PeptiCHIP: A Microfluidic Platform for Tumor Antigen Landscape Identification.

Identification of HLA class I ligands from the tumor surface (ligandome or immunopeptidome) is essential for designing T-cell mediated cancer therapeutic approaches. However, the sensitivity of the process for isolating MHC-I restricted tumor-specific peptides has been the major limiting factor for reliable tumor antigen characterization, making clear the need for technical improvement. Here, we describe our work from the fabrication and development of a microfluidic-based chip (PeptiCHIP) and its use to identify and characterize tumor-specific ligands on clinically relevant human samples. Specifically, we assessed the potential of immobilizing a pan-HLA antibody on solid surfaces via well-characterized streptavidin-biotin chemistry, overcoming the limitations of the cross-linking chemistry used to prepare the affinity matrix with the desired antibodies in the immunopeptidomics workflow. Furthermore, to address the restrictions related to the handling and the limited availability of tumor samples, we further developed the concept toward the implementation of a microfluidic through-flow system. Thus, the biotinylated pan-HLA antibody was immobilized on streptavidin-functionalized surfaces, and immune-affinity purification (IP) was carried out on customized microfluidic pillar arrays made of thiol-ene polymer. Compared to the standard methods reported in the field, our methodology reduces the amount of antibody and the time required for peptide isolation. In this work, we carefully examined the specificity and robustness of our customized technology for immunopeptidomics workflows. We tested this platform by immunopurifying HLA-I complexes from 1 × 106 cells both in a widely studied B-cell line and in patients-derived ex vivo cell cultures, instead of 5 × 108 cells as required in the current technology. After the final elution in mild acid, HLA-I-presented peptides were identified by tandem mass spectrometry and further investigated by in vitro methods. These results highlight the potential to exploit microfluidics-based strategies in immunopeptidomics platforms and in personalized immunopeptidome analysis from cells isolated from individual tumor biopsies to design tailored cancer therapeutic vaccines. Moreover, the possibility to integrate multiple identical units on a single chip further improves the throughput and multiplexing of these assays with a view to clinical needs.

Metallization of Organically Modified Ceramics for Microfluidic Electrochemical Assays.

Organically modified ceramic polymers (ORMOCERs) have attracted substantial interest in biomicrofluidic applications owing to their inherent biocompatibility and high optical transparency even in the near-ultraviolet (UV) range. However, the processes for metallization of ORMOCERs as well as for sealing of metallized surfaces have not been fully developed. In this study, we developed metallization processes for a commercial ORMOCER formulation, Ormocomp, covering several commonly used metals, including aluminum, silver, gold, and platinum. The obtained metallizations were systematically characterized with respect to adhesion (with and without adhesion layers), resistivity, and stability during use (in electrochemical assays). In addition to metal adhesion, the possibility for Ormocomp bonding over each metal as well as sufficient step coverage to guarantee conductivity over topographical features (e.g., over microchannel edges) was addressed with a view to the implementation of not only planar, but also three-dimensional on-chip sensing elements. The feasibility of the developed metallization for implementation of microfluidic electrochemical assays was demonstrated by fabricating an electrophoresis separation chip, compatible with a commercial bipotentiostat, and incorporating integrated working, reference, and auxiliary electrodes for amperometric detection of an electrochemically active pharmaceutical, acetaminophen.

Immobilization of proteolytic enzymes on replica-molded thiol-ene micropillar reactors via thiol-gold interaction.

We introduce rapid replica molding of ordered, high-aspect-ratio, thiol-ene micropillar arrays for implementation of microfluidic immobilized enzyme reactors (IMERs). By exploiting the abundance of free surface thiols of off-stoichiometric thiol-ene compositions, we were able to functionalize the native thiol-ene micropillars with gold nanoparticles (GNPs) and these with proteolytic α-chymotrypsin (CHT) via thiol-gold interaction. The micropillar arrays were replicated via PDMS soft lithography, which facilitated thiol-ene curing without the photoinitiators, and thus straightforward bonding and good control over the surface chemistry (number of free surface thiols). The specificity of thiol-gold interaction was demonstrated over allyl-rich thiol-ene surfaces and the robustness of the CHT-IMERs at different flow rates and reaction temperatures using bradykinin hydrolysis as the model reaction. The product conversion rate was shown to increase as a function of decreasing flow rate (increasing residence time) and upon heating of the IMER to physiological temperature. Owing to the effective enzyme immobilization onto the micropillar array by GNPs, no further purification of the reaction solution was required prior to mass spectrometric detection of the bradykinin hydrolysis products and no clogging problems, commonly associated with conventional capillary packings, were observed. The activity of the IMER remained stable for at least 1.5 h (continuous use), suggesting that the developed protocol may provide a robust, new approach to implementation of IMER technology for proteomics research. Graphical abstract.

Aqueous and non-aqueous microchip electrophoresis with on-chip electrospray ionization mass spectrometry on replica-molded thiol-ene microfluidic devices.

This work describes aqueous and non-aqueous capillary electrophoresis on thiol-ene-based microfluidic separation devices that feature fully integrated and sharp electrospray ionization (ESI) emitters. The chip fabrication is based on simple and low-cost replica-molding of thiol-ene polymers under standard laboratory conditions. The mechanical rigidity and the stability of the materials against organic solvents, acids and bases could be tuned by adjusting the respective stoichiometric ratio of the thiol and allyl ("ene") monomers, which allowed us to carry out electrophoresis separation in both aqueous and non-aqueous (methanol- and ethanol-based) background electrolytes. The stability of the ESI signal was generally ≤10% RSD for all emitters. The respective migration time repeatabilities in aqueous and non-aqueous background electrolytes were below 3 and 14% RSD (n=4-6, with internal standard). The analytical performance of the developed thiol-ene microdevices was shown in mass spectrometry (MS) based analysis of peptides, proteins, and small molecules. The theoretical plate numbers were the highest (1.2-2.4×104m-1) in ethanol-based background electrolytes. The ionization efficiency also increased under non-aqueous conditions compared to aqueous background electrolytes. The results show that replica-molding of thiol-enes is a feasible approach for producing ESI microdevices that perform in a stable manner in both aqueous and non-aqueous electrophoresis.

Thiol-ene microfluidic devices for microchip electrophoresis: Effects of curing conditions and monomer composition on surface properties.

Thiol-ene polymer formulations are raising growing interest as new low-cost fabrication materials for microfluidic devices. This study addresses their feasibility for microchip electrophoresis (MCE) via characterization of the effects of UV curing conditions and aging on the surface charge and wetting properties. A detailed comparison is made between stoichiometric thiol-ene (1:1) and thiol-ene formulations bearing 50% molar excess of allyls ("enes"), both prepared without photoinitiator or other polymer modifiers. Our results show that the surface charge of thiol-ene 1:1 increases along with increasing UV exposure dose until a threshold (here, about 200J/cm(2)), whereas the surface charge of thiol-ene 2:3 decreases as a function of increasing UV dose. However, no significant change in the surface charge upon storage in ambient air was observed over a period of 14 days (independent of the curing conditions). The water contact angles of thiol-ene 2:3 (typically 70-75°) were found to be less dependent on the UV dose and storing time. Instead, water contact angles of thiol-ene 1:1 slightly decrease (from initial 90 to 95° to about 70°) as a function of UV increasing exposure dose and storing time. Most importantly, both thiol-ene formulations remain relatively hydrophilic over extended periods of time, which favors their use in MCE applications. Here, MCE separation of biologically active peptides and selected fluorescent dyes is demonstrated in combination with laser-induced fluorescence detection showing high separation efficiency (theoretical plates 8200 per 4cm for peptides and 1500-2700 per 4cm for fluorescent dyes) and lower limits of detection in the sub-µM (visible range) or low-µM (near-UV range) level.

Stable neutral double hydrophilic block copolymer capillary coating for capillary electrophoretic separations.

Quaternized diblock copolymer, poly(N-methyl-2-vinylpyridinium iodide-block-ethylene oxide), was successfully used as a neutral, dynamic coating to suppress the electroosmotic flow. The block copolymer consisted of two polymers that were linked covalently together. The cationic block (poly(N-methyl-2-vinylpyridinium iodide)) was bound efficiently to the negatively charged capillary wall via electrostatic interactions, and the hydrophilic block (ethylene oxide) stabilized the system and created a neutral capillary surface with ultralow electroosmotic flow (+2.0 ± 4.5 × 10(-10) m(2)/Vs). The main advantages of the coating were simple and fast preparation, easy regeneration and automation, and stable electroosmotic flow. To emphasize the potential of this type of coating its stability was measured at a wide pH range demonstrating a high stability in the pH range of 4.0-10.5 and lifetime up to 8 days. The successful studies carried out with beta-blockers, basic proteins, and lipoproteins proved the suitability of the coating for the separation of different sized analytes. Furthermore, the neutral coating developed is useful in a wide range of protein analysis and biological interaction studies under physiological condition.

Partial-filling affinity capillary electrophoresis and quartz crystal microbalance with adsorption energy distribution calculations in the study of biomolecular interactions with apolipoprotein E as interaction partner.

Adsorption energy distribution (AED) calculations were successfully applied to partial-filling affinity capillary electrophoresis (PF-ACE) to facilitate more detailed studies of biomolecular interactions. PF-ACE with AED calculations was employed to study the interactions between two isoforms of apolipoprotein E (apoE) and dermatan sulfate (DS), and a quartz crystal microbalance (QCM) was used in combination with AED calculations to examine the interactions of the 15-amino-acid peptide fragment of apoE with DS. The heterogeneity of the interactions was elucidated. Microscale thermophoresis was used to validate the results. The interactions studied are of interest because, in vivo, apolipoprotein E localizes on DS-containing regions in the extracellular matrix of human vascular subendothelium. Two-site binding was demonstrated for the isoform apoE3 and DS, but only one-site binding for apoE2-DS. Comparable affinity constants were obtained for the apoE2-DS, apoE3-D3, and 15-amino-acid peptide of apoE-DS using the three techniques. The results show that combining AED calculations with modern biosensing techniques can open up another dimension in studies on the heterogeneity and affinity constants of biological molecules.

Diblock-copolymer-mediated self-assembly of protein-stabilized iron oxide nanoparticle clusters for magnetic resonance imaging.

Superparamagnetic iron oxide nanoparticles (SPIONs) can be used as efficient transverse relaxivity (T2 ) contrast agents in magnetic resonance imaging (MRI). Organizing small (D<10 nm) SPIONs into large assemblies can considerably enhance their relaxivity. However, this assembly process is difficult to control and can easily result in unwanted aggregation and precipitation, which might further lead to lower contrast agent performance. Herein, we present highly stable protein-polymer double-stabilized SPIONs for improving contrast in MRI. We used a cationic-neutral double hydrophilic poly(N-methyl-2-vinyl pyridinium iodide-block-poly(ethylene oxide) diblock copolymer (P2QVP-b-PEO) to mediate the self-assembly of protein-cage-encapsulated iron oxide (γ-Fe2 O3 ) nanoparticles (magnetoferritin) into stable PEO-coated clusters. This approach relies on electrostatic interactions between the cationic N-methyl-2-vinylpyridinium iodide block and magnetoferritin protein cage surface (pI≈4.5) to form a dense core, whereas the neutral ethylene oxide block provides a stabilizing biocompatible shell. Formation of the complexes was studied in aqueous solvent medium with dynamic light scattering (DLS) and cryogenic transmission electron microcopy (cryo-TEM). DLS results indicated that the hydrodynamic diameter (Dh ) of the clusters is approximately 200 nm, and cryo-TEM showed that the clusters have an anisotropic stringlike morphology. MRI studies showed that in the clusters the longitudinal relaxivity (r1 ) is decreased and the transverse relaxivity (r2 ) is increased relative to free magnetoferritin (MF), thus indicating that clusters can provide considerable contrast enhancement.