Characterization of Sample Loss Caused by Competitive Adsorption of Proteins in Vials Using Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis

Evaluating Cryopreservation Methods in Biobanking: Impacts on Biomarker Integrity and Omics Data Reliability

Objectives: Personalized medicine emphasizes prevention and early diagnosis by developing genetic screening and biomarker assessment tools. Biobanks, including University of Piemonte Orientale (UPO) Biobank, support this effort by providing high-quality biological samples collected, processed, and stored using optimized standardized protocols. To determine the optimal long-term storage conditions for biospecimens used in biomedical research, we evaluated plasma and serum samples cryopreserved using two storage methods, cryovials and straws, across various analytical methodologies with differing sensitivity and robustness. Design and Methods: Plasma and serum samples cryopreserved in liquid nitrogen in vials and straw at the UPO Biobank were subjected to multiple analyses including standard biochemical laboratory analysis, targeted lipidomics, untargeted proteomics, and targeted metabolites quantification through mass spectrometry-based analytical techniques. Results: Our data demonstrate the robustness and applicability of both storage methods for standard laboratory analyses in evaluating clinically relevant markers in plasma and serum. Lipidomic analysis revealed slight disparities in lipid abundance, though these differences were mostly confined to specific lipid species, particularly fatty acids. Conversely, proteomic and metabolomic analyses uncovered variations in abundance in a significant, albeit limited, fraction of analytes between vials and straw-derived samples. Conclusions: By highlighting similarities and differences in samples stored in these conditions, this study provides significant insights into optimizing biobanking practices and understanding the factors that influence the integrity of cryopreserved biospecimens and the reliability of the data derived from them. Both straws and vials are convenient and efficient cryopreservation methods, essentially equivalent for samples dedicated to robust and relatively low-sensitive standardized analyses. However, our findings emphasize the need for caution when interpreting omics data from samples subjected to different cryopreservation methods, as subtle variations can arise even with different types of containers.

Development of an Absolute Quantification Method for hERG Using PRM with Single Isotopologue in-Sample Calibration

The human ether-à-go-go-related gene (KCNH2)-encoded protein hERG constitutes the α subunit of the Kv11.1 channel and contributes to the I kr current, which plays an important role in the cardiac action potential. Genetically and xenobiotically triggered malfunctions of hERG can cause arrhythmia. The expression of hERG in various study systems was assessed mainly as the fold change relative to the corresponding control. Here, we developed a simple and sensitive quantitation method using targeted mass spectrometry, i.e., the parallel reaction monitoring approach, to measure the absolute quantity of hERG in copy number. Such measurements do not require controls, and the obtained values can be compared with similar results for any other protein. To effectively avoid matrix effects, we used the heavy-match-light (HML) in-sample calibration approach that requires only a single isotopologue to achieve copy-number quantitation. No significant difference was observed in the results obtained by HML and by the classic standard addition in-sample calibration approach. Using four proteotypic peptides, we quantified the average number of copies of hERG in the HEK293T heterologous expression system as 3.6 ± 0.5 × 106 copies/cell, i.e., 1 million copies/cell for the fully assembled Kv11.1 channel.

Electrophoretic Microplate Protein Identification Based on Gold Staining of Molybdenum Disulfide Hydrogels

Numerous high-performance nanotechnologies have been developed, but their practical applications are largely restricted by the nanomaterials' low stabilities and high operation complexity in aqueous substrates. Herein, we develop a simple and high-reliability hydrogel-based nanotechnology based on the in situ formation of Au nanoparticles in molybdenum disulfide (MoS2)-doped agarose (MoS2/AG) hydrogels for electrophoresis-integrated microplate protein recognition. After the incubation of MoS2/AG hydrogels in HAuCl4 solutions, MoS2 nanosheets spontaneously reduce Au ions, and the hydrogels are remarkably stained with the color of as-synthetic plasmonic Au hybrid nanomaterials (Au staining). Proteins can precisely mediate the morphologies and optical properties of Au/MoS2 heterostructures in the hydrogels. Consequently, Au staining-based protein recognition is exhibited, and hydrogels ensure the comparable stabilities and sensitivities of protein analysis. In comparison to the fluorescence imaging and dye staining, enhanced sensitivity and recognition performances of proteins are implemented by Au staining. In Au staining, exfoliated MoS2 semiconductors directly guide the oriented growth of plasmonic Au nanostructures in the presence of formaldehyde, showing environment-friendly features. The Au-stained hydrogels merge the synthesis and recognition applications of plasmonic Au nanomaterials. Significantly, the one-step incubation of the electrophoretic hydrogels leads to high simplicity of operation, largely challenging those multiple-step Ag staining routes which were performed with high complexity and formaldehyde toxicity. Due to its toxic-free, simple, and sensitive merits, the Au staining integrated with electrophoresis-based separation and microplate-based high-throughput measurements exhibits highly promising and improved practicality of those developing nanotechnologies and largely facilitates in-depth understanding of biological information.

Protein Adsorption Loss─The Bottleneck of Single-Cell Proteomics

Single-cell proteomics is a promising field to provide direct yet comprehensive molecular insights into cellular functions without averaging effects. Here, we address a grand technical challenge impeding the maturation of single-cell proteomics─protein adsorption loss (PAL). Even though widely known, there is currently no quantitation on how profoundly and selectively PAL has affected single-cell proteomics. Therefore, the mitigations to this challenge have been generic, and their efficacy was only evaluated by the size of the resolved proteome with no specificity on individual proteins. We use the existing knowledge of PAL, protein expression, and the typical surface area used in single-cell proteomics to discuss the severity of protein loss. We also summarize the current solutions to this challenge and briefly review the available methods to characterize the physical and chemical properties of protein surface adsorption. By citing successful strategies in single-cell genomics for measurement errors in individual transcripts, we pinpoint the urgency to benchmark PAL at the proteome scale with individual protein resolution. Finally, orthogonal single-cell proteomic techniques that have the potential to cross validate PAL are proposed. We hope these efforts can promote the fruition of single-cell proteomics in the near future.

Absolute Quantification of Nav1.5 Expression by Targeted Mass Spectrometry

Nav1.5 is the pore forming α-subunit of the cardiac voltage-gated sodium channel that initiates cardiac action potential and regulates the human heartbeat. A normal level of Nav1.5 is crucial to cardiac function and health. Over- or under-expression of Nav1.5 can cause various cardiac diseases ranging from short PR intervals to Brugada syndromes. An assay that can directly quantify the protein amount in biological samples would be a priori to accurately diagnose and treat Nav1.5-associated cardiac diseases. Due to its large size (>200 KD), multipass transmembrane domains (24 transmembrane passes), and heavy modifications, Nav1.5 poses special quantitation challenges. To date, only the relative quantities of this protein have been measured in biological samples. Here, we describe the first targeted and mass spectrometry (MS)-based quantitative assay that can provide the copy numbers of Nav1.5 in cells with a well-defined lower limit of quantification (LLOQ) and precision. Applying the developed assay, we successfully quantified transiently expressed Nav1.5 in as few as 1.5 million Chinese hamster ovary (CHO) cells. The obtained quantity was 3 ± 2 fmol on the column and 3 ± 2 × 104 copies/cell. To our knowledge, this is the first absolute quantity of Nav1.5 measured in a biological sample.

Improved intact peptide and protein quantitation by LC-MS: Battling the deleterious effects of analyte adsorption

Peptide and protein quantitation by liquid chromatography-mass spectrometry relies on the assumption of linear signal response with concentration. At low concentrations, analyte adsorption to pipette tips, sample vials and equipment can have significant deleterious effects on signal response. Meanwhile at high concentrations, linearity breaks down due to competitive ionization, signal suppression, and the formation of peptide or protein multimers. These effects result in calibration curves that are more sigmoidal than linear. Linearity at low protein levels for identification and quantitation is of paramount importance in the discovery and validation of biomarker molecules. Herein, we demonstrate the benefits of using commercial low-bind microcentrifuge tubes and LC vials on the response of a 27-mer peptide, Vn96, and the intact proteins apomyoglobin and carbonic anhydrase. Linear curves were acquired for Vn96 while apomyoglobin required the addition of intact carbonic anhydrase as an adsorption competitor to achieve linearity. A linear calibration curve for carbonic anhydrase was also acquired by using the polypeptide ubiquitin as an adsorption competitor and internal standard. Linear response was recorded for approximately two orders of magnitude for apomyoglobin and carbonic anhydrase and three orders of magnitude for Vn96 with detection limits ranging from 0.33 to 19 fmol/µL. Finally, we used low-bind vials for the online enzymatic digestion of apomyoglobin where a high concentration of apomyoglobin acted as an adsorption blocker for the low level trypsin enzyme. Fortunately, the liberated tryptic peptides showed no affinity for the walls of the low-bind vials. In this study, we take a comprehensive approach to combat analyte adsorption by showing the significance of utilizing low-bind vials and adsorption competitors to greatly improve upon signal sensitivity at low concentrations of target molecules. The use of these methodologies should improve the low-level detection of molecules by mass spectrometry.

Adsorbed protein film on pump surfaces leads to particle formation during fill-finish manufacturing

During fill-finish manufacturing, therapeutic proteins may aggregate or form subvisible particles in response to the physical stresses encountered within filling pumps. Understanding and quantitating this risk is important since filling may be the last unit operation before the patient receives their dose. We studied particle formation from lab-scale to manufacturing-scale using sensitive and robust protein formulations. Filling experiments with a ceramic rotary piston pump were integrated with a rinse-stripping method to investigate the relationship between protein adsorption and particle formation. For a sensitive protein, multilayer film formation on the piston surface correlated with high levels of subvisible particles in solution. For a robust protein formulation, adsorption and subvisible particle formation were minimal. These results support an aggregation mechanism that is initiated by adsorption to pump surfaces and propagated by mechanical and/or hydrodynamic disruption of the film. The elemental analysis confirmed that ceramic wear debris remained at trace levels and did not contribute appreciably to protein aggregation.

Poly(2-hydroxyethyl methacrylate)/β-cyclodextrin-hyaluronan contact lens with tear protein adsorption resistance and sustained drug delivery for ophthalmic diseases

A series of poly(2-hydroxyethyl methacrylate) (pHEMA) hydrogels containing cross-linked β-cyclodextrin-hyaluronan (β-CD-crHA), with tear protein adsorption resistance and sustained drug delivery, were developed as contact lens materials for eye diseases. β-CD-HA was synthesized from aminated β-CD and HA and then crosslinked within pHEMA hydrogel using polyethylenimine as a crosslinker. The synthesized β-CD-HA was characterized by ¹H NMR analysis, and β-CD-crHA immobilized in pHEMA hydrogel was confirmed by FT-IR, SEM, and AFM analyses. The incorporation of β-CD-crHA significantly improved the surface hydrophilicity, water uptake ability, oxygen permeability, and flexibility of pHEMA hydrogel, but did not compromise light transmission. pHEMA/β-CD-crHA hydrogels not only decreased the tear protein adsorption because of the electrostatically mutual repulsion and the improved hydrophilicity, leading to the reduced adhesion of Staphylococcus aureus on the hydrogel surface, but also enhanced the encapsulation capacity and the sustainable delivery of diclofenac due to the formation of inclusion complexes between β-CD and drugs. All the hydrogels were nontoxic to 3T3 mouse fibroblasts by in vitro cell viability analysis. Among these hydrogels with different β-CD-crHA contents, pHEMA/β-CD-crHA₁₀ hydrogel showed the lowest water contact angle of 52 °, the highest water content of 65%, the largest Dk value of 36.4 barrer, and the optimal modulus of 1.8 MPa, as well as a good light transmission of over 90%. The in vivo conjunctivitis treatment of rabbits for 72 h indicated that drug-loaded pHEMA/β-CD-crHA₁₀ hydrogel presented a better therapeutic effect than both one dose administration of drug solution per day and drug-loaded pHEMA hydrogel. Thus, pHEMA/β-CD-crHA₁₀ hydrogel is a promising contact lens material for ophthalmic diseases. STATEMENT OF SIGNIFICANCE: Topical eye drops are currently the most popular treatment for ophthalmic diseases, but frequent dosing is necessary to acquire the desirable clinical effect at the expense of systemic side-effects. Drug-loaded contact lenses, as an alternative of eye drops, possess many good performances and show potential applications. However, the sustained drug delivery and the tear protein adsorption resistance are still challenging for contact lenses. Hence, we developed a novel pHEMA/β-CD-crHA hydrogel by incorporating β-CD-crHA crosslinked network into pHEMA hydrogel. Besides the improvements in surface hydrophilicity, water uptake ability, oxygen permeability, and flexibility, pHEMA/β-CD-crHA hydrogel also reduced the adsorption of tear proteins and the adhesion of Staphylococcus aureus, enhanced the drug encapsulation, and prolonged the drug delivery, with better effect in the conjunctivitis treatment of rabbits. Thus, pHEMA/β-CD-crHA hydrogel is a potential contact lens material for treating ophthalmic diseases.

Enhanced electrophoretic separation of proteins by tethered SiO2 nanoparticles in an SDS-polyacrylamide gel network

Nanoparticles (NPs) are able to improve the separation efficiency of proteins in SDS-polyacrylamide gel electrophoresis (SDS-PAGE) due to their capability of enhancing heat dissipation during electrophoresis. However, the intrinsic surface charges of NPs (at buffer pH or charge induced due to the SDS coating) make them acquire electrophoretic mobility and movement in the gel. Such a movement leads to viscosity and temperature gradients in the gel and deteriorates the separation. In this work, we proposed a novel method by using tethered NPs in the gel. Silica NPs, as the model NPs, were prepared and their surfaces were modified using 3-[(methacryloxy)propyl] trimethoxysilane (MPS) which locks the NPs in the gel via covalent bonds (M-SiO₂/PA (polyacrylamide)). SiO₂ NPs were embedded into the gel (SiO₂/PA) as the positive control, while pure PA gel was chosen as the negative control. The results showed that at a relatively high voltage of 250 V, although the Joule heat generated during electrophoresis disturbed the separation in the pure gel, the SiO₂/PA and M-SiO₂/PA nanocomposite gels showed better performances. In comparison with the pure PA gel, the resolution increased by 3 and 32% for SiO₂/PA and M-SiO₂/PA, respectively, in a relatively short separation time of 35 min. The gel with tethered NPs presented a more efficient separation in terms of band broadening and resolution compared with the gel with free NPs probably due to the movement of free charged particles in the gel. Evidently, the migration speed of protein bands in the gels decreased especially for larger proteins in the presence of the NPs compared to the pristine gel due to the steric hindrance of the NPs. Finally, we separated E. coli proteins, as a real sample. Among the three gels (pure PA, SiO₂/PA, and M-SiO₂/PA), the gel containing M-SiO₂ showed the best performance.