Comparative Analysis of Protein Quantification Methods for the Rapid Determination of Protein Loading in Liposomal Formulations

An antibody fragment-decorated liposomal conjugate targets Philadelphia-like acute lymphoblastic leukemia

Philadelphia-like acute lymphoblastic leukemia (Ph-like ALL) is an aggressive B-ALL malignancy associated with high rates of relapse and inferior survival rate. While targeted treatments against the cell surface proteins CD22 or CD19 have been transformative in the treatment of refractory B-ALL, patients may relapse due to antigen loss, necessitating targeting alternative antigens. Cytokine receptor-like factor 2 (CRLF2) is overexpressed in half of Ph-like ALL cases conferring chemoresistance and enhancement of leukemia cell survival. Therefore, targeting CRLF2 may reduce the likelihood of relapse associated with antigen loss. We developed a CRLF2-targeting single-chain variable fragment modified by the fragment crystallizable region (CRLF2 scFv-Fc) conjugated to a drug maytansinoid 1 (DM1)-DOPC liposomal conjugate, creating homogeneous CRLF2-targeted liposomes (CRLF2-DM1 LIP). Cellular association and internalization studies in a Ph-like ALL cell line, MHH-CALL-4, compared to its lentivirally transduced CRLF2-knockdown counterpart (KD-CALL-4) revealed excellent CRLF2-targeting efficiency of CRLF2-DM1 LIP. Moreover, CRLF2-DM1 LIP showed selective association and internalization ex vivo using Ph-like ALL patient-derived xenograft (PDX) cells with minimal reactivity with non-target cells. Cell apoptosis assays demonstrated the CRLF2-dependent potency of CRLF2-DM1 LIP in Ph-like ALL cell lines. This study is the first to highlight the therapeutic potential of a CRLF2-directed scFv-Fc-liposomal conjugate for targeting Ph-like ALL.

Fluorescent molecular rotors as versatile in situ sensors for protein quantitation

Accurate protein quantitation is essential for many cellular mechanistic studies. Existing technology relies on extrinsic sample evaluation that requires significant volumes of sample as well as addition of assay-specific reagents and importantly, is a terminal analysis. This study exploits the unique chemical features of a fluorescent molecular rotor that fluctuates between twisted-to-untwisted states, with a subsequent intensity increase in fluorescence depending on environmental conditions (e.g., viscosity). Here we report the development of a rapid, sensitive in situ protein quantitation method using ARCAM-1, a representative fluorescent molecular rotor that can be employed in both non-terminal and terminal assays.

Development of a concise and reliable method for quantifying the antibody loaded onto lipid nanoparticles modified with Herceptin

Antibodies are essential components of the immune system with a wide range of molecular targets. They have been recognized as modalities for treating several diseases and more than 130 approved antibody-based therapeutics are available for clinical use. However, limitations remain associated with its efficacy, tissue permeability, and safety, especially in cancer treatment. Nanoparticles, particularly those responsive to external stimuli, have shown promise in improving the efficacy of antibody-based therapeutics and tissue-selective delivery. In this study, we developed a reliable and accurate method for quantifying the amount of antibody loaded onto lipid nanoparticles modified with Herceptin® (Trastuzumab), an antibody-based therapeutic used to treat HER2-positive cancers, using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by silver staining. This method proved to be a suitable alternative to commonly used protein quantification techniques, which are limited by lipid interference present in the samples. Furthermore, the amount of Herceptin modified on the liposomes, measured by this method, was confirmed by Herceptin's antibody-dependent cell-mediated cytotoxicity activity. Our results demonstrate the potential of this method as a critical tool for developing tissue-selective antibody delivery systems, leading to improved efficacy and reduced side effects of antibody-based therapeutics.

Development of tandem cation exchange chromatography for high purity extracellular vesicle isolation: The effect of ligand steric availability

Purification of extracellular vesicles for research and therapeutic applications requires updated methodology to address the limitations of traditional ultracentrifugation and other size-based separation techniques. Their downfalls include induced extracellular vesicle aggregation, low yields, poor scalability and one-dimensionality of the separation process, as the size or sedimentation speed of extracellular vesicles is often the only selection criterion. Ion exchange chromatography is a promising alternative or supplementary method candidate, as it offers a different approach for extracellular vesicle separation, which is surface charge. For now, mostly anion exchange chromatography has been evaluated for extracellular vesicle purification, as it successfully relies on the strongly negative surface charge of extracellular vesicles. However, as extracellular vesicles are very complex in their structure, also cation exchange chromatography could be applicable, due to individual cationic domains on the extracellular vesicle surface. Here, we compare anion exchange chromatography to different types of cation exchange chromatography for the purification of platelet extracellular vesicle samples also containing plasma-derived impurities. We found that the choice of resin structure used for cation exchange chromatography is critical for binding platelet extracellular vesicles, as a conventional-type cation exchanger was found to only capture and elute less than 20% of extracellular vesicles. With the tentacle-type resin, it was possible to obtain comparable platelet extracellular vesicle yields (over 90%) with cation exchange chromatography compared to anion exchange chromatography, as well as superior purity, especially when it was combined to conventional cation exchange resin.

Measuring Encapsulation Efficiency in Cell-Mimicking Giant Unilamellar Vesicles

One of the main drivers within the field of bottom-up synthetic biology is to develop artificial chemical machines, perhaps even living systems, that have programmable functionality. Numerous toolkits exist to generate giant unilamellar vesicle-based artificial cells. However, methods able to quantitatively measure their molecular constituents upon formation is an underdeveloped area. We report an artificial cell quality control (AC/QC) protocol using a microfluidic-based single-molecule approach, enabling the absolute quantification of encapsulated biomolecules. While the measured average encapsulation efficiency was 11.4 ± 6.8%, the AC/QC method allowed us to determine encapsulation efficiencies per vesicle, which varied significantly from 2.4 to 41%. We show that it is possible to achieve a desired concentration of biomolecule within each vesicle by commensurate compensation of its concentration in the seed emulsion. However, the variability in encapsulation efficiency suggests caution is necessary when using such vesicles as simplified biological models or standards.

Identification of transient receptor potential melastatin 3 proteotypic peptides employing an efficient membrane protein extraction method for natural killer cells

Introduction: Mutations and misfolding of membrane proteins are associated with various disorders, hence they make suitable targets in proteomic studies. However, extraction of membrane proteins is challenging due to their low abundance, stability, and susceptibility to protease degradation. Given the limitations in existing protocols for membrane protein extraction, the aim of this investigation was to develop a protocol for a high yield of membrane proteins for isolated Natural Killer (NK) cells. This will facilitate genetic analysis of membrane proteins known as transient receptor potential melastatin 3 (TRPM3) ion channels in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) research.

Methods: Two protocols, internally identified as Protocol 1 and 2, were adapted and optimized for high yield protein extraction. Protocol 1 utilized ultrasonic and salt precipitation, while Protocol 2 implemented a detergent and chloroform/methanol approach. Protein concentrations were determined by the Pierce Bicinchoninic Acid (BCA) and the Bio-Rad DC (detergent compatible) protein assays according to manufacturer’s recommendation. Using Protocol 2, protein samples were extracted from NK cells of n = 6 healthy controls (HC) and n = 4 ME/CFS patients. In silico tryptic digest and enhanced signature peptide (ESP) predictor were used to predict high-responding TRPM3 tryptic peptides. Trypsin in-gel digestion was performed on protein samples loaded on SDS-PAGE gels (excised at 150–200 kDa). A liquid chromatography-multiple reaction monitoring (LC-MRM) method was optimized and used to evaluate the detectability of TRPM3 n = 5 proteotypic peptides in extracted protein samples.

Results: The detergent-based protocol protein yield was significantly higher (p < 0.05) compared with the ultrasonic-based protocol. The Pierce BCA protein assay showed more reproducibility and compatibility compared to the Bio-Rad DC protein assay. Two high-responding tryptic peptides (GANASAPDQLSLALAWNR and QAILFPNEEPSWK) for TRPM3 were detectable in n = 10 extracted protein samples from NK cells isolated from HC and ME/CFS patients.

Conclusion: A method was optimized for high yield protein extraction from human NK cells and for the first time TRPM3 proteotypic peptides were detected using LC-MRM. This new method provides for future research to assess membrane protein structural and functional relationships, particularly to facilitate proteomic investigation of TRPM3 ion channel isoforms in NK cells in both health and disease states, such as ME/CFS.

Optimization of a Liposomal DNase I Formulation with an Extended Circulating Half-Life

Drug delivery systems such as liposomes are widely used to stabilize and increase the plasma half-life of therapeutics. In this article, we have investigated two strategies to increase the half-life of deoxyribonuclease I, an FDA-approved enzyme used for the treatment of cystic fibrosis, and a potential candidate for the reduction of uncontrolled inflammation induced by neutrophil extracellular traps. We demonstrate that our optimized preparation procedure resulted in nanoparticles with improved plasma half-life and total exposure relative to native protein, while maintaining enzymatic activity.

Rapid, high throughput protein estimation method for saponin and alhydrogel adjuvanted R21 VLP Malaria vaccine based on intrinsic fluorescence

Protein content estimation of recombinant vaccines at drug product (DP) stage is a crucial lot release and stability indicating assay in biopharmaceutical industries. Regulatory bodies such as US-FDA and WHO necessitates the quantitation of protein content to assess process parameters as well as formulation losses. Estimation of protein content at DP stage in presence of adjuvants (e.g AlOOH, AlPO₄, saponin and squalene) is quite challenging, and the challenge intensifies when the target protein is in Virus like particles (VLP) form, owing to its size and structural complexity. Methods available for protein estimation of adjuvanted vaccines mostly suffer from inaccuracy at lower protein concentrations and in most cases require antigen desorption before analysis. Present research work is based on the development of a rapid plate-based method for protein estimation through intrinsic fluorescence by using Malaria vaccine R21 VLP as a model protein. Present method exhibited linearity for protein estimation of R21, in the range of 5-30 µg/mL in Alhydrogel and 4-20 µg/mL for Matrix M adjuvant. The method was validated as per ICH guidelines. The limit of quantification was found to be 0.94 µg/mL for both Alhydrogel and Matrix M adjuvanted R21. The method was found specific, precise and repeatable. This method is superior in terms of less sample quantity requirement, multiple sample analysis, short turnaround time and is non-invasive. This method was found to be stability indicating, works for other proteins containing tryptophan residues and operates well even in presence of host cell proteins. Based on the study, present method can be used in vaccine industries for routine in-process sample analysis (both inline and offline), lot release of VLP based drug products in presence of Alhydrogel and saponin based adjuvant systems.

Sustained Release of a Streptococcus pneumoniae Endolysin from Liposomes for Potential Otitis Media Treatment

Local delivery of antimicrobials for otitis media treatment would maximize therapeutic efficacy while minimizing side effects. However, drug transport across the tympanic membrane in the absence of a delivery system is challenging. In this study, the MSlys endolysin was encapsulated in deformable liposomes for a targeted treatment of S. pneumoniae, one of the most important causative agents of otitis media. MSlys was successfully encapsulated in liposomes composed of l-alpha-lecithin and sodium cholate (5:1) or l-alpha-lecithin and PEG2000 PE (10:1), with encapsulation efficiencies of about 35%. The PEGylated and sodium cholate liposomes showed, respectively, mean hydrodynamic diameters of 85 and 115 nm and polydispersity indices of 0.32 and 0.42, both being stable after storage at 4 °C for at least one year. Both liposomal formulations showed a sustained release of MSlys over 7 days. Cytotoxicity studies against fibroblast and keratinocyte cell lines revealed the biocompatible nature of both MSlys and MSlys-loaded liposomes. Additionally, the encapsulated MSlys showed prompt antipneumococcal activity against planktonic and biofilm S. pneumoniae, thus holding great potential for transtympanic treatment against S. pneumoniae otitis media.

Accurate characterization of β-amyloid (Aβ40, Aβ42) standards using species-specific isotope dilution by means of HPLC-ICP-MS/MS

The amyloid β peptide, as one of the main components in senile plaque, represents a defining pathological feature for Alzheimer’s disease, and is therefore commonly used as a biomarker for this disease in clinical analysis. However, the selection of suitable standards is limited here, since only a few are commercially available, and these suffer from varying purity. Hence, the accurate characterization of these standards is of great importance. In this study, we developed a method for the traceable quantification of the peptide content using species-specific isotope dilution and ICP-MS/MS detection. It is based on the separation of the sulfur-containing amino acids methionine and cysteine after oxidation and hydrolysis of the peptide. Using a strong anion exchange column, both amino acids could be separated from each other, as well as from their oxidized forms and sulfate. The sulfur content was determined via ICP-MS/MS using oxygen as reaction gas. Species-specific isotope dilution was enabled by using a ³⁴S-labeled yeast hydrolysate, containing methionine sulfone and cysteic acid with different isotopic composition. The peptide contents of Aβ standards (Aβ40,42), as well as myoglobin and lysozyme with different degrees of purity, were determined. For validation purposes, the standard reference material NIST 2389a, which contains the amino acids in a similar concentration, was subjected to the developed sample preparation and analysis method. In addition to accounting for errors during sample preparation, high levels of accuracy and precision could be obtained using this method, making it fit-for-purpose for the characterization of peptide standards.

Edge-Enhanced Microwell Immunoassay for Highly Sensitive Protein Detection

Highly sensitive biosensors that can detect low concentrations of protein biomarkers at the early stages of diseases or proteins secreted from single cells are of importance for disease diagnosis and treatment assessment. This work reports a new signal amplification mechanism, that is, edge enhancement based on the vertical sidewalls of microwells for ultra-sensitive protein detection. The fluorescence emission at the edge of the microwells is highly amplified due to the microscopic axial resolution (depth of field) and demonstrates a microring effect. The enhanced fluorescence intensity from microrings is calibrated for bovine serum albumin detection, which shows a 6-fold sensitivity enhancement and a lower limit of detection at the microwell edge, compared to those obtained on a flat surface. The microwell chip is used to separate single cells, and the wall of each microwell is used to detect interferon-γ secretion from T cells stimulated with a peptide and whole cancer cells. Given its edge-enhancement ability, the microwell technique can be a highly sensitive biosensing platform for disease diagnosis at an early stage and for assessing potential treatments at the single-cell level.

Simultaneous quantification of total carbohydrate and protein amounts from aqueous solutions by the sulfuric acid ultraviolet absorption method (SA-UV method)

Based on the sulfuric acid-ultraviolet assay (SA-UV, developed by Albalasmeh et al., 2013), we have further expanded this method for the simultaneous quantification of saccharides (carbohydrates) and proteins by ultraviolet spectrophotometry. The absorbance of saccharides depends on the formation of furfurals by dehydration in the presence of concentrated sulfuric acid, whereas proteins are unaffected and can be quantified by UV active peptide bonds and aromatic amino acid residues. In saccharide/protein mixtures the SA-UV assay offers a good alternative and substitutes the need for two different methods, like the phenol-sulfuric acid (PSA, developed by DuBois et al., 1951) and bicinchoninic acid (BCA, developed by Smith et al., 1985) assays. For the development of this method, we used glucose and BSA as model substrates and performed a method validation in terms of linearity, LOD, LOQ, accuracy, and precision. Simultaneous quantification in glucose/BSA mixtures is possible down to 20 mg/L from 30 μL sample volumes, and even low content mixtures with concentrations down to 2 mg/L can appropriately be quantified from higher volumes by an evaporation technique.

Advances in monitoring and control of refolding kinetics combining PAT and modeling

Overexpression of recombinant proteins in Escherichia coli results in misfolded and non-active protein aggregates in the cytoplasm, so-called inclusion bodies (IB). In recent years, a change in the mindset regarding IBs could be observed: IBs are no longer considered an unwanted waste product, but a valid alternative to produce a product with high yield, purity, and stability in short process times. However, solubilization of IBs and subsequent refolding is necessary to obtain a correctly folded and active product. This protein refolding process is a crucial downstream unit operation-commonly done as a dilution in batch or fed-batch mode. Drawbacks of the state-of-the-art include the following: the large volume of buffers and capacities of refolding tanks, issues with uniform mixing, challenging analytics at low protein concentrations, reaction kinetics in non-usable aggregates, and generally low re-folding yields. There is no generic platform procedure available and a lack of robust control strategies. The introduction of Quality by Design (QbD) is the method-of-choice to provide a controlled and reproducible refolding environment. However, reliable online monitoring techniques to describe the refolding kinetics in real-time are scarce. In our view, only monitoring and control of re-folding kinetics can ensure a productive, scalable, and versatile platform technology for re-folding processes. For this review, we screened the current literature for a combination of online process analytical technology (PAT) and modeling techniques to ensure a controlled refolding process. Based on our research, we propose an integrated approach based on the idea that all aspects that cannot be monitored directly are estimated via digital twins and used in real-time for process control. KEY POINTS: • Monitoring and a thorough understanding of refolding kinetics are essential for model-based control of refolding processes. • The introduction of Quality by Design combining Process Analytical Technology and modeling ensures a robust platform for inclusion body refolding.

Microfluidic production of protein loaded chimeric stealth liposomes

The addition of polyethylene glycol (PEG) on the surface of liposomes increases their circulation time when administered intravenously. However, the inclusion of PEG using PEGylated phospholipids could result in a possible micelles formation. The development of chimeric systems mixing synthetic biocompatible and biodegradable PEG-containing copolymers with lipids is a strategy to obtain as well PEGylated liposomes. Microfluidics is an innovative manufacturing technology easy to scale up that presents high reproducibility, low batch-to-batch variation, and better control over particles characteristics. Taking advantage of this technique, in this research work, chimeric stealth liposomes were produced mixing five different synthesized methoxy-poly(ethylene glycol)-block-poly(δ-decalactone) (mPEG-PDL, varying in polymer length) with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and cholesterol. The obtained chimeric formulations were around 150 nm in size with a narrow distribution and an almost neutral surface charge. Ovalbumin (OVA) was used as a model protein to evaluate the loading potential reaching an encapsulation efficiency of 41 ± 4%. The prepared systems showed no cytotoxicity in vitro on THP-1 cell with an uptake up to 89 ± 4% after 3 h. Finally, protein integrity after encapsulation was confirmed with DQ-OVA. In this work, we demonstrated that using microfluidics, it is possible to produce stable and highly protein-loaded chimeric stealth liposomes with good physicochemical characteristics, no toxicity, protein integrity, and effective uptake by endocytosis.

Nanosized Delivery Systems for Therapeutic Proteins: Clinically Validated Technologies and Advanced Development Strategies

The impact of protein therapeutics in healthcare is steadily increasing, due to advancements in the field of biotechnology and a deeper understanding of several pathologies. However, their safety and efficacy are often limited by instability, short half-life and immunogenicity. Nanodelivery systems are currently being investigated for overcoming these limitations and include covalent attachment of biocompatible polymers (PEG and other synthetic or naturally derived macromolecules) as well as protein nanoencapsulation in colloidal systems (liposomes and other lipid or polymeric nanocarriers). Such strategies have the potential to develop next-generation protein therapeutics. Herein, we review recent research progresses on these nanodelivery approaches, as well as future directions and challenges.

The Impact of Solvent Selection: Strategies to Guide the Manufacturing of Liposomes Using Microfluidics

The aim of this work was to assess the impact of solvent selection on the microfluidic production of liposomes. To achieve this, liposomes were manufactured using small-scale and bench-scale microfluidics systems using three aqueous miscible solvents (methanol, ethanol or isopropanol, alone or in combination). Liposomes composed of different lipid compositions were manufactured using these different solvents and characterised to investigate the influence of solvents on liposome attributes. Our studies demonstrate that solvent selection is a key consideration during the microfluidics manufacturing process, not only when considering lipid solubility but also with regard to the resultant liposome critical quality attributes. In general, reducing the polarity of the solvent (from methanol to isopropanol) increased the liposome particle size without impacting liposome short-term stability or release characteristics. Furthermore, solvent combinations such as methanol/isopropanol mixtures can be used to modify solvent polarity and the resultant liposome particle size. However, the impact of solvent choice on the liposome product is also influenced by the liposome formulation; liposomes containing charged lipids tended to show more sensitivity to solvent selection and formulations containing increased concentrations of cholesterol or pegylated-lipids were less influenced by the choice of solvent. Indeed, incorporation of 14 wt% or more of pegylated-lipid was shown to negate the impact of solvent selection.

Electrostatically Driven Encapsulation of Hydrophilic, Non-Conformational Peptide Epitopes into Liposomes

Since the first use of liposomes as carriers for antigens, much work has been done to elucidate the mechanisms involved in the encapsulation of vaccine-relevant biomolecules. However, only a few studies have specifically investigated the encapsulation of hydrophilic, non-conformational peptide epitopes. We performed comprehensive and systematic screening studies, in order to identify conditions that favor the electrostatic interaction of such peptides with lipid membranes. Moreover, we have explored bi-terminal sequence extension as an approach to modify the isoelectric point of peptides, in order to modulate their membrane binding behavior and eventually shift/expand the working range under which they can be efficiently encapsulated in an electrostatically driven manner. The findings of our membrane interaction studies were then applied to preparing peptide-loaded liposomes. Our results show that the magnitude of membrane binding observed in our exploratory in situ setup translates to corresponding levels of encapsulation efficiency in both of the two most commonly employed methods for the preparation of liposomes, i.e., thin-film hydration and microfluidic mixing. We believe that the methods and findings described in the present studies will be of use to a wide audience and can be applied to address the ongoing relevant issue of the efficient encapsulation of hydrophilic biomolecules.