Augmented Placental Protein 13 in Placental-Associated Extracellular Vesicles in Term and Preterm Preeclampsia Is Further Elevated by Corticosteroids

Placental protein 13 (PP13) is a regulatory protein involved in remodeling the vascular system of the pregnancy and extending the immune tolerance of the mother to the growing fetus. PP13 is localized on the surface of the syncytiotrophoblast. An ex vivo placental model shows that the PP13 is released via placental-associated extracellular vesicles (PEVs) to the maternal uterine vein. This exploratory study aimed to determine PEV-associated PP13 in the maternal circulation as compared to the known soluble fraction since each has a specific communication pathway. Patients admitted to Bnai Zion Medical Center for delivery were recruited, and included 19 preeclampsia (PE) patients (7 preterm PE gestational age < 37 weeks' gestation), 16 preterm delivery (PTD, delivery at GA < 37 weeks' gestation), and 15 matched term delivery controls. Treatment by corticosteroids (Celestone), which is often given to patients with suspected preterm PE and PTD, was recorded. The PEV proteome was purified from the patients' plasma by size exclusion chromatography (SEC) to separate the soluble and PEV-associated PP13. The total level of PP13 (soluble and PEV-associated) was determined using mild detergent that depleted the PEV proteome. PP13 fractions were determined by ELISA with PP13 specific antibodies. ELISA with alkaline phosphatase (PLAP)- and cluster differentiation 63 (CD63)-specific antibodies served to verify the placental origin of the PEVs. SPSS was used for statistical analysis. The patients' medical, pregnancy, and delivery records in all groups were similar except, as expected, that a larger number of PE and PTD patients had smaller babies who were delivered earlier, and the PE patients had hypertension and proteinuria. The SEC analysis detected the presence of PP13 in the cargo of the PEVs and on their surface, in addition to the known soluble fraction. The median soluble PP13 was not significantly different across the PE, PTD, and term delivery control groups. However, after depleting the PEV of their proteome, the total PP13 (soluble and PEV-associated) was augmented in the cases of preterm PE, reaching 2153 pg/mL [IQR 1866-2838] but not in cases of PTD reaching 1576 pg/mL [1011-2014] or term delivery groups reaching 964 pg/mL [875-1636]), p < 0.01. On the surface of the circulating PEV from PTD patients, there was a decrease in PP13. Corticosteroid treatment was accompanied by a massive depletion of PP13 from the PEV, especially in preterm PE patients. This exploratory study is, thus, the first to determine PEV-associated PP13 in maternal circulation, providing a quantitative determination of the soluble and the PEV-associated fractions, and it shows that the latter is the larger. We found an increase in the amount of PP13 carried via the PEV-associated pathway in PE and PTD patients compared to term delivery cases, which was further augmented when the patients were treated with corticosteroids, especially in preterm PE. The signal conveyed by this novel communication pathway warrants further research to investigate these two differential pathways for the liberation of PP13.

A Combination of Native LC-MS Approaches for the Comprehensive Characterization of the Antibody-Drug Conjugate Trastuzumab Deruxtecan

BACKGROUND

Native mass spectrometry (nMS) approaches appear attractive to complement bottom-up strategies traditionally used in biopharmaceutical industries thanks to their quite straightforward and rapid workflows, especially through online hyphenation of non-denaturing liquid chromatography (LC) to nMS. The present work provides an overview of the state-of-the-art chromatographic tools available for the detailed characterization of monoclonal antibody (mAb) formats, exemplified on the antibody-drug conjugate (ADC) trastuzumab deruxtecan (T-DXd).

METHODS

T-DXd was first characterized by conventional reversed phase LC (rpLC) and peptide mapping. Couplings of size exclusion chromatography (SEC), cation exchange chromatography (CEX), and hydrophobic interaction chromatography (HIC) to nMS were used to gain further insights into size, hydrophobic, and charge variants of T-DXd and its parental mAb trastuzumab, at intact and middle-up levels.

RESULTS

SEC-nMS first offered a direct snapshot of the homogeneous conjugation of T-DXd, with an average drug-to-antibody ratio (DAR) of 8 in agreement with a conjugation on cysteines after reduction of all interchain disulfide bonds. Moreover, SEC-nMS afforded precise identification and quantification of aggregates and fragments. Middle-up level experiments performed after IdeS digestion confirmed that drug conjugation occurs in the Fab region of the mAb, as seen with rpLC. HIC separated two DAR8 species that could not be differentiated by nMS. Although middle-up HIC-nMS proved to be more informative for oxidized forms, the identification of minor variants was still difficult because of poor MS signal quality, showing how the coupling of HIC to nMS remains challenging. Lastly, middle-up CEX-nMS provided accurate determination and localization of post-translational modifications, with several acidic/basic variants within Fab and Fc regions of T-DXd that were also identified by peptide mapping.

CONCLUSIONS

This study illustrates the strengths and drawbacks of each LC-nMS coupling. By combining SEC-, HIC-, and CEX-nMS, we were able to achieve a comprehensive characterization of T-DXd without extensive sample preparation prior to MS analysis.

The Past, the Present, and the Future of the Size Exclusion Chromatography in Extracellular Vesicles Separation

Extracellular vesicles (EVs) are cell-derived membranous particles secreted by all cell types (including virus infected and uninfected cells) into the extracellular milieu. EVs carry, protect, and transport a wide array of bioactive cargoes to recipient/target cells. EVs regulate physiological and pathophysiological processes in recipient cells and are important in therapeutics/drug delivery. Despite these great attributes of EVs, an efficient protocol for EV separation from biofluids is lacking. Numerous techniques have been adapted for the separation of EVs with size exclusion chromatography (SEC)-based methods being the most promising. Here, we review the SEC protocols used for EV separation, and discuss opportunities for significant improvements, such as the development of novel particle purification liquid chromatography (PPLC) system capable of tandem purification and characterization of biological and synthetic particles with near-single vesicle resolution. Finally, we identify future perspectives and current issues to make PPLC a tool capable of providing a unified, automated, adaptable, yet simple and affordable particle separation resource.

[Applications of separation technology in novel coronavirus research, epidemic prevention and detection]

新型冠状病毒肺炎(COVID-19)疫情的爆发给世界公共卫生安全带来前所未有的挑战。随着新型冠状病毒(SARS-CoV-2)相关研究的不断深入,众多分析检测技术相继被应用,推动了病毒检测、疫苗和创新疗法的研发,从而使疫情早日得到控制。分离技术作为生命科学、医学、药学领域的关键技术,操作简单,分离效率高,选择性强,在新型冠状病毒的分离、检测、诊疗及防疫中起到不可替代的作用。该文以SARS-CoV-2或COVID-19为关键词在ISI Web of Science中进行主题检索,归纳了2020年度新型冠状病毒相关的研究论文,简要介绍主要的研究方向,并对国际顶级学术期刊Nature, Science, Cell的论文发表情况进行了统计。通过检索影响因子较高的期刊,综述了新型冠状病毒研究中主要应用的分离技术,并从亲和色谱和尺寸排阻色谱、液相色谱、磁珠分离、离心、微纳分离以及电泳6个方面进行说明。综述统计了亲和色谱和尺寸排阻色谱纯化的病毒相关蛋白,并介绍了其在新型冠状病毒传播、感染机制以及药物筛选中的应用;介绍了液相色谱对病毒候选药物评估以及复杂基质中单一成分的鉴定;介绍了磁珠分离在细胞分离、核酸提取和免疫学检测中的应用;介绍了离心对病毒颗粒、细胞以及血清的分离;介绍了微纳分离结合其他技术以实现病毒蛋白的高灵敏检测;简要介绍了电泳在聚合酶链式反应(PCR)产物分析中的应用。该文综述了2020年度新型冠状病毒研究和防疫检测中分离技术的应用情况,分析了分离技术在新型冠状病毒检测中发挥的作用,旨在为从事分离研究的科研工作者提供一些参考。

[Quantitative analysis of nine types of virus-like particles in human papilloma virus bulk by size-exclusion chromatography]

据统计,5%以上的人类癌症由人乳头瘤病毒(HPV)导致。HPV疫苗的使用,尤其是多价HPV疫苗的使用,可有效预防HPV感染和肿瘤的发生。例如,9价HPV疫苗可有效预防90%以上HPV相关癌前病变。人乳头瘤病毒样颗粒(VLP)是HPV疫苗的唯一抗原。VLP由360份衣壳蛋白L1组成。VLP的含量测定对HPV原液和HPV疫苗的质量评价至关重要。该文发展了一种以体积排阻色谱(SEC)为基础的9种型别人乳头病毒样颗粒的定量方法。实验优化了包括色谱柱类型、色谱柱孔径、流动相离子强度和流动相pH值在内的色谱条件。经过考察,以SHIMSEN Ankylo SEC-300色谱柱(300 mm×7.8 mm, 3 μm)为固定相,以含有300 mmol/L NaCl和50 mmol/L磷酸盐(pH 7.0)的缓冲溶液为流动相时,VLP的色谱峰更窄,从而可获得更高的响应和更好的灵敏度,因此选择该色谱条件用于VLP与基质的分离。优化所得的方法具有较宽的线性范围,良好的重复性(峰面积的相对标准偏差不大于5.0%)和灵敏度(定量限为4.58~15.24 μg/mL)。将方法用于HPV原液中VLP的含量测定,监测VLP的稳定性。结果显示,HPV原液中VLP颗粒不稳定,于4 ℃放置一周后,VLP含量与生产后立即测得的含量相比存在一定程度的降解。此外,方法还可用于疫苗上清液中游离蛋白质的分析,监测铝佐剂对VLP的吸附情况。被测厂家的铝佐剂可较好的吸附VLP,无明显残余蛋白质检出。与传统的蛋白质定量方法相比,如Folin-酚法(Lowry法),该法具有操作简单、自动化程度高、分析通量高等优点,可实现VLP含量的批量化分析。

[Size exclusion-reverse liquid column chromatography-mass spectrometry and its application in the identification of post-translationally modified proteins in rat kidney]

Proteomics is an emerging field that has been shown to play a crucial role in unveiling the mechanisms underlying physiological and pathological processes, and liquid chromatography-mass spectrometry (LC-MS) is one of the most important methods employed in this field. However, in complex biological systems, such as eukaryotes, it is challenging to perform a comprehensive and unbiased proteome analysis due to the high complexity of biological samples and enormous differences in sample contents. For example, post-translational modifications (PTMs) in proteins are imperative for cell signaling, but post-translationally modified proteins account for about 1% of the total proteins in a single cell, making their identification extremely difficult. Therefore, chromatographic separation methods based on different principles are generally applied to reduce the complexity of biological samples and enrich trace proteins for their identification through mass spectrometry (MS). In this study, we developed a new proteomics method by combining size exclusion chromatography (SEC) and reversed-phase chromatography (RPLC), to separate and identify trace proteins in complex systems. SEC was used to separate and enrich kidney-specific proteins. After optimization of the method, it was found that 30 mmol/L of ammonium acetate could efficiently separate rat kidney proteins from the total protein fraction so that they could be eluted based on their relative molecular mass. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis and LC-MS results showed that our SEC separation method not only refined the protein composition of the biological sample but also enhanced the relative contents of trace proteins through multiple injections. The collected protein fractions were further concentrated through ultrafiltration centrifugation followed by freeze-drying, which further improved the recovery of trace proteins by approximately 90% and largely decreased the time required with the use of freeze-drying alone. Thereafter, five protein fractions were separately digested using trypsin, and the resultant peptides were further analyzed by reverse phase chromatography-MS analysis. In the RPLC column, the peptides were isolated mainly based on their hydrophobicity. As a result, by combining SEC and RPLC, 23621 peptides and 1345 proteins were identified from the kidney, with an increase in numbers by 69% and 27%, respectively, when compared to those obtained using the common 2D strong cation exchange (SCX)-RPLC-MS method. However, no significant difference was observed in the pI and grand average of hydropathicity (GRAVY) values. Gene ontology (GO) analysis revealed an increase in the number of proteins in each cell component, especially the membrane. Furthermore, identification of a higher rate of identified peptides than proteins suggested that the protein coverage was also improved, thereby facilitating the detection of PTM proteins. Consequently, five common PTMs in biological processes, including methylation, acetylation, carbamylation, oxidation, and phosphorylation, were examined and compared between the two methods. As expected, the number of post-translationally modified peptides identified using SEC-RPLC-MS were 1.7-1.9 times more than those determined using the SCX-RPLC-MS method. Especially for the identification of phosphorylated peptides, we could achieve the level of the targeted enrichment strategy; however no significant difference was observed in the extents of phosphorylation among serine, threonine, and tyrosine. These results further indicate that upon combining SEC and RPLC, high efficiency could be achieved by decreasing the complexity of the protein sample, and the identification was unbiased. Finally, the phosphorylation of some kidney proteins, such as spectrin, L-lactate dehydrogenase, and ATPases, was found, which is critical for their functions. In summary, the SEC-RPLC-MS approach was developed for the identification of rat kidney proteins and is especially applicable for the identification of PTM proteins. Using this method, the identification efficiency for PTM peptides increased significantly. Therefore, this method has potential for better understanding the impact of PTM on kidney proteins and further elucidating the potential mechanisms underlying its physiological and pathological functions.

Probing Membrane Protein Assembly into Nanodiscs by In Situ Dynamic Light Scattering: A2A Receptor as a Case Study

Simple Summary

Located within the biological cell membranes, integral membrane proteins are responsible for a large variety of vital cellular processes. In humans, nearly a quarter of the genome codes integral membrane proteins, therefore malfunction of these proteins is associated with a variety of symptoms and diseases such as obesity, cancer and Parkinson’s disease. Clearly, knowledge of membrane proteins behaviour, in both structural and functional terms, is important not only in medicine but also in the design of better drugs with improved pharmaceutical properties. Nevertheless, much still remains unknown about these proteins, mainly because of the technical challenges associated with their production and stability in vitro once removed from their native lipidic environment. Recently, several membrane mimetic systems have been developed including nanodisc lipid particles. Nanodiscs are self-assembled lipidic structures that “trap” membrane proteins into a disc shaped phospholipid bilayer that is stabilised by a belt made of a protein know as membrane scaffold protein (MSP). Membrane proteins assembled into lipidic nanodiscs can maintain their structural and functional integrity and are compatible with most biophysical methods. Here we demonstrate the use of in situ dynamic light scattering as a high-throughput screening tool to assess the best conditions for nanodisc assembly and protein incorporation.

Abstract

Membrane proteins play a crucial role in cell physiology by participating in a variety of essential processes such as transport, signal transduction and cell communication. Hence, understanding their structure–function relationship is vital for the improvement of therapeutic treatments. Over the last decade, based on the development of detergents, amphipoles and styrene maleic-acid lipid particles (SMALPs), remarkable accomplishments have been made in the field of membrane protein structural biology. Nevertheless, there are still many drawbacks associated with protein–detergent complexes, depending on the protein in study or experimental application. Recently, newly developed membrane mimetic systems have become very popular for allowing a structural and functional characterisation of membrane proteins in vitro. The nanodisc technology is one such valuable tool, which provides a more native-like membrane environment than detergent micelles or liposomes. In addition, it is also compatible with many biophysical and biochemical methods. Here we describe the use of in situ dynamic light scattering to accurately and rapidly probe membrane proteins’ reconstitution into nanodiscs. The adenosine type 2A receptor (A_2AR) was used as a case study.

Emulsifiers from Partially Composted Olive Waste

Partial (one month) composting of solid olive processing waste is shown to produce extractable emulsifiers. Size exclusion chromatography (SEC) and Fourier-transform infra-red spectroscopy (FTIR) show that these consist of polysaccharides and proteins from the composted waste. Aqueous extraction at pH 5, pH 7, and pH 9 all yield extracts rich in oligosacchrides and oligopeptides which derive from the break-down of the macromolecules under composting, with the extract obtained at pH 5 being the richer in such components. Fourier-transform infra-red (FTIR) spectroscopy also confirms that these materials consist of proteinic and poly/oligosaccharidic populations. These materials can emulsify stable oil-in-water emulsions at pH 3 for a few days, while the same emulsions collapse in less than 24 h at pH 7. Confocal microscopy and droplet size distribution data suggest that Ostwald ripening, rather than coalescence, is the major course of emulsion instability. The above point to a short-process alternative to full composting in producing a high added value product from solid olive processing waste.

[Control of Coagulant Dosing for Humic Substances Based on Ultraviolet Spectrum Analysis]

Humic substance (HS) is a main component of dissolved organic matter in the aquatic environment and significantly affects water treatment processes. To investigate the applicability and principle of UV spectrum analysis for coagulation control, laboratory jar tests were conducted with synthetic waters that had varying concentrations of HS and kaolinite. Thus, the influence of water quality conditions on the optimal coagulant dose (OCD) was determined and further correlated to Specific Ultraviolet Absorbance (SUVA₂₅₄) and the ultraviolet spectral slopes of the coagulated water. Subsequently, the relationship between the UV spectral slopes and organic fractionation was further identified by using size exclusion chromatography (SEC). The results showed that the coagulant demands of the synthetic waters were positively related to dissolved organic carbon (DOC). Consequently, a stoichiometric relationship (0.61 mg·mg^-1 calculated as Al/DOC) was found between the coagulant demand and initial DOC of the synthetic water. As the coagulant dose increased, SUVA₂₅₄ decreased from 8.9 L·(mg·m)^-1 to a steady level of 2.0 L·(mg·m)^-1 and the removal efficiency of DOC was positively correlated with SUVA₂₅₄. Spectral slopes in different wavelength ranges had showed similar tendencies, with S_275-295 having the best correlation with SUVA₂₅₄ (R²=0.81). Furthermore, SEC results demonstrated that coagulation preferentially removed humic substances, leading to reduced humification. As a result, S_275-295 had the highest correlation with the portion of UVA₂₅₄ contributed by humic substances in water. Therefore, online measurement of ultraviolet spectral slopes was an important aspect in the control of coagulant dosing.

Efficient analysis of mammalian polysomes in cells and tissues using Ribo Mega-SEC

We describe Ribo Mega-SEC, a powerful approach for the separation and biochemical analysis of mammalian polysomes and ribosomal subunits using Size Exclusion Chromatography and uHPLC. Using extracts from either cells, or tissues, polysomes can be separated within 15 min from sample injection to fraction collection. Ribo Mega-SEC shows translating ribosomes exist predominantly in polysome complexes in human cell lines and mouse liver tissue. Changes in polysomes are easily quantified between treatments, such as the cellular response to amino acid starvation. Ribo Mega-SEC is shown to provide an efficient, convenient and highly reproducible method for studying functional translation complexes. We show that Ribo Mega-SEC is readily combined with high-throughput MS-based proteomics to characterize proteins associated with polysomes and ribosomal subunits. It also facilitates isolation of complexes for electron microscopy and structural studies.

SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics

We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.

Using an FPLC to promote active learning of the principles of protein structure and purification

The concepts of protein purification are often taught in undergraduate biology and biochemistry lectures and reinforced during laboratory exercises; however, very few reported activities allow students to directly gain experience using modern protein purification instruments, such as Fast Protein Liquid Chromatography (FPLC). This laboratory exercise uses size exclusion chromatography (SEC) and ion exchange (IEX) chromatography to separate a mixture of four different proteins. Students use an SEC chromatogram and corresponding SDS-PAGE gel to understand how protein conformations change under different conditions (i.e. native and non-native). Students explore strategies to separate co-eluting proteins by IEX chromatography. Using either cation or anion exchange, one protein is bound to the column while the other is collected in the flow-through. In this exercise, undergraduate students gain hands-on experience with experimental design, buffer and sample preparation, and implementation of instrumentation that is commonly used by experienced researchers while learning and applying the fundamental concepts of protein structure, protein purification, and SDS-PAGE. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):60-68, 2017.