Speciation analysis for trace levels of selenoproteins in cultured human cells

Omics insights into the responses to dietary selenium

Selenium is a well-known health-relevant element related with cancer chemoprevention, neuroprotective roles, beneficial in diabetes, and in several infectious diseases, among others. It is naturally present in some foods, but deficiency in people led to the production of nutraceuticals, supplements, and functional food enriched in this element. There is a U-shaped link between selenium levels and health and a narrow range between toxic and essential levels, and thus, supplementation should be performed carefully. Omics methodologies have become valuable approaches to delve into the responses of dietary selenium in mammals that allowed a deeper knowledge about the metabolism of this element as well as its biological role. In this review, we discuss omics approaches from the workflows to their applications that has been previously used to deep insight into the metabolism of dietary selenium. There is a special focus on selenoproteins, metabolomics responses in blood and tissues (e.g., brain, reproductive organs, etc.) as well as the impact on gut microbiota and its metabolites profile. Thus, we mainly reviewed heteroatom-tagged proteomics, metallomics, metabolomics, and metataxonomics, usually combined with transcriptomics, genomics, and other molecular methods.

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS)-based strategies applied for the analysis of metal-binding protein in biological samples: an update on recent advances

New analytical strategies for metal-binding protein facilitate researchers learning about how metals play a significant role in life. Laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS) offers many advantages for the metal analysis of biological samples and shows a promising future in protein analysis, but recent advances in LA-ICP-MS-based strategies for identifying metal-binding proteins via endogenous metals remain less updated yet. To present the current status in this field, the main analytical strategies for metal-binding proteins with LA-ICP-MS are reviewed here, including in situ analysis of biospecimens and ex situ analysis with gel electrophoresis. A critical discussion of challenges and future perspectives is also given. Multifarious laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS)-based strategies have been developed and applied to investigate the metal-binding proteins in biospecimens in situ or through gel electrophoresis ex situ over the past decades, facilitating researchers disclosing how essential metals are implicated in life or what proteins toxic metals will target.

Antagonistic Interaction of Selenium and Cadmium in Human Hepatic Cells Through Selenoproteins

Cadmium (Cd) is a highly toxic heavy metal for humans and animals, which is associated with acute hepatotoxicity. Selenium (Se) confers protection against Cd-induced toxicity in cells, diminishing the levels of ROS and increasing the activity of antioxidant selenoproteins such as glutathione peroxidase (GPx). The aim of this study was to evaluate the antagonistic effect of selenomethionine (SeMet) against Cd toxicity in HepG2 cells, through the modulation of selenoproteins. To this end, the cells were cultured in the presence of 100 µM SeMet and 5 μM, 15 µM, and 25 µM CdCl₂ and a combination of both species for 24 h. At the end of the experiment, cell viability was determined by MTT assay. The total metal content of Cd and Se was analyzed by triple-quadrupole inductively coupled plasma–mass spectrometry (ICP-QqQ-MS). To quantify the concentration of three selenoproteins [GPx, selenoprotein P (SELENOP), and selenoalbumin (SeAlb)] and selenometabolites, an analytical methodology based on column switching and a species-unspecific isotopic dilution approach using two-dimensional size exclusion and affinity chromatography coupled to ICP-QqQ-MS was applied. The co-exposure of SeMet and Cd in HepG2 cells enhanced the cell viability and diminished the Cd accumulation in cells. Se supplementation increased the levels of selenometabolites, GPx, SELENOP, and SeAlb; however, the presence of Cd resulted in a significant diminution of selenometabolites and SELENOP. These results suggested that SeMet may affect the accumulation of Cd in cells, as well as the suppression of selenoprotein synthesis induced by Cd.

Natural Deep Eutectic Solvents as a Key Metal Extractant for Fractionation in Speciation Analysis

The research aimed to use natural deep eutectic solvents (NADES) as an extractant for fractionation of compounds of selected elements from young barley and to compare it with the fractionation of elements from certified element materials. The use of such a comparison made it possible to prove the possibility of extracting the same forms of elements (species) from different materials, which confirmed the option of using NADES as extractants in speciation analysis. The research was conducted with hyphenated techniques—separation by high-performance chromatography coupled to an isotope-specific detector, mass spectrometry (MS) with ionization in inductively coupled plasma (ICP)—which are widely used in speciation analysis. Natural deep eutectic solvents also help introduce Green Analytical Chemistry principles (GAC). According to the results of our studies, the use of different NADES permit the extraction of various metals from a single sample. Moreover, using other natural solvents of eutectic properties helps extract different species of a given metal.

Selenoproteome Expression Studied by Non-Radioactive Isotopic Selenium-Labeling in Human Cell Lines

Selenoproteins, in which the selenium atom is present in the rare amino acid selenocysteine, are vital components of cell homeostasis, antioxidant defense, and cell signaling in mammals. The expression of the selenoproteome, composed of 25 selenoprotein genes, is strongly controlled by the selenium status of the body, which is a corollary of selenium availability in the food diet. Here, we present an alternative strategy for the use of the radioactive ⁷⁵Se isotope in order to characterize the selenoproteome regulation based on (i) the selective labeling of the cellular selenocompounds with non-radioactive selenium isotopes (⁷⁶Se, ⁷⁷Se) and (ii) the detection of the isotopic enrichment of the selenoproteins using size-exclusion chromatography followed by inductively coupled plasma mass spectrometry detection. The reliability of our strategy is further confirmed by western blots with distinct selenoprotein-specific antibodies. Using our strategy, we characterized the hierarchy of the selenoproteome regulation in dose–response and kinetic experiments.

Characterization and Quantification of Selenoprotein P: Challenges to Mass Spectrometry

Selenoprotein P (SELENOP) is an emerging marker of the nutritional status of selenium and of various diseases, however, its chemical characteristics still need to be investigated and methods for its accurate quantitation improved. SELENOP is unique among selenoproteins, as it contains multiple genetically encoded SeCys residues, whereas all the other characterized selenoproteins contain just one. SELENOP occurs in the form of multiple isoforms, truncated species and post-translationally modified variants which are relatively poorly characterized. The accurate quantification of SELENOP is contingent on the availability of specific primary standards and reference methods. Before recombinant SELENOP becomes available to be used as a primary standard, careful investigation of the characteristics of the SELENOP measured by electrospray MS and strict control of the recoveries at the various steps of the analytical procedures are strongly recommended. This review critically discusses the state-of-the-art of analytical approaches to the characterization and quantification of SELENOP. While immunoassays remain the standard for the determination of human and animal health status, because of their speed and simplicity, mass spectrometry techniques offer many attractive and complementary features that are highlighted and critically evaluated.

Chemical Biology Approaches to Interrogate the Selenoproteome

Selenoproteins are the family of proteins that contain the amino acid selenocysteine. Many selenoproteins, including glutathione peroxidases and thioredoxin reductases, play a role in maintaining cellular redox homeostasis. There are a number of examples of homologues of selenoproteins that utilize cysteine residues, raising the question of why selenocysteines are utilized. One hypothesis is that incorporation of selenocysteine protects against irreversible overoxidation, typical of cysteine-containing homologues under high oxidative stress. Studies of selenocysteine function are hampered by challenges both in detection and in recombinant expression of selenoproteins. In fact, about half of the 25 known human selenoproteins remain uncharacterized. Historically, selenoproteins were first detected via labeling with radioactive 75Se or by use of inductively coupled plasma-mass spectrometry to monitor nonradioactive selenium. More recently, tandem mass-spectrometry techniques have been developed to detect selenocysteine-containing peptides. For example, the isotopic distribution of selenium has been used as a unique signature to identify selenium-containing peptides from unenriched proteome samples. Additionally, selenocysteine-containing proteins and peptides were selectively enriched using thiol-reactive electrophiles by exploiting the increased reactivity of selenols relative to thiols, especially under low pH conditions. Importantly, the reactivity-based enrichment of selenoproteins can differentiate between oxidized and reduced selenoproteins, providing insight into the activity state. These mass spectrometry-based selenoprotein detection approaches have enabled (1) production of selenoproteome expression atlases, (2) identification of aging-associated changes in selenoprotein expression, (3) characterization of selenocysteine reactivity across the selenoprotein family, and (4) interrogation of selenoprotein targets of small-molecule drugs. Further investigations of selenoprotein function would benefit from recombinant expression of selenoproteins. However, the endogenous mechanism of selenoprotein production makes recombinant expression challenging. Primarily, selenocysteine is biosynthesized on its own tRNA, is dependent on multiple enzymatic steps, and is highly sensitive to selenium concentrations. Furthermore, selenocysteine is encoded by the stop codon UGA, and suppression of that stop codon requires a selenocysteine insertion sequence element in the selenoprotein mRNA. In order to circumvent the low efficiency of the endogenous machinery, selenoproteins have been produced in vitro through native chemical ligation and expressed protein ligation. Attempts have also been made to engineer the endogenous machinery for increased efficiency, including recoding the selenocysteine codon, and engineering the tRNA and the selenocysteine insertion sequence element. Alternatively, genetic code expansion can be used to generate selenoproteins. This approach allows for selenoprotein production directly within its native cellular environment, while bypassing the endogenous selenocysteine incorporation machinery. Furthermore, by incorporating a caged selenocysteine by genetic code expansion, selenoprotein activity can be spatially and temporally controlled. Genetic code expansion has allowed for the expression and uncaging of human selenoproteins in E. coli and more recently in mammalian cells. Together, advances in selenoprotein detection and expression should enable a better understanding of selenoprotein function and provide insight into the necessity for selenocysteine production.

Selenoproteome Identification in Inflamed Murine Primary Bone Marrow-Derived Macrophages by Nano-LC Orbitrap Fusion Tribrid Mass Spectrometry

Selenium (Se) functions as a cellular redox gatekeeper through its incorporation into proteins as the 21st amino acid, selenocysteine (Sec). Supplementation of macrophages with exogenous Se (as sodium selenite) downregulates inflammation and intracellular oxidative stress by effectively restoring redox homeostasis upon challenge with bacterial endotoxin lipopolysaccharide (LPS). Here, we examined the use of a standard Tandem Mass Tag (TMT)-labeling mass spectrometry-based proteomic workflow to quantitate and examine temporal regulation of selenoproteins in such inflamed cells. Se-deficient murine primary bone marrow-derived macrophages (BMDMs) exposed to LPS in the presence or absence of selenite treatment for various time periods (0-20 h) were used to analyze the selenoproteome expression using isobaric labeling and shotgun proteomic workflow. To overcome the challenge of identification of Sec peptides, we used the identification of non-Sec containing peptides downstream of Sec as a reliable evidence of ribosome readthrough indicating efficient decoding of Sec codon. Results indicated a temporal regulation of the selenoproteome with a general increase in their expression in inflamed cells in a Se-dependent manner. Selenow, Gpx1, Msrb1, and Selenom were highly upregulated upon stimulation with LPS when compared to other selenoproteins. Interestingly, Selenow appeared to be one amongst the highly regulated selenoproteins in macrophages that was previously thought to be mainly restricted to myocytes. Collectively, TMT-labeling method of non-Sec peptides offers a reliable method to quantitate and study temporal regulation of selenoproteins; however, further optimization to include Sec-peptides could make this strategy more robust and sensitive compared to other semi-quantitative or qualitative methods. Graphical Abstract.

Nonradioactive Isotopic Labeling and Tracing of Selenoproteins in Cultured Cell Lines

Selenium (Se) is an essential component of genetically encoded selenoproteins, in the form of a rare amino acid, namely the selenocysteine (Sec). Radioactive ⁷⁵Se has been widely used to trace selenoproteins in vitro and in vivo (cell models and animals). Alternatively, its unique isotopic pattern can be used to detect and characterize nonradioactive Se-compounds in cellular extracts using molecular or elemental mass spectrometry at ppm levels. However, when studying trace levels of Se-compounds, such as selenoproteins (ppt levels), the distribution of the signal between its six naturally abundant isotopes reduces its sensitivity. Here, we describe the use of isotopically enriched forms of Se as an alternative strategy to radioactive ⁷⁵Se, for the labeling and tracing of selenoproteins in cultured cell lines.

Detection of Selenoproteins by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP MS) in Immobilized pH Gradient (IPG) Strips

In contrast to other trace elements that are cofactors of enzymes and removed from proteins under denaturing conditions, Se is covalently bound to proteins when incorporated into selenoproteins, since it is a component of selenocysteine aminoacid. It implies that selenoproteins can undergo several biochemical separation methods in stringent and chaotropic conditions and still maintain the presence of selenium in the primary sequence. This feature has been used to develop a method for the detection of trace levels of human selenoproteins in cell extracts without the use of radioactive isotopes. The selenoproteins are separated as a function of their isoelectric point (pI) using iso-electrofocusing (IEF) electrophoretic strips and detected by laser ablation-inductively coupled plasma mass spectrometry (LA-ICP MS). This method, therefore referred to as IEF-LA-ICP MS, allowed the detection of several selenoproteins in human cell lines, including Gpx1, Gpx4, TXNRD1, TXNRD2, and SELENOF.

Selenium-regulated hierarchy of human selenoproteome in cancerous and immortalized cells lines

BACKGROUND

Selenoproteins (25 genes in human) co-translationally incorporate selenocysteine using a UGA codon, normally used as a stop signal. The human selenoproteome is primarily regulated by selenium bioavailability with a tissue-specific hierarchy.

METHODS

We investigated the hierarchy of selenoprotein expression in response to selenium concentration variation in four cell lines originating from kidney (HEK293, immortalized), prostate (LNCaP, cancer), skin (HaCaT, immortalized) and liver (HepG2, cancer), using complementary analytical methods. We performed (i) enzymatic activity, (ii) RT-qPCR, (iii) immuno-detection, (iv) selenium-specific mass spectrometric detection after non-radioactive ⁷⁶Se labeling of selenoproteins, and (v) luciferase-based reporter constructs in various cell extracts.

RESULTS

We characterized cell-line specific alterations of the selenoproteome in response to selenium variation that, in most of the cases, resulted from a translational control of gene expression. We established that UGA-selenocysteine recoding efficiency, which depends on the nature of the SECIS element, dictates the response to selenium variation.

CONCLUSIONS

We characterized that selenoprotein hierarchy is cell-line specific with conserved features. This analysis should be done prior to any experiments in a novel cell line.

GENERAL SIGNIFICANCE

We reported a strategy based on complementary methods to evaluate selenoproteome regulation in human cells in culture.

Comparison of analytical methods using enzymatic activity, immunoaffinity and selenium-specific mass spectrometric detection for the quantitation of glutathione peroxidase 1

Glutathione peroxidase 1 (Gpx1), one of the most responsive selenoproteins to the variation of selenium concentration, is often used to evaluate "selenium status" at a cellular or organismal level. The four major types of analytical methodologies to quantify Gpx1 were revisited. They include (i) an enzymatic assay, (ii, iii) polyacrylamide gel electrophoresis (PAGE) with (ii) western blot detection of protein or (iii) inductively coupled plasma mass spectrometry (ICP MS) detection of selenium, and (iv) size-exclusion chromatography with ICP MS detection. Each of the four methods was optimized for the quantification of Gpx1 with maximum sensitivity. The methods based on the enzymatic and immunodetection offer a much higher sensitivity but their accuracy is compromised by the limited selectivity and limited dynamic range. The advantages, drawbacks and sources of error of each technique are critically discussed and the need for the cross-validation of the results using the different techniques to assure the quality assurance of quantitative analysis is emphasized.

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

Mass spectrometry-based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.

Stable isotope labelling methods in mass spectrometry-based quantitative proteomics

Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.