detection via immunoassays.

Evaluation of alpha-D-mannopyranoside glycolipid micelles-lectin interactions by surface plasmon resonance method.

It is established that achieving higher binding affinities in carbohydrate-protein interactions requires multivalent presentations of the sugar ligands at the receptor binding site. Several inhibition, calorimetric, mass balance, and other studies have reiterated the beneficial effects of molecular level clustering of the sugar ligands for tight binding to the receptors. We have undertaken an effort to study the multivalent effects involving larger assemblies, represented by micelles, and their lectin interactions. The micelles were constituted with monomer bearing one- or two-sugar moieties at the monomolecular level and with varying the distances between the sugar moieties. Micellar aggregation studies and dynamic light scattering (DLS) studies afforded details of the aggregation numbers and the hydrodynamic diameters of various glycolipid (GL) micelles. The GL micelles were used as analytes of surface plasmon resonance (SPR) experiments on a lectin concanavalin A (Con A)-immobilized surface. SPR studies of the micelle-lectin interactions demonstrate that the ligand-receptor binding can be fit into the bivalent analyte model of interaction. Furthermore, micelles formed from two-sugar containing GLs are able to elicit favorable kinetic association rate constants in comparison to the micelles constituted with one-sugar containing GLs. The kinetic rate constants across the micelles and the effect of the sugar valencies in the GLs are discussed.