A Guide to Transient Expression of Membrane Proteins in HEK-293 Cells for Functional Characterization

Advanced applications of Nanodiscs-based platforms for antibodies discovery

Due to their fundamental biological importance, membrane proteins (MPs) are attractive targets for drug discovery, with cell surface receptors, transporters, ion channels, and membrane-bound enzymes being of particular interest. However, due to numerous challenges, these proteins present underutilized opportunities for discovering biotherapeutics. Antibodies hold the promise of exquisite specificity and adaptability, making them the ideal candidates for targeting complex membrane proteins. They can target specific conformations of a particular membrane protein and can be engineered into various formats. Generating specific and effective antibodies targeting these proteins is no easy task due to several factors. The antigen's design, antibody-generation strategies, lead optimization technologies, and antibody modalities can be modified to tackle these challenges. The rational employment of cutting-edge lipid nanoparticle systems for retrieving the membrane antigen has been successfully implemented to simplify the mechanism-based therapeutic antibody discovery approach. Despite the highlighted MP production challenges, this review unequivocally underscores the advantages of targeting complex membrane proteins with antibodies and designing membrane protein antigens. Selected examples of lipid nanoparticle success have been illustrated, emphasizing the potential of therapeutic antibody discovery in this regard. With further research and development, we can overcome these challenges and unlock the full potential of therapeutic antibodies directed to target complex MPs.

Prolonged Activation of the GLP-1 Receptor via Covalent Capture

The incretin gut hormone glucagon-like peptide-1 (GLP-1) has become a household name because of its ability to induce glucose-dependent insulin release with accompanying weight loss in patients. Indeed, derivatives of the peptide exert numerous pleiotropic actions that favorably affect other metabolic functions, and consequently, such compounds are being considered as treatments for a variety of ailments. The ability of native GLP-1 to function as a clinical drug is severely limited because of its short half-life in vivo. All of the beneficial effects of GLP-1 come from its agonism at the cognate receptor, GLP-1R. In our quest for long-lived activation of the receptor, we hypothesized that an agonist that had the ability to covalently cross-link with GLP-1R would prove useful. We here report the structure-guided design of peptide analogues containing an electrophilic warhead that could be covalently captured by a resident native nucleophile on the receptor. The compounds were evaluated using washout experiments, and resistance to such washing serves as an index of prolonged activation and covalent capture, which we use to tabulate longevity and robust long-lived GLP-1R agonism. The addition of SulF (cross-linkable warhead), an N-terminal trifluoroethyl group (for protease protection), and a C18 diacid lipid (protractor) all contributed to the increased wash resistance of GLP-1. The most effective compound based on the wash resistance metric, C2K26DAC18_K34SulF, has all three elements outlined and may serve as a blueprint and a proof-of-concept scaffold for the design of clinically useful molecules.

Molecular determinants for brain targeting by peptides: a meta-analysis approach with experimental validation

Blood-brain barrier (BBB) peptide-shuttles (BBBpS) are able to translocate the BBB and reach the brain. Despite the importance of brain targeting in pharmacology, BBBpS are poorly characterized. Currently, their development relies on the empiric assumption that cell-penetrating peptides (CPPs), with proven ability to traverse lipid membranes, will likewise behave as a BBBpS. The relationship between CPPs/BBBpS remains elusive and, to the best of our knowledge, has not hitherto been subject to thorough experimental scrutiny. In this work, we have identified/quantified the main physicochemical properties of BBBpS and then searched for CPPs with these properties, hence potential BBBpS. The specific features found for BBBpS are: (i) small size, (ii) none or few aromatic residues, (iii) hydrophobic, and (iv) slight cationic nature. Then, we selected the 10 scoring best in an ordinary least squares analysis, and tested them in vitro and in vivo. Overall, we identified the molecular determinants for brain targeting by peptides, devised a methodology that can be used to assist in the design of peptides with potential brain penetration from amino acid residue sequences, and found four new BBBpS within the CPP library.

New insights into the physiology and pathophysiology of the atypical sodium leak channel NALCN

Cell excitability and its modulation by hormones and neurotransmitters involve the concerted action of a large repertoire of membrane proteins, especially ion channels. Unique complements of coexpressed ion channels are exquisitely balanced against each other in different excitable cell types, establishing distinct electrical properties that are tailored for diverse physiological contributions, and dysfunction of any component may induce a disease state. A crucial parameter controlling cell excitability is the resting membrane potential (RMP) set by extra- and intracellular concentrations of ions, mainly Na+, K+, and Cl-, and their passive permeation across the cell membrane through leak ion channels. Indeed, dysregulation of RMP causes significant effects on cellular excitability. This review describes the molecular and physiological properties of the Na+ leak channel NALCN, which associates with its accessory subunits UNC-79, UNC-80, and NLF-1/FAM155 to conduct depolarizing background Na+ currents in various excitable cell types, especially neurons. Studies of animal models clearly demonstrate that NALCN contributes to fundamental physiological processes in the nervous system including the control of respiratory rhythm, circadian rhythm, sleep, and locomotor behavior. Furthermore, dysfunction of NALCN and its subunits is associated with severe pathological states in humans. The critical involvement of NALCN in physiology is now well established, but its study has been hampered by the lack of specific drugs that can block or agonize NALCN currents in vitro and in vivo. Molecular tools and animal models are now available to accelerate our understanding of how NALCN contributes to key physiological functions and the development of novel therapies for NALCN channelopathies.

Generation of a Cell Line Selectively Producing Functionally Active OATP1B1 Transporter

The solute carrier organic anion transporter family member, OATP1B1, is one of the most important transporter proteins, which mediate penetration of many endogenous substances and xenobiotics into hepatocytes. A model system providing expression of the functional protein is needed to assess interaction of OATP1B1 with various substances. Based on the HEK293 cells, we obtained the HEK293-OATP1B1 cell line, constitutively expressing the SLCO1B1 gene encoding the OATP1B1 transporter. Expression of the SLCO1B1 gene was confirmed by real-time PCR analysis and Western blotting. Functionality of the transporter was assessed by the transport of atorvastatin, which is a substrate of OATP1B1. Cells of the resulting cell line, which selectively express the functionally active recombinant OATP1B1 transporter, can be used to study functions of the protein and to test drugs for being substrates, inducers, and inhibitors of OATP1B1, and to assess the risks of drug interactions.

Chitosan functionalized Mn3O4 nanoparticles counteracts ulcerative colitis in mice through modulation of cellular redox state

Recent findings suggest a key role for reactive oxygen species (ROS) in the pathogenesis and progression of ulcerative colitis (UC). Several studies have also highlighted the efficacy of citrate functionalized Mn3O4 nanoparticles as redox medicine against a number of ROS-mediated disorders. Here we show that synthesized nanoparticles consisting of chitosan functionalized tri-manganese tetroxide (Mn3O4) can restore redox balance in a mouse model of UC induced by dextran sulfate sodium (DSS). Our in-vitro characterization of the developed nanoparticle confirms critical electronic transitions in the nanoparticle to be important for the redox buffering activity in the animal model. A careful administration of the developed nanoparticle not only reduces inflammatory markers in the animals, but also reduces the mortality rate from the induced disease. This study provides a proof of concept for the use of nanomaterial with synergistic anti-inflammatory and redox buffering capacity to prevent and treat ulcerative colitis.

Passive Recording of Bioelectrical Signals from Non-Excitable Cells by Fluorescent Mirroring

Bioelectrical variations trigger different cell responses, including migration, mitosis, and mutation. At the tissue level, these actions result in phenomena such as wound healing, proliferation, and pathogenesis. Monitoring these mechanisms dynamically is highly desirable in diagnostics and drug testing. However, existing technologies are invasive: either they require physical access to the intracellular compartments, or they imply direct contact with the cellular medium. Here, we present a novel approach for the passive recording of electrical signals from non-excitable cells adhering to 3D microelectrodes, based on optical mirroring. Preliminary results yielded a fluorescence intensity output increase of the 5,8% in the presence of a HEK-293 cell on the electrode compared to bare microelectrodes. At present, this technology may be employed to evaluate cell-substrate adhesion and monitor cell proliferation. Further refinements could allow extrapolating quantitative data on surface charges and resting potential to investigate the electrical phenomena involved in cell migration and cancer progression.

Pitfalls of using sequence databases for heterologous expression studies - a technical review

Synthesis of DNA fragments based on gene sequences that are available in public resources has become an efficient and affordable method that has gradually replaced traditional cloning efforts such as PCR cloning from cDNA. However, database entries based on genome sequencing results are prone to errors which can lead to false sequence information and, ultimately, errors in functional characterisation of proteins such as ion channels and transporters in heterologous expression systems. We have identified five common problems that repeatedly appear in public resources: (1) Not every gene has yet been annotated; (2) not all gene annotations are necessarily correct; (3) transcripts may contain automated corrections; (4) there are mismatches between gene, mRNA and protein sequences; and (5) splicing patterns often lack experimental validation. This technical review highlights and provides a strategy to bypass these issues in order to avoid critical mistakes that could impact future studies of any gene/protein of interest in heterologous expression systems.

Identification of Inflammatory Proteomics Networks of Toll-like Receptor 4 through Immunoprecipitation-Based Chemical Cross-Linking Proteomics

Toll-like receptor 4 (TLR4) is a receptor on an immune cell that can recognize the invasion of bacteria through their attachment with bacterial lipopolysaccharides (LPS). Hence, LPS is a pro-immune response stimulus. On the other hand, statins are lipid-lowering drugs and can also lower immune cell responses. We used human embryonic kidney (HEK 293) cells engineered to express HA-tagged TLR-4 upon treatment with LPS, statin, and both statin and LPS to understand the effect of pro- and anti-inflammatory responses. We performed a monoclonal antibody (mAb) directed co-immunoprecipitation (CO-IP) of HA-tagged TLR4 and its interacting proteins in the HEK 293 extracted proteins. We utilized an ETD cleavable chemical cross-linker to capture weak and transient interactions with TLR4 protein. We tryptic digested immunoprecipitated and cross-linked proteins on beads, followed by liquid chromatography–mass spectrometry (LC-MS/MS) analysis of the peptides. Thus, we utilized the label-free quantitation technique to measure the relative expression of proteins between treated and untreated samples. We identified 712 proteins across treated and untreated samples and performed protein network analysis using Ingenuity Pathway Analysis (IPA) software to reveal their protein networks. After filtering and evaluating protein expression, we identified macrophage myristoylated alanine-rich C kinase substrate (MARCKSL1) and creatine kinase proteins as a potential part of the inflammatory networks of TLR4. The results assumed that MARCKSL1 and creatine kinase proteins might be associated with a statin-induced anti-inflammatory response due to possible interaction with the TLR4.

Fluorescence-Based Measurements of Membrane-Bound Angiotensin Converting Enzyme 2 Activity Using Xenopus Laevis Oocytes

Functional investigations of enzymes involving cellular expression systems are important for pharmacological studies. The precise control of expression is challenging in transiently transfected mammalian cell lines. Here, we explored the ability of Xenopus laevis oocytes to express a membrane-bound enzyme for functional characterization using standard 96-well plates and a fluorescence-based plate reader assay. We microinjected oocytes with cRNA encoding the angiotensin converting enzyme 2 (ACE2) and measured the enzymatic activity in single oocytes using a commercial fluorescence-based assay. The injected oocytes showed up to a 50-fold increase in fluorescence compared to uninjected oocytes. This fluorescence intensity was dose-dependent on the amount of ACE2 cRNA. These results suggest that Xenopus oocytes can be used for the functional evaluation of membrane-bound enzymes, decreasing the experimental workload.

Endogenous ion channels expressed in human embryonic kidney (HEK-293) cells

Mammalian expression systems, particularly the human embryonic kidney (HEK-293) cells, combined with electrophysiological studies, have greatly benefited our understanding of the function, characteristic, and regulation of various ion channels. It was previously assumed that the existence of endogenous ion channels in native HEK-293 cells could be negligible. Still, more and more ion channels are gradually reported in native HEK-293 cells, which should draw our attention. In this regard, we summarize the different ion channels that are endogenously expressed in HEK-293 cells, including voltage-gated Na⁺ channels, Ca²⁺ channels, K⁺ channels, Cl^- channels, nonselective cation channels, TRP channels, acid-sensitive ion channels, and Piezo channels, which may complicate the recording of the heterogeneously expressed ion channels to a certain degree. We noted that the expression patterns and channel profiles varied with different studies, which may be due to the distinct originality of the cells, cell culture conditions, passage numbers, and different recording protocols. Therefore, a better knowledge of endogenous ion channels may help minimize potential problems in characterizing heterologously expressed ion channels. Based on this, it is recommended that HEK-293 cells from unknown sources should be examined before transfection for the characterization of their functional profile, especially when the expression level of exogenous ion channels does not overwhelm the endogenous ion channels largely, or the current amplitude is not significantly higher than the native currents.

B2M gene knockout in HEK293T cells by non-viral delivery of CRISPR-Cas9 system for the generation of universal cells

Background

Allogeneic stem cells are the most potent sources for replacing cell, tissue, and organ malfunctions. The clinical use of these stem cells has been limited due to the risk of immune system rejection due to the incompatibility of human leukocyte (HLA) antigens between donors and recipients. To overcome this limitation, we used the CRISPR/Cas9 system to eliminate the β2 microglobulin (B2M) gene, which plays a vital role in the expression of HLA class I.

Results

Non-viral transfer of two gRNAs targeting the first exon and intron in the B2M gene results in large deletions in the target region. In addition, the results of this study showed that 11.11% and 22.22% of cells received genomic changes as homozygous and heterozygous, respectively.

Conclusion

In conclusion, we have shown that the dual guide RNA strategy is a simple and efficient method for modifying genes. As a result, these cells can be proposed as universal cells that are not detectable in the cell therapy system and transplantation by the receptor immune system.

From In Vitro Data to In Vivo Interspecies Danger Communication: A Study of Chemosensing via the Mouse Grueneberg Ganglion

Simple Summary

The mouse olfactory system is essential for danger detection with a critical role in the Grueneberg ganglion subsystem. This organ, which is localized at the tip of the nose, is implicated in the recognition of kairomones, or chemical cues released by predators which allow interspecies communication. These kairomones, which are present in the secretions of predators, will induce fear-related behaviours in mice. It is not yet known how the Grueneberg ganglion neurons can detect these molecules; however, three specific bitter taste receptors, known as TAS2Rs, that are present in the Grueneberg ganglion play a role in this detection. Here, using in vitro, ex vivo and in vivo experimental approaches, we identified two novel and potent sources of kairomones that are recognized by the mouse Grueneberg ganglion neurons, namely the biological secretions from the raccoon (Procyon lotor) and the skunk (Mephitis mephitis).

Abstract

In the wild, mice have developed survival strategies to detect volatile cues that warn them of potential danger. Specific olfactory neurons found in the Grueneberg ganglion olfactory subsystem can detect alarm pheromones emitted by stressed conspecifics, as well as kairomones involuntarily released by their predators. These volatile chemical cues allow intra- and interspecies communication of danger, respectively. Alarm pheromones, kairomones and bitter taste ligands share a common chemical motif containing sulfur or nitrogen. Interestingly, three specific bitter taste receptors (TAS2Rs) have been found in the Grueneberg ganglion neurons that are implicated in danger signalling pathways. We have recently developed a TAS2R–expressing heterologous system that mimics the Grueneberg ganglion neuron responses after kairomone stimulation. Here, we demonstrated by in vitro, ex vivo and in vivo experiments that the biological secretions from the raccoon (Procyon lotor) and the skunk (Mephitis mephitis) were acting as potent sources of kairomones. They activated the Grueneberg ganglion neurons and induced fear-related behaviours in mice. Identification of new sources of semiochemicals is a first step towards an understanding of the interspecies danger communication that takes place in the Grueneberg ganglion.

The role of oviduct-specific glycoprotein (OVGP1) in modulating biological functions of gametes and embryos

Diverse lines of evidence indicate that the mammalian oviduct makes important contributions to the complex process of reproduction other than being simply a conduit for the transport of gametes and embryos. The cumulative synthesis and transport of proteins secreted by oviductal secretory cells into the oviductal lumen create a microenvironment supporting important reproductive events, including sperm capacitation, fertilization, and early embryo development. Among the components that have been identified in the oviductal fluid is a family of glycosylated proteins known collectively as oviduct-specific glycoprotein (OVGP1) or oviductin. OVGP1 has been identified in several mammalian species, including humans. The present review summarizes the work carried out, in various mammalian species, by many research groups revealing the synthesis and secretion of OVGP1, its fate in the female reproductive tract upon secretion by the oviductal epithelium, and its role in modulating biological functions of gametes and embryos. The production and functions of recombinant human OVGP1 and recombinant OVGP1 of other mammalian species are also discussed. Some of the findings obtained with immunocytochemistry will be highlighted in the present review. It is hoped that the findings obtained from recent studies carried out with recombinant OVGP1 from various species will rekindle researchers’ interest in pursuing further the role of the oviductal microenvironment, of which OVGP1 is a major component, in contributing to the successful occurrence of early reproductive events, and the potential use of OVGP1 in improving the current assisted reproductive technology in alleviating infertility.

Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS

Undruggability of RAS proteins has necessitated alternative strategies for the development of effective inhibitors. In this respect, phosphorylation has recently come into prominence as this reversible post-translational modification attenuates sensitivity of RAS towards RAF. As such, in this study, we set out to unveil the impact of phosphorylation on dynamics of HRAS^WT and aim to invoke similar behavior in HRAS^G12D mutant by means of small therapeutic molecules. To this end, we performed molecular dynamics (MD) simulations using phosphorylated HRAS and showed that phosphorylation of Y32 distorted Switch I, hence the RAS/RAF interface. Consequently, we targeted Switch I in HRAS^G12D by means of approved therapeutic molecules and showed that the ligands enabled detachment of Switch I from the nucleotide-binding pocket. Moreover, we demonstrated that displacement of Switch I from the nucleotide-binding pocket was energetically more favorable in the presence of the ligand. Importantly, we verified computational findings in vitro where HRAS^G12D/RAF interaction was prevented by the ligand in HEK293T cells that expressed HRAS^G12D mutant protein. Therefore, these findings suggest that targeting Switch I, hence making Y32 accessible might open up new avenues in future drug discovery strategies that target mutant RAS proteins.

Vimentin Targeted Nano-gene Carrier for Treatment of Renal Diseases

BACKGROUND

Chronic kidney disease (CKD) is a global health problem, and there is no permanent treatment for reversing kidney failure; thus, early diagnosis and effective treatment are required. Gene therapy has outstanding potential; however, the lack of safe gene delivery vectors, a reasonable transfection rate, and kidney targeting ability limit its application. Nanoparticles can offer innovative ways to diagnose and treat kidney diseases as they facilitate targetability and therapeutic efficacy.

METHODS

Herein, we developed a proximal renal tubule-targeting gene delivery system based on alternative copolymer (PS) of sorbitol and polyethyleneimine (PEI), modified with vimentin-specific chitobionic acid (CA), producing PS-conjugated CA (PSC) for targeting toward vimentin-expressing cells in the kidneys. In vitro studies were used to determine cell viability, transfection efficiency, serum influence, and specific uptake in the human proximal renal tubular epithelial cell line (HK-2). Finally, the targeting efficiency of the prepared PSC gene carriers was checked in a murine model of Alport syndrome.

RESULTS

Our results suggested that the prepared polyplex showed low cytotoxicity, enhanced transfection efficiency, specific uptake toward HK-2 cells, and excellent targeting efficiency toward the kidneys.

CONCLUSION

Collectively, from these results it can be inferred that the PSC can be further evaluated as a potential gene carrier for the kidney-targeted delivery of therapeutic genes for treating diseases.

Electrophysiological study of Arabidopsis ABCB4 and PIN2 auxin transporters: Evidence of auxin activation and interaction enhancing auxin selectivity

Polar auxin transport through plant tissue strictly requires polarly localized PIN proteins and uniformly distributed ABCB proteins. A functional synergy between the two types of membrane protein where their localizations overlap may create the degree of asymmetric auxin efflux required to produce polar auxin transport. We investigated this possibility by expressing ABCB4 and PIN2 in human embryonic kidney cells and measuring whole-cell ionic currents with the patch-clamp technique and CsCl-based electrolytes. ABCB4 activity was 1.81-fold more selective for Cl- over Cs+ and for PIN2 the value was 2.95. We imposed auxin gradients and determined that ABCB4 and PIN2 were 12-fold more permeable to the auxin anion (IAA-) than Cl-. This measure of the intrinsic selectivity of the transport pathway was 21-fold when ABCB4 and PIN2 were co-expressed. If this increase occurs in plants, it could explain why asymmetric PIN localization is not sufficient to create polar auxin flow. Some form of co-action or synergy between ABCB4 and PIN2 that increases IAA- selectivity at the cell face where both occur may be important. We also found that auxin stimulated ABCB4 activity, which may contribute to a self-reinforcement of auxin transport known as canalization.

Transient Transfection and Expression of Eukaryotic Membrane Proteins in Expi293F Cells and Their Screening on a Small Scale: Application for Structural Studies

Cancers, neurodegenerative and infectious diseases remain some of the leading causes of deaths worldwide. The structure-guided drug design is essential to advance drug development for these important diseases. One of the key challenges in the structure determination workflow is the production of eukaryotic membrane proteins (drug targets) of high quality. A number of expression systems have been developed for the production of eukaryotic membrane proteins. In this chapter, an optimized detailed protocol for transient transfection and expression of eukaryotic membrane proteins in Expi293F cells is presented. Testing expression and purification on a small scale allow optimizing conditions for sample preparation for downstream structural (cryo-EM) elucidation.

Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook

Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.

Affecting HEK293 Cell Growth and Production Performance by Modifying the Expression of Specific Genes

The HEK293 cell line has earned its place as a producer of biotherapeutics. In addition to its ease of growth in serum-free suspension culture and its amenability to transfection, this cell line’s most important attribute is its human origin, which makes it suitable to produce biologics intended for human use. At the present time, the growth and production properties of the HEK293 cell line are inferior to those of non-human cell lines, such as the Chinese hamster ovary (CHO) and the murine myeloma NSO cell lines. However, the modification of genes involved in cellular processes, such as cell proliferation, apoptosis, metabolism, glycosylation, secretion, and protein folding, in addition to bioprocess, media, and vector optimization, have greatly improved the performance of this cell line. This review provides a comprehensive summary of important achievements in HEK293 cell line engineering and on the global engineering approaches and functional genomic tools that have been employed to identify relevant genes for targeted engineering.

Transfection types, methods and strategies: a technical review

Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells’ genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.

The role of PQL genes in response to salinity tolerance in Arabidopsis and barley

While soil salinity is a global problem, how salt enters plant root cells from the soil solution remains underexplored. Non-selective cation channels (NSCCs) are suggested to be the major pathway for the entry of sodium ions (Na+), yet their genetic constituents remain unknown. Yeast PQ loop (PQL) proteins were previously proposed to encode NSCCs, but the role of PQLs in plants is unknown. The hypothesis tested in this research is that PQL proteins constitute NSCCs mediating some of the Na+ influx into the root, contributing to ion accumulation and the inhibition of growth in saline conditions. We identified plant PQL homologues, and studied the role of one clade of PQL genes in Arabidopsis and barley. Using heterologous expression of AtPQL1a and HvPQL1 in HEK293 cells allowed us to resolve sizable inwardly directed currents permeable to monovalent cations such as Na+, K+, or Li+ upon membrane hyperpolarization. We observed that GFP-tagged PQL proteins localized to intracellular membrane structures, both when transiently over-expressed in tobacco leaf epidermis and in stable Arabidopsis transformants. Expression of AtPQL1a, AtPQL1b, and AtPQL1c was increased by salt stress in the shoot tissue compared to non-stressed plants. Mutant lines with altered expression of AtPQL1a, AtPQL1b, and AtPQL1c developed larger rosettes in saline conditions, while altered levels of AtPQL1a severely reduced development of lateral roots in all conditions. This study provides the first step toward understanding the function of PQL proteins in plants and the role of NSCC in salinity tolerance.

Quantitative Bio-Imaging Tools to Dissect the Interplay of Membrane and Cytoskeletal Actin Dynamics in Immune Cells

Cellular function is reliant on the dynamic interplay between the plasma membrane and the actin cytoskeleton. This critical relationship is of particular importance in immune cells, where both the cytoskeleton and the plasma membrane work in concert to organize and potentiate immune signaling events. Despite their importance, there remains a critical gap in understanding how these respective dynamics are coupled, and how this coupling in turn may influence immune cell function from the bottom up. In this review, we highlight recent optical technologies that could provide strategies to investigate the simultaneous dynamics of both the cytoskeleton and membrane as well as their interplay, focusing on current and future applications in immune cells. We provide a guide of the spatio-temporal scale of each technique as well as highlighting novel probes and labels that have the potential to provide insights into membrane and cytoskeletal dynamics. The quantitative biophysical tools presented here provide a new and exciting route to uncover the relationship between plasma membrane and cytoskeletal dynamics that underlies immune cell function.

Contextualized Protein-Protein Interactions

Protein-protein interaction (PPI) databases are an important bioinformatics resource, yet existing literature-curated databases usually represent cell-type-agnostic interactions, which is at variance with our understanding that protein dynamics are context specific and highly dependent on their environment. Here, we provide a resource derived through data mining to infer disease- and tissue-relevant interactions by annotating existing PPI databases with cell-contextual information extracted from reporting studies. This resource is applicable to the reconstruction and analysis of disease-centric molecular interaction networks. We have made the data and method publicly available and plan to release scheduled updates in the future. We expect these resources to be of interest to a wide audience of researchers in the life sciences.

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We present PPI Context: contextualization of existing literature-curated PPIs

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A resource for filtering PPIs by cell-line information mined from reporting studies

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A fast and flexible pipeline implementing the presented data mining method

Existing literature-curated protein-protein interaction (PPI) databases usually aggregate cell-type-agnostic interactions, yet PPIs are dependent on environmental conditions. Thus, new methods and resources for inferring the context in which a PPI is reported will extend their application and use in disease-centric modeling. We expect the resource presented in this article to be of high interest to those querying known interactions of proteins of interest, reconstruction and analyses of molecular interaction networks, and multi-omics data integration approaches.

Effects of GABAA Receptor α3 Subunit Epilepsy Mutations on Inhibitory Synaptic Signaling

Missense mutations T166M, Q242L, T336M, and Y474C in the GABA_A receptor (GABA_AR) α3 subunit gene are associated with epileptic seizures, dysmorphic features, intellectual disability, and developmental delay. When incorporated into GABA_ARs expressed in oocytes, all mutations are known to reduce GABA-evoked whole-cell currents. However, their impact on the properties of inhibitory synaptic currents (IPSCs) is unknown, largely because it is difficult to establish, much less control, the stoichiometry of GABA_AR expressed in native neuronal synapses. To circumvent this problem, we employed a HEK293 cell-neuron co-culture expression system that permits the recording of IPSCs mediated by a pure population of GABA_ARs with a defined stoichiometry. We first demonstrated that IPSCs mediated by α3-containing GABA_ARs (α3β3γ2) decay significantly slower than those mediated by α1-containing isoforms (α1β2γ2 or α1β3γ2). GABA_AR α3 mutations did not affect IPSC peak amplitudes or 10-90% rise times, but three of the mutations affected IPSC decay. T336M significantly accelerated the IPSC decay rate whereas T166M and Y474C had the opposite effect. The acceleration of IPSC decay kinetics caused by the T366M mutation was returned to wild-type-like values by the anti-epileptic medication, midazolam. Quantification experiments in HEK293 cells revealed a significant reduction in cell-surface expression for all mutants, in agreement with previous oocyte data. Taken together, our results show that impaired surface expression and altered IPSC decay rates could both be significant factors underlying the pathologies associated with these mutations.

Effects of Decomplexation Rates on Ternary Gene Complex Transfection with α-Poly(l-Lysine) or ε-Poly(l-Lysine) as a Decomplexation Controller in An Easy-To-Transfect Cell or A Hard-To-Transfect Cell

The tight binding of pDNA with a cationic polymer is the crucial requirement that prevents DNA degradation from undesired DNase attack to safely deliver the pDNA to its target site. However, cationic polymer-mediated strong gene holding limits pDNA dissociation from the gene complex, resulting in a reduction in transfection efficiency. In this study, to control the decomplexation rate of pDNA from the gene complex in a hard-to-transfect cell or an easy-to-transfect cell, either α-poly(l-lysine) (APL) or ε-poly(l-lysine) (EPL) was incorporated into branched polyethylenimine (bPEI)-based nanocomplexes (NCs). Compared to bPEI/pDNA NCs, the addition of APL or EPL formed smaller bPEI-APL/pDNA NCs with similar zeta potentials or larger bPEI-EPL/pDNA NCs with reduced zeta potentials, respectively, due to the different characteristics of the primary amines in the two poly(l-lysine)s (PLs). Interestingly, although both bPEI-APL/pDNA NCs and bPEI-EPL/pDNA NCs showed similar pDNA compactness to bPEI/pDNA NCs, the addition of APL or EPL resulted in slower or faster pDNA release, respectively, from the bPEI-PL/pDNA NCs than from the bPEI/pDNA NCs. bPEI-EPL/pDNA NCs with a decomplexation enhancer (i.e., EPL) improved the transfection efficiency (TE) in both a hard-to-transfect HepG2 cell and an easy-to-transfect HEK293 cell. However, although a decomplexation inhibitor (i.e., APL) reduced the TE of bPEI-APL/pDNA NCs in both cells, the degree of reduction in the TE could be compensated by PL-mediated enhanced nuclear delivery, particularly in HepG2 cells but not HEK293 cells, because both PLs facilitate nuclear localization of the gene complex per its cellular uptake. In conclusion, a decomplexation rate controller could be a potential factor to establish a high TE and design clinically available gene complex systems.

Generating therapeutic monoclonal antibodies to complex multi-spanning membrane targets: Overcoming the antigen challenge and enabling discovery strategies

Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning helices, encompass families of proteins which are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels and transporters. Although these proteins have typically been targeted by small molecule drugs and peptides, the high specificity of monoclonal antibodies offers a significant opportunity to selectively modulate these target proteins. However, it remains the case that isolation of antibodies with desired pharmacological function(s) has proven difficult due to technical challenges in preparing membrane protein antigens suitable to support antibody drug discovery. In this review recent progress in defining strategies for generation of membrane protein antigens is outlined. We also highlight antibody isolation strategies which have generated antibodies which bind the membrane protein and modulate the protein function.

Different morphologies of human embryonic kidney 293T cells in various types of culture dishes

Human embryonic kidney 293T (HEK293T) cells are used in various biological experiments and researches. In this study, we investigated the effect of cell culture environments on morphological and functional properties of HEK293T cells. We used several kinds of dishes made of polystyrene or glass for cell culture, including three types of polystyrene dishes provided from different manufacturers for suspension and adherent cell culture. In addition, we also investigated the effect of culturing on gelatin-coated surfaces on the cell morphology. We found that HEK293T cells aggregated and formed into three-dimensional (3-D) multicellular spheroids (MCS) when non-coated polystyrene dishes were used for suspension culture. In particular, the non-coated polystyrene dish from Sumitomo bakelite is the most remarkable characteristic for 3-D MCS among the polystyrene dishes. On the other hand, HEK293T cells hardly aggregated and formed 3-D MCS on gelatin-coated polystyrene dishes for suspension culture. HEK293T cells adhered on the non- or gelatin-coated polystyrene dish for adherent culture, but they did not form 3-D MCS. HEK293T cells also adhered to non- or gelatin-coated glass dishes and did not form 3-D MCS in serum-free medium. These results suggest that HEK293T cells cultured on non-coated polystyrene dish may be useful for the tool to analyze the characteristics of 3D-MCS.

Galectin 3-binding protein suppresses amyloid-β production by modulating β-cleavage of amyloid precursor protein

Alzheimer's disease (AD) is the most common type of dementia, and its pathogenesis is associated with accumulation of β-amyloid (Aβ) peptides. Aβ is produced from amyloid precursor protein (APP) that is sequentially cleaved by β- and γ-secretases. Therefore, APP processing has been a target in therapeutic strategies for managing AD; however, no effective treatment of AD patients is currently available. Here, to identify endogenous factors that modulate Aβ production, we performed a gene microarray–based transcriptome analysis of neuronal cells derived from human induced pluripotent stem cells, because Aβ production in these cells changes during neuronal differentiation. We found that expression of the glycophosphatidylinositol-specific phospholipase D1 (GPLD1) gene is associated with these changes in Aβ production. GPLD1 overexpression in HEK293 cells increased the secretion of galectin 3–binding protein (GAL3BP), which suppressed Aβ production in an AD model, neuroglioma H4 cells. Mechanistically, GAL3BP suppressed Aβ production by directly interacting with APP and thereby inhibiting APP processing by β-secretase. Furthermore, we show that cells take up extracellularly added GAL3BP via endocytosis and that GAL3BP is localized in close proximity to APP in endosomes where amyloidogenic APP processing takes place. Taken together, our results indicate that GAL3BP may be a suitable target of AD-modifying drugs in future therapeutic strategies for managing AD.

Plant Membrane Transport Research in the Post-genomic Era

Membrane transport processes are indispensable for many aspects of plant physiology including mineral nutrition, solute storage, cell metabolism, cell signaling, osmoregulation, cell growth, and stress responses. Completion of genome sequencing in diverse plant species and the development of multiple genomic tools have marked a new era in understanding plant membrane transport at the mechanistic level. Genes coding for a galaxy of pumps, channels, and carriers that facilitate various membrane transport processes have been identified while multiple approaches are developed to dissect the physiological roles as well as to define the transport capacities of these transport systems. Furthermore, signaling networks dictating the membrane transport processes are established to fully understand the regulatory mechanisms. Here, we review recent research progress in the discovery and characterization of the components in plant membrane transport that take advantage of plant genomic resources and other experimental tools. We also provide our perspectives for future studies in the field.

Unravelling the Regions of Mutant F508del-CFTR More Susceptible to the Action of Four Cystic Fibrosis Correctors

Cystic fibrosis (CF) is a genetic disease associated with the defective function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that causes obstructive disease and chronic bacterial infections in airway epithelia. The most prevalent CF-causing mutation, the deletion of phenylalanine at position 508 (F508del), leads to CFTR misfolding, trafficking defects and premature degradation. A number of correctors that are able to partially rescue F508del-CFTR processing defects have been identified. Clinical trials have demonstrated that, unfortunately, mono-therapy with the best correctors identified to date does not ameliorate lung function or sweat chloride concentration in homozygous F508del patients. Understanding the mechanisms exerted by currently available correctors to increase mutant F508del-CFTR expression is essential for the development of new CF-therapeutics. We investigated the activity of correctors on the mutant F508del and wild type (WT) CFTR to identify the protein domains whose expression is mostly affected by the action of correctors, and we investigated their mechanisms of action. We found that the four correctors under study, lumacaftor (VX809), the quinazoline derivative VX325, the bithiazole compound corr4a, and the new molecule tezacaftor (VX661), do not influence either the total expression or the maturation of the WT-CFTR transiently expressed in human embryonic kidney 293 (HEK293) cells. Contrarily, they significantly enhance the expression and the maturation of the full length F508del molecule. Three out of four correctors, VX809, VX661 and VX325, seem to specifically improve the expression and the maturation of the mutant CFTR N-half (M1N1, residues 1–633). By contrast, the CFTR C-half (M2N2, residues 837–1480) appears to be the region mainly affected by corr4a. VX809 was shown to stabilize both the WT- and F508del-CFTR N-half isoforms, while VX661 and VX325 demonstrated the ability to enhance the stability only of the mutant F508del polypeptide.

Analysis of Alpina officinarum Hance, chemically and biologically

Alpinia officinarum Hance is one of the most commonly used herbs belongs to Family Zingiberaceae. The current work deals with the qualitative and quantitative chemical study of this plant rhizomes in addition to the investigation of its anticancer activities. The results of the qualitative analysis showed a variation of phytochemical contents in this plant. While quantitative analysis showed a very promising percentage of active materials and Pharmacopeial constants. Analysis of elements like Cu, Zn & Mg were variable chromium was the lowest (0.680 ppm). The active constituents showed the highest percentage of carbohydrate (20.25 ± 1.11) and the lowest was of lipid (2.79 ± 1.03), other constituents percentage ranged from 5.11 ± 1.31 to 18.26 ± 1.24 for protein and flavonoids respectively. The pharmacopeial constant determinations reported the highest in moisture content (11.02 ± 1.05), Total ash, water-soluble ash, and acid insoluble ash were varied in values (5.64 ± 1.31 to 2.01 ± 1.12).

The evaluation of the antitumor activities (in vitro) of the investigated plant rhizomes extract showed that; it exhibited a direct cytotoxic effect on the growth of some cell lines compared to the standard drug vinblastine sulphate. The activities were recorded against two cell lines; A-549 (Lung carcinoma) and CACO (colorectal carcinoma) with IC50 6.72 ± 0.5 and 7.6 ± 0.3 µg/ml respectively, these effects were better than the standard drug vinblastine sulphate (IC₅₀ were 24.6 ± 0.7& 30.3 ± 1.4 µg/ml). Moreover, the effect of the investigated extract was also promising on the other three cell lines (HCT-116 (Colon carcinoma, Hela (Cervical carcinoma) & Pc3 (prostate cancer) the best effect was on Hela with IC₅₀ of 24.5 ± 1.1 µg/ml better than vinblastine sulphate (59.7 ± 2.1 µg/ml).

Cross-linking Proteomics Indicates Effects of Simvastatin on the TLR2 Interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade

Toll-like receptor 2 (TLR2) is a pattern recognition receptor that, upon ligation by microbial molecules, interacts with other proteins to initiate pro-inflammatory responses by the cell. Statins (hydroxymethylglutaryl coenzyme A reductase inhibitors), drugs widely prescribed to reduce hypercholesterolemia, are reported to have both pro- and anti-inflammatory effects upon cells. Some of these responses are presumed to be driven by effects on signaling proteins at the plasma membrane, but the underlying mechanisms remain obscure. We reasoned that profiling the effect of statins on the repertoire of TLR2-interacting proteins might provide novel insights into the mechanisms by which statins impact inflammation. In order to study the TLR2 interactome, we designed a coimmunoprecipitation (IP)-based cross-linking proteomics study. A hemagglutinin (HA)-tagged-TLR2 transfected HEK293 cell line was used to precipitate the TLR2 interactome upon cell exposure to the TLR2 agonist Pam3CSK4 and simvastatin, singly and in combination. To stabilize protein interactors, we used two different chemical cross-linkers with different spacer chain lengths. Proteomic analysis revealed important combinatorial effects of simvastatin and Pam3CSK4 on the TLR2 interactome. After stringent data filtering, we identified alpha-centractin (ACTR1A), an actin-related protein and subunit of the dynactin complex, as a potential interactor of TLR2. The interaction was validated using biochemical methods. RNA interference studies revealed an important role for ACTR1A in induction of pro-inflammatory cytokines. Taken together, we report that statins remodel the TLR2 interactome, and we identify ACTR1A, a part of the dynactin complex, as a novel regulator of TLR2-mediated immune signaling pathways.

The Arabidopsis thaliana K+-Uptake Permease 5 (AtKUP5) Contains a Functional Cytosolic Adenylate Cyclase Essential for K+ Transport

Potassium (K⁺) is the most abundant cation in plants, and its uptake and transport are key to growth, development and responses to the environment. Here, we report that Arabidopsis thaliana K⁺ uptake permease 5 (AtKUP5) contains an adenylate cyclase (AC) catalytic center embedded in its N-terminal cytosolic domain. The purified recombinant AC domain generates cAMP in vitro; and when expressed in Escherichia coli, increases cAMP levels in vivo. Both the AC domain and full length AtKUP5 rescue an AC-deficient E. coli mutant, cyaA, and together these data provide evidence that AtKUP5 functions as an AC. Furthermore, full length AtKUP5 complements the Saccharomyces cerevisiae K⁺ transport impaired mutant, trk1 trk2, demonstrating its function as a K⁺ transporter. Surprisingly, a point mutation in the AC center that impairs AC activity, also abolishes complementation of trk1 trk2, suggesting that a functional catalytic AC domain is essential for K⁺ uptake. AtKUP5-mediated K⁺ uptake is not affected by cAMP, the catalytic product of the AC, but, interestingly, causes cytosolic cAMP accumulation. These findings are consistent with a role for AtKUP5 as K⁺ flux sensor, where the flux-dependent cAMP increases modulate downstream components essential for K⁺ homeostasis, such as cyclic nucleotide gated channels.

Anticancer effect of Cenchrus ciliaris L

Cenchrus ciliaris L total alcohol and successive extracts of both aerial and root parts were tested for their anticancer activities against lung (A-549), intestinal (CACO), colon (HCT-116), cervical (Hela), hepatocellular (HepG-2), and breast (MCF-7) (PC3) cell lines and compared with the standard drug vinblastine sulphate. The obtained results exhibited direct cytotoxic effect with variable inhibiting effect on the growth of the listed cell lines comparing to vinblastine sulphate as reference standard drug, these effects showed different IC₅₀ ranged from 11.1 ± 0.3 to 267 ± µg/ml.

All root extracts showed the best activities against most of the tested cell lines specially HepG-2 (Hepatocellular carcinoma) (9 ± 2.1 µg/ml) which was somewhat closely related to the effect of vinblastine sulphate (2.93 ± 0.3 µg/ml).

The highest anticancer effect of Cenchrus ciliaris L aerial parts and root extracts were recorded on HepG-2 (Hepatocellular carcinoma) their IC₅₀ were 12 ± 0.8 & 9 ± 2.1 respectively, CACO (colorectal carcinoma) their IC₅₀ were 27.2 ± 1.6 & 20.5 ± 0.6 respectively, A-549 (Lung carcinoma) their IC₅₀ were 14.5 ± 0.7& 11.1 ± 0.3 respectively which were better than the standard drug especially in case the anticancer effect on CACO (colorectal carcinoma) and A-549 (Lung carcinoma). Chloroform extracts of both aerial and roots achieved the best anticancer activities on all of the cell lines especially with colorectal (CACO) and Lung carcinoma (A-549). Cenchrus ciliaris could be a promising source of new chemical moieties used to target cancer cells.

Human Embryonic Kidney 293 Cells: A Vehicle for Biopharmaceutical Manufacturing, Structural Biology, and Electrophysiology

Mammalian cells, e.g., CHO, BHK, HEK293, HT-1080, and NS0 cells, represent important manufacturing platforms in bioengineering. They are widely used for the production of recombinant therapeutic proteins, vaccines, anticancer agents, and other clinically relevant drugs. HEK293 (human embryonic kidney 293) cells and their derived cell lines provide an attractive heterologous system for the development of recombinant proteins or adenovirus productions, not least due to their human-like posttranslational modification of protein molecules to provide the desired biological activity. Secondly, they also exhibit high transfection efficiency yielding high-quality recombinant proteins. They are easy to maintain and express with high fidelity membrane proteins, such as ion channels and transporters, and thus are attractive for structural biology and electrophysiology studies. In this article, we review the literature on HEK293 cells regarding their origins but also stress their advancements into the different cell lines engineered and discuss some significant aspects which make them versatile systems for biopharmaceutical manufacturing, drug screening, structural biology research, and electrophysiology applications.

Purification and characterization of a bioactive alpha-fetoprotein produced by HEK-293 cells

Alpha-fetoprotein (AFP) is a biomarker that is used to diagnose hepatocellular carcinoma (HCC) and can promote malignancy in HCC. AFP is an important target in the treatment of liver cancer. To obtain enough AFP to screen for AFP inhibitors, we expressed and purified AFP in HEK-293 cells. In the present study, we produced AFP in the cells and harvested highly pure rAFP (or recombinant expression AFP in HEK-293 cells). We also analysed the bioactivity of rAFP and found that rAFP promoted growth of the human HCC cells, antagonize paclitaxel inhibition of HCC cell proliferation, suppress expression of active caspase-3, and promote expression of Ras and survivin. This study provides a method to produce significant amounts of AFP for use in biochemical assays and functional studies and to screen AFP inhibitors for use in HCC therapy.

Controllable Ion Channel Expression through Inducible Transient Transfection

Transfection, the delivery of foreign nucleic acids into a cell, is a powerful tool in protein research. Through this method, ion channels can be investigated through electrophysiological analysis, biochemical characterization, mutational studies, and their effects on cellular processes. Transient transfections offer a simple protocol in which the protein becomes available for analysis within a few hours to days. Although this method presents a relatively straightforward and time efficient protocol, one of the critical components is calibrating the expression of the gene of interest to physiological relevant levels or levels that are suitable for analysis. To this end, many different approaches that offer the ability to control the expression of the gene of interest have emerged. Several stable cell transfection protocols provide a way to permanently introduce a gene of interest into the cellular genome under the regulation of a tetracycline-controlled transcriptional activation. While this technique produces reliable expression levels, each gene of interest requires a few weeks of skilled work including calibration of a killing curve, selection of cell colonies, and overall more resources. Here we present a protocol that uses transient transfection of the Transient Receptor Potential cation channel subfamily V member 1 (TRPV1) gene in an inducible system as an efficient way to express a protein in a controlled manner which is essential in ion channel analysis. We demonstrate that using this technique, we are able to perform calcium imaging, whole cell, and single channel analysis with controlled channel levels required for each type of data collection with a single transfection. Overall, this provides a replicable technique that can be used to study ion channels structure and function.