Combining immunofluorescence with in situ proximity ligation assay: a novel imaging approach to monitor protein–protein interactions in relation to subcellular localization

Early divergent modulation of NLRP2's and NLRP3's inflammasome sensors vs. AIM2's one by signals from Aβ·Calcium-sensing receptor complexes in human astrocytes

Alzheimer's disease (AD), the most prevalent human dementia, is driven by accruals of extracellular Aβ42 senile patches and intracellular neurofibrillary tangles of hyperphosphorylated Tau (p-Tau) proteins. AD's concurrent neuroinflammation is prompted by innate immunity-related cytosolic protein oligomers named inflammasomes. Upon proper "first" (priming) and "second" (activating) signals, inflammasomes overproduce proinflammatory Interleukin (IL)-1β, and IL-18 while cleaving pyroptosis-promoting Gasdermin D's N-terminal fragments. Our earlier studies highlighted that in pure monocultures, exogenous Aβ25-35-treated nonproliferating human cortical astrocytes (HCAs) made and released surpluses of endogenous Aβ42-oligomers (-os) and p-Tau-os, just as alike-treated human cortical neurons did. Aβ25-35-exposed HCAs also over-released NO, VEGFA, and IL-6. Aβ•CaSR (Aβ·Calcium-Sensing Receptor) complexes generated intracellular signals mediating all such neurotoxic effects since CaSR's negative allosteric modulators (aka NAMs or calcilytics, e.g., NPS2143) fully suppressed them. However, it had hitherto remained unexplored whether signals from Aβ·CaSR complexes also induced the early expression and/or activation of NOD-like 2 (NLRP2) and 3 (NLRP3) and of PYHIN absent in melanoma 2 (AIM2) inflammasomes in monocultured HCAs. To clarify this topic, we used in-situ-Proximity Ligation, qRT-PCR, double antibody arrays, immunoblots, and Caspase 1/4 enzymatic assays. Aβ·CaSR complexes quickly assembled on HCAs surface and issued intracellular signals activating Akt and JAK/STAT axes. In turn, the latter upregulated NLRP2 and NLRP3 PRRs (pattern recognition receptors) yet downregulated AIM2. These effects were specific, being significantly hindered by NPS2143 and inhibitors of PI3K (LY294002), AMPKα (Dorsomorphin), mTOR (Torin1), and JAK/TYK (Brepoticinib). A wide-spectrum inhibitor, Bay11-7082, intensified the Aβ·CaSR/Akt/JAK/STAT axis-driven opposite control of NLRP3's and AIM2's PRR proteins without affecting NLRP2 PRR upregulation. However, the said effects on the PRRs proteins vanished within 24-h. Moreover, Aβ·CaSR signals neither concurrently changed ASC, pro-IL-1β, and Gasdermin-D (holo- and fragments) protein levels and Caspases 1 and 4 enzymatic activities nor induced pyroptosis. Therefore, Aβ·CaSR cues acted as "first (priming) signals" temporarily increasing NLRP2 and NLRP3 PRRs expression without activating the corresponding inflammasomes. The neatly divergent modulation of NLRP3's vs. AIM2's PRR proteins by Aβ·CaSR cues and by Bay11-7082 suggests that, when bacterial or viral DNA fragments are absent, AIM2 might play "anti-inflammasomal" or other roles in HCAs. However, Bay11-7082's no effect on NLRP2 PRR overexpression also reveals that CaSR's downstream mechanisms controlling inflammasomes' sensors are quite complex in HCAs, and hence, given AD's impact on human health, well worth further studies.

Current and Emerging Approaches to Study Microenvironmental Interactions and Drug Activity in Classical Hodgkin Lymphoma

Simple Summary

In classical Hodgkin Lymphoma (cHL), the tumor microenvironment (TME) plays an important role in tumor progression and treatment response, making its evaluation critical for determining prognosis, treatment strategies and predicting an increase in drug toxicity. Therefore, there is a need to utilize more complex systems to study the cHL-TME and its interplay with tumor cells. To evaluate new anticancer drugs and to find the mechanisms of drug resistance, this review summarizes emerging approaches for the analysis of the TME composition and to identify the state of the disease; the in vitro techniques used to determine the mechanisms involved in the building of an immunosuppressive and protective TME; new 3-dimensional (3D) models, the heterospheroids (HS), developed to mimic TME interactions. Here, we describe the present and likely future clinical applications indicated by the results of these studies and propose a classification for the in vitro culture methods used to study TME interactions in cHL.

Abstract

Classic Hodgkin lymphoma is characterized by a few tumor cells surrounded by a protective and immunosuppressive tumor microenvironment (TME) composed by a wide variety of noncancerous cells that are an active part of the disease. Therefore, new techniques to study the cHL-TME and new therapeutic strategies targeting specifically tumor cells, reactivating the antitumor immunity, counteracting the protective effects of the TME, were developed. Here, we describe new methods used to study the cell composition, the phenotype, and the spatial distribution of Hodgkin and Reed–Sternberg (HRS) cells and of noncancerous cells in tumor tissues. Moreover, we propose a classification, with increasing complexity, of the in vitro functional studies used to clarify the interactions leading not only to HRS cell survival, growth and drug resistance, but also to the immunosuppressive tumor education of monocytes, T lymphocytes and fibroblasts. This classification also includes new 3-dimensional (3D) models, obtained by cultivating HRS cells in extracellular matrix scaffolds or in sponge scaffolds, under non-adherent conditions with noncancerous cells to form heterospheroids (HS), implanted in developing chick eggs (ovo model). We report results obtained with these approaches and their applications in clinical setting.

Protein Kinase C-Mediated Phosphorylation and α2δ-1 Interdependently Regulate NMDA Receptor Trafficking and Activity

N-methyl-d-aspartate receptors (NMDARs) are important for synaptic plasticity associated with many physiological functions and neurologic disorders. Protein kinase C (PKC) activation increases the phosphorylation and activity of NMDARs, and α2δ-1 is a critical NMDAR-interacting protein and controls synaptic trafficking of NMDARs. In this study, we determined the relative roles of PKC and α2δ-1 in the control of NMDAR activity. We found that α2δ-1 coexpression significantly increased NMDAR activity in HEK293 cells transfected with GluN1/GluN2A or GluN1/GluN2B. PKC activation with phorbol 12-myristate 13-acetate (PMA) increased receptor activity only in cells coexpressing GluN1/GluN2A and α2δ-1. Remarkably, PKC inhibition with Gӧ6983 abolished α2δ-1-coexpression-induced potentiation of NMDAR activity in cells transfected with GluN1/GluN2A or GluN1/GluN2B. Treatment with PMA increased the α2δ-1-GluN1 interaction and promoted α2δ-1 and GluN1 cell surface trafficking. PMA also significantly increased NMDAR activity of spinal dorsal horn neurons and the amount of α2δ-1-bound GluN1 protein complexes in spinal cord synaptosomes in wild-type mice, but not in α2δ-1 knockout mice. Furthermore, inhibiting α2δ-1 with pregabalin or disrupting the α2δ-1-NMDAR interaction with the α2δ-1 C-terminus peptide abolished the potentiating effect of PMA on NMDAR activity. Additionally, using quantitative phosphoproteomics and mutagenesis analyses, we identified S929 on GluN2A and S1413 (S1415 in humans) on GluN2B as the phosphorylation sites responsible for NMDAR potentiation by PKC and α2δ-1. Together, our findings demonstrate the interdependence of α2δ-1 and PKC phosphorylation in regulating NMDAR trafficking and activity. The phosphorylation-dependent, dynamic α2δ-1-NMDAR interaction constitutes an important molecular mechanism of synaptic plasticity.SIGNIFICANCE STATEMENT A major challenge in studies of protein phosphorylation is to define the functional significance of each phosphorylation event and determine how various signaling pathways are coordinated in response to neuronal activity to shape synaptic plasticity. PKC phosphorylates transporters, ion channels, and G-protein-coupled receptors in signal transduction. In this study, we showed that α2δ-1 is indispensable for PKC-activation-induced surface and synaptic trafficking of NMDARs, whereas the α2δ-1-NMDAR interaction is controlled by PKC-induced phosphorylation. Our findings reveal that α2δ-1 mainly functions as a phospho-binding protein in the control of NMDAR trafficking and activity. This information provides new mechanistic insight into the reciprocal roles of PKC-mediated phosphorylation and α2δ-1 in regulating NMDARs and in the therapeutic actions of gabapentinoids.

Proximity ligation assay: an ultrasensitive method for protein quantification and its applications in pathogen detection

It is of great significance to establish sensitive and accurate pathogen detection methods, considering the continuous emergence or re-emergence of infectious diseases seriously influences the safety of human and animals. Proximity ligation assay (PLA) is developed for the sensitive protein detection and also can be used for the detection of pathogens. PLA employs aptamer or monoclonal/polyclonal antibody-nucleic acid complexes as proximity probes. When the paired proximity probes bind to the same target protein or protein complex, they will be adjacent to each other and form an amplifiable DNA sequence through ligation. Combining the specificity of enzyme-linked immunosorbent assay (ELISA) and sensitivity of polymerase chain reaction (PCR), PLA transforms the detection of protein into the detection of DNA nucleic acid sequence. Therefore, as an ultrasensitive protein assay, PLA has great potential for quantification, localization of protein, and clinical diagnostics. In this review, we summarize the basic principles of PLA and its applications in pathogen detection. KEY POINTS: • Different forms of proximity ligation assay are introduced. • Applications of proximity ligation assay in pathogen detection are summarized. • Proximity ligation assay is an ultrasensitive method to quantify protein and pathogen.

Coexistence of D3 R typical and atypical signaling in striatonigral neurons during dopaminergic denervation. Correlation with D3 nf expression changes

Dopamine D₃ R are widely expressed in basal ganglia where interact with D₁ R. D₃ R potentiate cAMP accumulation and GABA release stimulated by D₁ R in striatonigral neurons through "atypical" signaling. During dopaminergic denervation, D₃ R signaling changes to a "typical" in which antagonizes the effects of D₁ R, the mechanisms of this switching are unknown. D₃ nf splice variant regulates membrane anchorage and function of D₃ R and decreases in denervation; thus, it is possible that D₃ R signaling switching correlates with changes in D₃ nf expression and increases of membranal D₃ R that mask D₃ R atypical effects. We performed experiments in unilaterally 6-hydroxydopamine lesioned rats and found a decrease in mRNA and protein of D₃ nf, but not of D₃ R in the denervated striatum. Proximity ligation assay showed that D₃ R-D₃ nf interaction decreased after denervation, whereas binding revealed an increased B_max in D₃ R. The new D₃ R antagonized cAMP accumulation and GABA release stimulated by D₁ R; however, in the presence of N-Ethylmaleimide (NEM), to block G_i protein signaling, activation of D₃ R produced its atypical signaling stimulating D₁ R effects. Finally, we investigated if the typical and atypical effects of D₃ R modulating GABA release are capable of influencing motor behavior. Injections of D₃ R agonist into denervated nigra decreased D₁ R agonist-induced turning behavior but potentiated it in the presence of NEM. Our data indicate the coexistence of D₃ R typical and atypical signaling in striatonigral neurons during denervation that correlated with changes in the ratio of expression of D₃ nf and D₃ R isoforms. The coexistence of both atypical and typical signaling during denervation influences motor behavior.

D2 autoreceptor switches CB2 receptor effects on [3 H]-dopamine release in the striatum

CB₂ receptors (CB₂ R) are expressed in midbrain neurons. To evidence the control of dopamine release in dorsal striatum by CB₂ R, we performed experiments of [³ H]-dopamine release in dorsal striatal slices. We found a paradoxical increase in K⁺ -induced [³ H]-dopamine release by CB₂ R activation with GW 833972A and JWH 133 two selective agonist. To understand the mechanism involved, we tested for a role of the D₂ autoreceptor in this effect; because in pallidal structures, the inhibitory effect of CB₁ receptors (CB₁ R) on GABA release is switched to a stimulatory effect by D₂ receptors (D₂ R). We found that the blockade of D₂ autoreceptors with sulpiride prevented the stimulatory effect of CB₂ R activation; in fact, under this condition, CB₂ R decreased dopamine release, indicating the role of the D₂ autoreceptor in the paradoxical increase. We also found that the effect occurs in nigrostriatal terminals, since lesions with 6-OH dopamine in the middle forebrain bundle prevented CB₂ R effects on release. In addition, D₂ -CB₂ R interaction promoted cAMP accumulation, and the increase in [³ H]-dopamine release was prevented by PKA blockade. D₂ -CB₂ R coprecipitation and proximity ligation assay studies indicated a close interaction of receptors that could participate in the observed effects. Finally, intrastriatal injection of CB₂ R agonist induced contralateral turning in amphetamine-treated rats, which was prevented by sulpiride, indicating the role of the interaction in motor behavior. Thus, these data indicate that the D₂ autoreceptor switches, from inhibitory to stimulatory, the CB₂ R effects on dopamine release, involving the cAMP → PKA pathway in nigrostriatal terminals.

Electrochemiluminescence-Based Capacitance Microscopy for Label-Free Imaging of Antigens on the Cellular Plasma Membrane

Electrochemiluminescence (ECL)-based capacitance microscopy using a square-wave voltage is established unprecedentedly to realize the label-free visualization of species on electrode surfaces and cellular plasma membranes. The drop in the local capacitance upon the binding of species to the surface or to a cellular membrane is derived to induce a relatively larger potential drop ( V_dl) across the double layer on the local electrode surface, which is utilized to prompt enhanced ECL at the binding position. The square-wave voltage with a frequency of as high as 1.5 kHz is proven to be favorable for the discrimination of the local ECL from the surrounding signal. Using this new detection principle and resultant capacitance microscopy, carcinoembryonic antigens (CEA) at amounts of as low as 1 pg can be visualized. Further application of this approach permits the direct imaging of CEA antigens on single MCF-7 cells through the capacitance change after the formation of the antigen-antibody complex. Successful visualization of the analyte without any ECL tag will allow not only special capacitance microscopy for label-free bioassays but also a novel ECL detection approach for the sensitive detection of biomolecules.

p62-Dependent Phase Separation of Patient-Derived KEAP1 Mutations and NRF2

Cancer-derived loss-of-function mutations in the KEAP1 tumor suppressor gene stabilize the NRF2 transcription factor, resulting in a prosurvival gene expression program that alters cellular metabolism and neutralizes oxidative stress. In a recent genotype-phenotype study, we classified 40% of KEAP1 mutations as ANCHOR mutants. By immunoprecipitation, these mutants bind more NRF2 than wild-type KEAP1 and ubiquitylate NRF2, but they are incapable of promoting NRF2 degradation. BioID-based protein interaction studies confirmed increased abundance of NRF2 within the KEAP1 ANCHOR mutant complexes, with no other statistically significant changes to the complexes. Discrete molecular dynamic simulation modeling and limited proteolysis suggest that the ANCHOR mutations stabilize residues in KEAP1 that contact NRF2. The modeling supports an intramolecular salt bridge between the R470C ANCHOR mutation and E493; mutation of the E493 residue confirmed the model, resulting in the ANCHOR phenotype. In live cells, the KEAP1 R320Q and R470C ANCHOR mutants colocalize with NRF2, p62/SQSTM1, and polyubiquitin in structured spherical droplets that rapidly fuse and dissolve. Transmission electron microscopy coupled with confocal fluorescent imaging revealed membraneless phase-separated biomolecular condensates. We present a model wherein ANCHOR mutations form p62-dependent biomolecular condensates that may represent a transitional state between impaired proteasomal degradation and autophagy.

MDC1 methylation mediated by lysine methyltransferases EHMT1 and EHMT2 regulates active ATM accumulation flanking DNA damage sites

Chromatin dynamics mediated by post-translational modifications play a crucial role in cellular response to genotoxic stress for the maintenance of genome integrity. MDC1 is a pivotal chromatin adaptor in DNA damage response (DDR) and its methylation is essential to recruit repair factors at DNA double-strand break (DSB) sites, yet their precise molecular mechanisms remain elusive. Here we identified euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and EHMT2 as novel regulators of MDC1, which is required for the accumulation of DDR factors e.g. 53BP1 and RAP80, at the DSB sites. MDC1 interacts mainly with EHMT1, which is facilitated by DNA damage-initiated ATM signalling, and EHMT2 dominantly modulates methylation of MDC1 lysine 45. This regulatory modification promotes the interaction between MDC1 and ATM to expand activated ATM on damaged chromatin and dysfunctional telomere. These findings identify EHMT1 and EHMT2 as DDR components, with implications for genome-integrity maintenance through proper dynamic methylation of MDC1.

K63-Ubiquitylation and TRAF6 Pathways Regulate Mammalian P-Body Formation and mRNA Decapping

Signals and posttranslational modifications regulating the decapping step in mRNA degradation pathways are poorly defined. In this study we reveal the importance of K63-linked ubiquitylation for the assembly of decapping factors, P-body formation, and constitutive decay of instable mRNAs encoding mediators of inflammation by various experimental approaches. K63-branched ubiquitin chains also regulate IL-1-inducible phosphorylation of the P-body component DCP1a. The E3 ligase TRAF6 binds to DCP1a and indirectly regulates DCP1a phosphorylation, expression of decapping factors, and gene-specific mRNA decay. Mutation of six C-terminal lysines of DCP1a suppresses decapping activity and impairs the interaction with the mRNA decay factors DCP2, EDC4, and XRN1, but not EDC3, thus remodeling P-body architecture. The usage of ubiquitin chains for the proper assembly and function of the decay-competent mammalian decapping complex suggests an additional layer of control to allow a coordinated function of decapping activities and mRNA metabolism in higher eukaryotes.

Detection of Receptor Heteromerization Using In Situ Proximity Ligation Assay

Although G protein-coupled receptor (GPCR) heteromerization has been extensively demonstrated in vitro using heterologous cells that overexpress epitope-tagged receptors, their presence in endogenous systems is less well established. This is because a criterion to identify receptor heteromerization is the demonstration that the two interacting receptors are present not only in the same cell but also in the same subcellular compartment in close enough proximity to allow for direct receptor-receptor interaction. This has been difficult to study in native tissues due to a lack of sensitive and selective tools not only capable of detecting low-abundance proteins but also of demonstrating that they are in sufficiently close proximity to interact. The latter can be achieved using a proximity ligation assay (PLA). Detailed in this unit are protocols for demonstrating the presence of GPCR heteromers in endogenous cells as well as animal and human tissues, the controls required for these assays, and troubleshooting tips. © 2016 by John Wiley & Sons, Inc.

Current Approaches Toward Quantitative Mapping of the Interactome

Protein–protein interactions (PPIs) play a key role in many, if not all, cellular processes. Disease is often caused by perturbation of PPIs, as recently indicated by studies of missense mutations. To understand the associations of proteins and to unravel the global picture of PPIs in the cell, different experimental detection techniques for PPIs have been established. Genetic and biochemical methods such as the yeast two-hybrid system or affinity purification-based approaches are well suited to high-throughput, proteome-wide screening and are mainly used to obtain qualitative results. However, they have been criticized for not reflecting the cellular situation or the dynamic nature of PPIs. In this review, we provide an overview of various genetic methods that go beyond qualitative detection and allow quantitative measuring of PPIs in mammalian cells, such as dual luminescence-based co-immunoprecipitation, Förster resonance energy transfer or luminescence-based mammalian interactome mapping with bait control. We discuss the strengths and weaknesses of different techniques and their potential applications in biomedical research.

Bcl10 crucially nucleates the pro-apoptotic complexes comprising PDK1, PKCζ and caspase-3 at the nuclear envelope of etoposide-treated human cervical carcinoma C4-I cells

Protein kinase (PK)Cζ signaling at various subcellular levels affects cell survival, differentiation, growth and/or apoptosis. However, the mechanisms modulating PKCζ activity at the nuclear membrane (NM) are not yet fully understood. Previously, we demonstrated that PKCζ interacts with the B‑cell lymphoma 10 (Bcl10) protein at the NM of human cervical carcinoma (HCC) C4‑I cells. In the present study, we aimed to further clarify the interactions between PKCζ, Bcl10 and other proteins co-immunoprecipitated from NMs isolated from untreated and etoposide (also known as VP‑16; 2.0 µg/ml)‑treated C4‑I cells using biochemical and proteomics analyses. Aside from the Bcl10 protein, 3‑phosphoinositide‑dependent protein kinase‑1 (PDK1) also co-immunoprecipitated with PKCζ from NMs of C4‑I cells, indicating the assembly of a heterotrimeric complex, which increased with time in VP‑16‑exposed cells, as did the activity of PDK1‑phosphorylated‑PKCζ. In turn, PKCζ‑phosphorylated‑Bcl10 straddled an enlarged complex which comprised caspase‑3. Subsequently, activity‑enhanced caspase‑3 cleaved and inactivated PKCζ. Finally, the suppression of Bcl10 using specific siRNA or lentiviral transduction prevented the increase in the PDK1•PKCζ association, the increase in the activity of PKCζ and caspase‑3, as well as the caspase‑3‑mediated PKCζ proteolysis and inactivation from occurring at the NMs of the VP‑16‑exposed C4‑I cells. Our observations provide evidence that Bcl10 acts as a pivotal pro-apoptotic protein which crucially nucleates complexes comprising PDK1, PKCζ and active caspase‑3 at the NMs of VP‑16‑exposed C4‑I cells. Hence, our data suggest that Bcl10 and PKCζ are potential therapeutic targets in the treatment of HCC.

Thioredoxin Activates MKK4-NFκB Pathway in a Redox-dependent Manner to Control Manganese Superoxide Dismutase Gene Expression in Endothelial Cells

The mitogen-activated protein kinase kinase 4 (MKK4) is activated via phosphorylation of Ser-257 and Thr-261 by upstream MAP3Ks and activates JNK and p38 MAPKs in response to cellular stress. We show that thioredoxin (Trx), a cellular redox protein, activates MKK4 via Cys-246 and Cys-266 residues as mutation of these residues renders MKK4 insensitive to phosphorylation by MAP3Ks, TNFα, or Trx. MKK4 is activated in vitro by reduced Trx but not oxidized Trx in the absence of an upstream kinase, suggesting that autophosphorylation of this protein occurs due to reduction of Cys-246 and Cys-266 by Trx. Additionally, mutation of Cys-246 and Cys-266 resulted in loss of kinase activity suggesting that the redox state of Cys-246 and Cys-266 is a critical determinant of MKK4 activation. Trx induces manganese superoxide dismutase (MnSOD) gene transcription by activating MKK4 via redox control of Cys-246 and Cys-266, as mutation of these residues abrogates MKK4 activation and MnSOD expression. We further show that MKK4 activates NFκB for its binding to the MnSOD promoter, which leads to AP-1 dissociation followed by MnSOD transcription. Taken together, our studies show that the redox status of Cys-246 and Cys-266 in MKK4 controls its activities independent of MAP3K, demonstrating integration of the endothelial redox environment to MAPK signaling.

The Histochemistry and Cell Biology pandect: the year 2014 in review

This review encompasses a brief synopsis of the articles published in 2014 in Histochemistry and Cell Biology. Out of the total of 12 issues published in 2014, two special issues were devoted to "Single-Molecule Super-Resolution Microscopy." The present review is divided into 11 categories, providing an easy format for readers to quickly peruse topics of particular interest to them.