Peripheral Blood CD8+ T-Lymphocyte Immune Response in Benign and Subpopulations of Breast Cancer Patients.

Peripheral blood CD8+ T lymphocytes play a crucial role in cell-mediated immunity and tumor-related immune responses in breast cancer. In this study, label-free quantification analysis and gene set enrichment analysis (GSEA) of CD8+ T lymphocytes in the peripheral blood of benign patients and patients with different breast cancer (BC) subtypes, i.e., luminal A, luminal B, and triple-negative breast cancer (TNBC), were performed using nano-UHPLC and Orbitrap mass spectrometry. Differential protein expression in CD8+ T lymphocytes revealed significant downregulation (log2 FC ≥ 0.38 or ≤-0.38, adj. p < 0.05), particularly in proteins involved in cytotoxicity, cytolysis, and proteolysis, such as granzymes (GZMs) and perforin 1 (PRF1). This downregulation was observed in the benign group (GZMH, GZMM, and PRF1) and luminal B (GZMA, GZMH) subtypes, whereas granzyme K (GZMK) was upregulated in TNBC in comparison to healthy controls. The RNA degradation pathway was significantly downregulated (p < 0.05, normalized enrichment score (NES) from -1.47 to -1.80) across all BC subtypes, suggesting a potential mechanism for regulating gene expression during T cell activation. Also, the Sm-like proteins (LSM2, LSM3, and LSM5) were significantly downregulated in the RNA degradation pathway. Proteomic analysis of CD8+ T lymphocytes in peripheral blood across different breast cancer subtypes provides a comprehensive view of the molecular mechanisms of the systemic immune response that can significantly contribute to advancements in the diagnosis, treatment, and prognosis of this disease.

Human peripheral blood mononuclear cells as a valuable source of disease-related biomarkers: Evidence from comparative proteomics studies.

PURPOSE: The discovery of specific and sensitive disease-associated biomarkers for early diagnostic purposes of many diseases is still highly challenging due to various complex molecular mechanisms triggered, high variability of disease-related interactions, and an overlap of manifestations among diseases. Human peripheral blood mononuclear cells (PBMCs) contain protein signatures corresponding to essential immunological interplay. Certain diseases stimulate PBMCs and contribute towards modulation of their proteome which can be effectively identified and evaluated via the comparative proteomics approach. EXPERIMENTAL DESIGN: In this review, we made a detailed survey of the PBMCS-derived protein biomarker candidates for a variety of diseases, published in the last 15 years. Articles were preselected to include only comparative proteomics studies. RESULTS: PBMC-derived biomarkers were investigated for cancer, glomerular, neurodegenerative/neurodevelopmental, psychiatric, chronic inflammatory, autoimmune, endocrinal, infectious, and other diseases. A detailed review of these studies encompassed the proteomics platforms, proposed candidate biomarkers, their immune cell type specificity, and potential clinical application. CONCLUSIONS: Overall, PBMCs have shown a solid potential in giving early diagnostic and prognostic biomarkers for many diseases. The future of PBMC biomarker research should reveal its full potential through well-designed comparative studies and extensive testing of the most promising protein biomarkers identified so far.

Liquid-Phase Microextraction Approaches for Preconcentration and Analysis of Chiral Compounds: A Review on Current Advances.

Chirality is a critical issue in pharmaceutics, forensic chemistry, therapeutic drug monitoring, doping control, toxicology, or environmental investigations as enantiomers of a chiral compound can exhibit different activities, i.e., one enantiomer can have the desired effect while the other one can be inactive or even toxic. To monitor enantioselective metabolism or toxicokinetic/toxicodynamic mechanisms in extremely low content in biological or environmental matrices, sample preparation is vital. The present review describes current status of development of liquid-phase microextraction approaches such as hollow fiber liquid-phase microextraction (HF-LPME), electromembrane extraction (EME), dispersive liquid-liquid microextraction (DLLME), and supramolecular solvent-based microextraction (SSME), used for sample preparation of enantiomers/chiral compounds. The advantages and limitations of the above techniques are discussed. Attention is also focused on chiral separation approaches commonly applied to study the stereo-selective metabolism or toxicokinetic/toxicodynamic mechanisms of enantiomers in the biological and environmental samples.

Human peripheral blood mononuclear cells: A review of recent proteomic applications.

Human peripheral blood mononuclear cells (PBMCs) represent a sentinel blood sample which reacts to different pathophysiological stimuli in the form of immunological responses/immunophenotypic changes. The study of molecular content of PBMCs can provide better understanding of immune processes giving the possibility of monitoring the health conditions of the host organism. Proteomic analysis of PBMCs can achieve mentioned goal as important immune-related biomarkers are easily accessible for analysis. PBMCs have been gaining attention in different research areas including preclinical or clinical investigations. In this review, recent applications of proteomic analysis of PBMCs are described and discussed. Approaches are divided based on different proteomic workflows such as in-gel, in-solution and on-filter modes. The effect of various diseases such as autoimmune, cancer, neurodegenerative, viral, metabolic, and various immune stimulations such as radiation, vaccine, corticosteroids over PBMCs proteome, are described with emphasis on promising protein biomarker candidates.

A low-voltage electro-membrane extraction for quantification of imatinib and sunitinib in biological fluids.

Aim: Hollow-fiber-based supported liquid membrane was modified utilizing nanostructures such as graphite, graphene oxide or nitrogen-doped graphene oxide, for electro-membrane extraction (EME) of imatinib and sunitinib from biological fluids. By applying these conductive nanostructures, a low-voltage EME device (6.0 V) was fabricated. Materials & methods: A response surface methodology through central composite design was used to evaluate and optimize effects of various essential factors that influence on normalized recovery. Results: Optimal extraction conditions were set as, 1-octanol with 0.01 % (w/v) graphene oxide functioning as the supported liquid membrane, an extraction time of 17.0 min, pH of the acceptor and the donor phase of 2.8 and 7.9, respectively. Conclusion: The method was successfully applied to quantify imatinib and sunitinib in biological fluids.

Automation of single-cell proteomic sample preparation.

Molecular heterogeneity exists at different spatial scales in biological samples and is an important parameter in the development of pathologies and resistances to therapies. When aiming to reach molecular heterogeneity of cells at extremely low spatial scales, single-cell analysis can be the ultimate choice. Proteomics performed in bulk population of cells (macroproteomics) is prone to mask molecular heterogeneity. Mass spectrometry-based single cell proteomics (SCP-MS) is the right solution to overcome this issue. Three main problems can be identified using SCP-MS: (i) analytical loss during sample preparation, (ii) inefficient microinjection/delivery of proteins/peptides from samples to MS and (iii) low analytical throughput. Technologies for automation of SCP have recently gained attention to improve methods accuracy, sensitivity, throughput and in-depth and low-biased proteome analysis. In this minireview, we therefore overview the state-of-the-art of automation of SCP-MS sample preparation approaches.

Microproteomic sample preparation.

Multiple applications of proteomics in life and health science, pathology and pharmacology, require handling size-limited cell and tissue samples. During proteomic sample preparation, analyte loss in these samples arises when standard procedures are used. Thus, specific considerations have to be taken into account for processing, that are summarised under the term microproteomics (µPs). Microproteomic workflows include: sampling (e.g., flow cytometry, laser capture microdissection), sample preparation (possible disruption of cells or tissue pieces via lysis, protein extraction, digestion in bottom-up approaches, and sample clean-up) and analysis (chromatographic or electrophoretic separation, mass spectrometric measurements and statistical/bioinformatic evaluation). All these steps must be optimised to reach wide protein dynamic ranges and high numbers of identifications. Under optimal conditions, sampling is adapted to the studied sample types and nature, sample preparation isolates and enriches the whole protein content, clean-up removes salts and other interferences such as detergents or chaotropes, and analysis identifies as many analytes as the instrumental throughput and sensitivity allow. In the suggested review, we present and discuss the current state in µP applications for processing of small number of cells (cell µPs) and microscopic tissue regions (tissue µPs).

Two-phase agarose gel-electromembrane extraction: Effect of organic solvent as an acceptor phase in electroendosmosis flow phenomenon.

In this study, a new mode of gel electromembrane extraction (G-EME) namely as "Two-phase G-EME", is suggested for the sensitive quantification of five basic drugs (desipramine, clomipramine, trimipramine, citalopram and clozapine) in biological samples. Compared to classical G-EME which is based on aqueous-gel-aqueous layout, herein, the aqueous acceptor phase (AP) was replaced with organic solvent. Briefly, negative electrode was immersed into the organic AP (with low conductivity) and positive electrode into the aqueous donor phase (DP). Based on our results, this simple adjustment significantly reduced electroendosmosis (EEO) flow phenomenon which is considered as the main issue in G-EME. In the workflow, target analytes were extracted from the 7.0 mL sample, across the fabricated agarose gel membrane, to the 100 µL of the AP under the optimized extraction conditions (organic solvent type: acetonitrile; pH of gel membrane: 5.0, pH of sample solution: 4.0, voltage: 45 V and extraction time: 22 min). Then, the organic AP with analytes was analyzed by gas chromatography (GC) instrument with flame-ionization detector (FID). The methodology offered limits of detection (LODs) and recoveries in the range of 1.0-1.5 ng mL-1 and 48.5-89.0 %, respectively. Finally, we note that two-phase G-EME assembly was able to extract analytes-of-interest in the convenient and safe manner from the hazardous and difficult-to-process biological specimens such as human serum and urine.

An overview on the recent applications of agarose as a green biopolymer in micro-extraction-based sample preparation techniques.

Introducing a myriad array of chemicals in different industrial fields has made sample preparation inevitable for trace analysis. Classical extraction techniques such as solid phase extraction (SPE) and liquid-liquid extraction (LLE) techniques often suffer from tedious procedures (huge workload) and hazards to personnel and environment (samples and reagents are often user-unfriendly and processed in high amounts). For addressing these problems, microextraction techniques have been introduced. These systems benefit from using a minute amount of sample, reduced consumption of organic solvents, enhanced clean-up, high recovery and high enrichment factors. Moreover, approaches based on the use of natural materials have emerged during the last 10 years. Agarose is a natural biopolymer used as a green material in the form of gel-based separation medium. It has been recently utilized in the microextraction schemes. Easy fabrication, adjustability to get various dimensions and shapes, high inertness and biodegradability are of its main attributes. The present overview is focused on applications of agarose in solid phase microextraction (SPME), micro-solid phase extraction (µ-SPE) and liquid phase microextraction (LPME) - agarose film-liquid phase microextraction (AF-LPME) and gel electromembrane extraction (G-EME) since 2012. Besides, the pros and cons of agarose employment in the mentioned techniques will be described in depth.

Recent advances in robotic protein sample preparation for clinical analysis and other biomedical applications.

Discovery of new protein biomarker candidates has become a major research goal in the areas of clinical chemistry, analytical chemistry, and biomedicine. These important species constitute the molecular target when it comes to diagnosis, prognosis, and further monitoring of disease. However, their analysis requires powerful, selective and high-throughput sample preparation and product (analyte) characterisation approaches. In general, manual sample processing is tedious, complex and time-consuming, especially when large numbers of samples have to be processed (e.g., in clinical studies). Automation via microtiter-plate platforms involving robotics has brought improvements in high-throughput performance while comparable or even better precisions and repeatability (intra-day, inter-day) were achieved. At the same time, waste production and exposure of laboratory personnel to hazards were reduced. In comprehensive protein analysis workflows (e.g., liquid chromatography-tandem mass spectrometry analysis), sample preparation is an unavoidable step. This review surveys the recent achievements in automation of bottom-up and top-down protein and/or proteomics approaches. Emphasis is put on high-end multi-well plate robotic platforms developed for clinical analysis and other biomedical applications. The literature from 2013 to date has been covered.

Evaluation of dispersive liquid-liquid microextraction by coupling with green-based agarose gel-electromembrane extraction: An efficient method to the tandem extraction of basic drugs from biological fluids.

Nowadays, developing new methods for the effective extraction/separation of drugs (present at trace levels) from complicated matrices (as biological fluids) is certainly a great challenge for many operators. In this regard, green-based agarose gel electromembrane extraction (G-EME) was for the first time combined with dispersive liquid-liquid microextraction (DLLME) toward G-EME/DLLME methodology (i.e., tandem extraction approach). Two basic drugs such as trimipramine (TRI) and clomipramine (CLO) extracted from the urine samples, were used as model compounds. Regarding method workflow, analytes were extracted from the 5 mL sample, through a synthesized agarose gel membrane, to the 700 µL aqueous acceptor phase under the optimized conditions (pH of acceptor phase: 2.0; pH of gel membrane: 2.0; pH of donor phase: 4.0, voltage value: 30 V, and extraction time: 25 min). In the next step, acceptor solution was poured to a conic vial and mixed with 100 µL alkaline solution (NaOH, 1 M). Afterwards, DLLME procedure took place again at optimal conditions, i.e., extraction solvent was carbon tetrachloride (10 µL), and dispersive solvent was acetone (100 µL). Ultimately, gas chromatography (GC) was applied for the detection and quantification of drugs. Such G-EME/DLLME configuration has brought two main advantages. Firstly, interferences such as proteins and other large biological molecules were eliminated from biological fluids via G-EME. Further, high enrichment factors (EFs of 260-370 refer to extraction recoveries of 52-74%) were obtained using DLLME with acceptable detection limits (1.0-3.0 ng mL-1). Finally, the suggested approach was successfully utilized to determine drugs at trace levels in urine samples.

The unfolded protein response controls endoplasmic reticulum stress-induced apoptosis of MCF-7 cells via a high dose of vitamin C treatment.

Recent in vitro studies have shown that vitamin C (Vit C) with pro-oxidative properties causes cytotoxicity of breast cancer cells by selective oxidative stress. However, the effect of Vit C in itself at different concentration levels on MCF-7 breast cancer cell line after 24 h, has not yet been described. We aimed to examine the effect of Vit C on the viability and signalling response of MCF-7/WT (MCF-7 wild-type) cells that were exposed to various concentrations (0.125-4 mM) of Vit C during 24 h. The cytotoxic effect of Vit C on MCF-7/VitC (MCF-7/WT after added 2 mM Vit C) was observed, resulting in a decrease of cell index after 12 h. Also, the cytotoxicity of Vit C (2 mM) after 24 h was confirmed by flow cytometry, i.e., increase of dead, late apoptotic, and depolarized dead MCF-7/VitC cells compared to MCF-7/WT cells. Moreover, changes in proteomic profile of MCF-7/VitC cells compared to the control group were investigated via label-free quantitative mass spectrometry and post-translational modification. Using bioinformatics assessment (i.e., iPathwayGuide and SPIA R packages), a significantly impacted pathway in MCF-7/VitC was identified, namely the protein processing in endoplasmic reticulum. The semi-quantitative change (log2fold change = 4.5) and autophosphorylation at Thr-446 of protein kinase (PKR) (involved in this pathway) indicates that PKR protein could be responsible for the unfolded protein response and inhibition of the cell translation during endoplasmic reticulum stress, and eventually, for cell apoptosis. These results suggest that increased activity of PKR (Thr-446 autophosphorylation) related to cytotoxic effect of Vit C (2 mM) may cause the MCF-7 cells death.

RHOA and mDia1 Promotes Apoptosis of Breast Cancer Cells Via a High Dose of Doxorubicin Treatment.

BACKGROUND: Transforming RhoA proteins (RHOA) and their downstream Diaphanous homolog 1 proteins (DIAPH1) or mDia1 participate in the regulation of actin cytoskeleton which plays critical role in cells, i.e., morphologic changes and apoptosis. METHODOLOGY: To determine the cell viability the real time cell analysis (RTCA) and flow cytometry were used. To perform proteomic analysis, the label-free quantitative method and post-translation modification by the nano-HPLC and ESI-MS ion trap mass analyser were used. RESULTS: The results of the cell viability showed an increase of dead cells (around 30 %) in MCF-7/DOX-1 (i.e., 1µM of doxorubicin was added to MCF-7/WT breast cancer cell line) compared to MCF-7/WT (control) after 24 h doxorubicin (DOX) treatment. The signalling pathway of the Regulation of actin cytoskeleton (p<0.0026) was determined, where RHOA and mDia1 proteins were up-regulated. Also, post-translational modification analysis of these proteins in MCF-7/DOX-1 cells revealed dysregulation of the actin cytoskeleton, specifically the collapse of actin stress fibbers due to phosphorylation of RHOA at serine 188 and mDia1 at serine 22, resulting in their deactivation and cell apoptosis. CONCLUSION: These results pointed to an assumed role of DOX to dysregulation of actin cytoskeleton and cell death.

Recent developments in green membrane-based extraction techniques for pharmaceutical and biomedical analysis.

Monitoring of target analytes (e.g., pharmaceuticals, endogenous compounds) present in biological samples usually requires a preliminary step toward analyte isolation from surrounding matrix and enrichment for trace analysis. Evident developments have been recently made to introduce novel "green" analytical approaches (which keep the requirements of Green Analytical Chemistry - GAC) being effective, economical, eco-friendly, and amenable to hyphenated analytical instrumentations. Modern membrane-based extraction techniques provide the smart options against classical sample preparations e.g., liquid-liquid extraction (LLE).These approaches are more stable and allow trace determination of analytes in complex matrices (e.g., biological samples), with high extraction recovery and selectivity. Simultaneously, drawbacks of LLE such as large consumption of organic solvents and the need for tedious handling are eliminated. This paper thoroughly overviews important features and applications of membrane- based extraction techniques with special focus on pharmaceutical and biomedical analysis since 2013. Different driving forces of mass transfer across the membrane were summarized and membrane-based extraction techniques were described along with their advantages/disadvantages as well.

Achievements in robotic automation of solvent extraction and related approaches for bioanalysis of pharmaceuticals.

Currently, the growing demand on quick, easy and ecological sample pretreatment methods is unquestionable. Such challenge involves also approaches focusing on the analysis of pharmaceuticals and other endogenous compounds in biological matrices, termed as Bioanalysis. Solvent extraction such as liquid-liquid extraction (LLE), derived liquid phase microextraction (LPME) and related approaches such as solid liquid extraction (SLE), proved to be applicable in bioanalysis, as numerous papers have been published in this field. However, their manual performances may suffer from a long-term and laborious preparation, due to the inherent complexity of the biological samples. A high sample-throughput (enabling measurement of tens or hundreds of samples on a daily basis) can be achieved when automation of sample pretreatment is performed, resulting in decreased imprecision and low waste production of hazardous solvents and risky biological materials. Here, robotic systems have a key role, especially when multiple processing (e.g., 96-well plate format) and coupling to modern analytical instrumentation (e.g. LC-MS) are combined. A thorough overview on the up-to-date automations of LLE, LPME, SLE and solid LLE via robotics, is therefore presented. Pharmaceuticals and related compounds determined in classical liquid biological samples (i.e. plasma/serum, whole blood, urine, saliva etc.) and modern dried matrix spots (DMS) were considered as analytes of interest. The methodologies were critically compared to manual setups and among themselves.

Salivary Protein Roles in Oral Health and as Predictors of Caries Risk.

This work describes the current state of research on the potential relationship between protein content in human saliva and dental caries, which remains among the most common oral diseases and causes irreversible damage in the oral cavity. An understanding the whole saliva proteome in the oral cavity could serve as a prerequisite to obtaining insight into the etiology of tooth decay at early stages. To date, however, there is no comprehensive evidence showing that salivary proteins could serve as potential indicators for the early diagnosis of the risk factors causing dental caries. Therefore, proteomics indicates the promising direction of future investigations of such factors, including diagnosis and thus prevention in dental therapy.

Proteomic analysis of the vitamin C effect on the doxorubicin cytotoxicity in the MCF-7 breast cancer cell line.

PURPOSE: Doxorubicin is an anthracycline drug which inhibits the growth of breast cancer cell lines. However, a major factor limiting its use is a cumulative, dose-dependent cardiotoxicity, resulting in a permanent loss of cardiomyocytes. Vitamin C was found to potentiate the cytotoxic effects of a variety of chemotherapeutic drugs including doxorubicin. The aim of the study was to describe the changes in protein expression and proliferation of the MCF-7 cells induced by the vitamin C applied with doxorubicin. METHODS: Label-free quantitative proteomics and real-time cell analysis methods were used to search for proteome and cell proliferation changes. These changes were induced by the pure DOX and by DOX combined with vitamin C applied on the MCF-7 cell line. RESULTS: From the real-time cell analysis experiments, it is clear that the highest anti-proliferative effect occurs with the addition of 200 µM of vitamin C to 1 µM of doxorubicin. By applying both the label-free protein quantification method and total ion current assay, we found statistically significant changes (p ≤ 0.05) of 26 proteins induced by the addition of vitamin C to doxorubicin on the MCF-7 cell line. These differentially expressed proteins are involved in processes such as structural molecule activity, transcription and translation, immune system process and antioxidant, cellular signalling and transport. CONCLUSION: The detected proteins may be capable of predicting response to DOX therapy. This is a key tool in the treatment of breast cancer, and the combination with vit C seems to be of particular interest due to the fact that it can potentiate anti-proliferative effect of DOX.

Automation of static and dynamic non-dispersive liquid phase microextraction. Part 1: Approaches based on extractant drop-, plug-, film- and microflow-formation.

Simplicity, effectiveness, swiftness, and environmental friendliness - these are the typical requirements for the state of the art development of green analytical techniques. Liquid phase microextraction (LPME) stands for a family of elegant sample pretreatment and analyte preconcentration techniques preserving these principles in numerous applications. By using only fractions of solvent and sample compared to classical liquid-liquid extraction, the extraction kinetics, the preconcentration factor, and the cost efficiency can be increased. Moreover, significant improvements can be made by automation, which is still a hot topic in analytical chemistry. This review surveys comprehensively and in two parts the developments of automation of non-dispersive LPME methodologies performed in static and dynamic modes. Their advantages and limitations and the reported analytical performances are discussed and put into perspective with the corresponding manual procedures. The automation strategies, techniques, and their operation advantages as well as their potentials are further described and discussed. In this first part, an introduction to LPME and their static and dynamic operation modes as well as their automation methodologies is given. The LPME techniques are classified according to the different approaches of protection of the extraction solvent using either a tip-like (needle/tube/rod) support (drop-based approaches), a wall support (film-based approaches), or microfluidic devices. In the second part, the LPME techniques based on porous supports for the extraction solvent such as membranes and porous media are overviewed. An outlook on future demands and perspectives in this promising area of analytical chemistry is finally given.

Automation of static and dynamic non-dispersive liquid phase microextraction. Part 2: Approaches based on impregnated membranes and porous supports.

A critical overview on automation of modern liquid phase microextraction (LPME) approaches based on the liquid impregnation of porous sorbents and membranes is presented. It is the continuation of part 1, in which non-dispersive LPME techniques based on the use of the extraction phase (EP) in the form of drop, plug, film, or microflow have been surveyed. Compared to the approaches described in part 1, porous materials provide an improved support for the EP. Simultaneously they allow to enlarge its contact surface and to reduce the risk of loss by incident flow or by components of surrounding matrix. Solvent-impregnated membranes or hollow fibres are further ideally suited for analyte extraction with simultaneous or subsequent back-extraction. Their use can therefore improve the procedure robustness and reproducibility as well as it "opens the door" to the new operation modes and fields of application. However, additional work and time are required for membrane replacement and renewed impregnation. Automation of porous support-based and membrane-based approaches plays an important role in the achievement of better reliability, rapidness, and reproducibility compared to manual assays. Automated renewal of the extraction solvent and coupling of sample pretreatment with the detection instrumentation can be named as examples. The different LPME methodologies using impregnated membranes and porous supports for the extraction phase and the different strategies of their automation, and their analytical applications are comprehensively described and discussed in this part. Finally, an outlook on future demands and perspectives of LPME techniques from both parts as a promising area in the field of sample pretreatment is given.

Visual detection and sequential injection determination of aluminium using a cinnamoyl derivative.

A cinnamoyl derivative, 3-[4-(dimethylamino)cinnamoyl]-4-hydroxy-6-methyl-3,4-2H-pyran-2-one, was used as a ligand for the determination of aluminium. Upon the addition of an acetonitrile solution of the ligand to an aqueous solution containing Al(III) and a buffer solution at pH 8, a marked change in colour from yellow to orange is observed. The colour intensity is proportional to the concentration of Al(III); thus, the 'naked-eye' detection of aluminium is possible. The reaction is also applied for sequential injection determination of aluminium. Beer׳s law is obeyed in the range from 0.055 to 0.66 mg L(-1) of Al(III). The limit of detection, calculated as three times the standard deviation of the blank test (n=10), was found to be 4 µg L(-1) for Al(III). The method was applied for the determination of aluminium in spiked water samples and pharmaceutical preparations.