Sensors and regulators of intracellular pH

Sulfonium perchlorate based near-infrared fluorescent probe targeting lysosome for pH imaging in living cells and tumor-bearing mice

Due to the accumulation of lactate and other acidic metabolites from insufficient blood supply and hypoxia, the acidic microenvironment of tumors not only accelerates tumor growth and spread but may also affect immune cell function, thereby aiding tumor development. Therefore, real-time monitoring of pH fluctuations in intracellular and living systems provides crucial insights into physiological and pathological processes. This research introduced a novel NIR fluorescent probe, termed SOH, for pH imaging in living cells and tumor-bearing mice. This sulfonium perchlorate probe exhibited excellent optical properties, including large Stokes shift, significant lysosome-targeting capability, and superior photostability. SOH was effectively used for real-time pH imaging in HepG2 cells and for visualizing the weakly acidic microenvironment within tumor tissue in mice. It shows promising potential as an early tumor diagnostic tool in vivo.

Intrinsic dual-emitting Si dots for high-precision and broad-range pH detection

BACKGROUND

High-precision and broad-range pH detection is critical for health status assessment, such as signal transduction, enzyme activity, endocytosis, and cell proliferation and apoptosis. Although pH-responsive ratiometric fluorescent probes offer an effective pH monitoring strategy, their preparation often requires multi-step modification and decreases fluorescence efficiency and stability. Herein, we developed a simple method to prepare fluorescent Si dots with dual emission centers for high-precision and broad-range pH monitoring, and the detection of urease based on pH-responsive Si dots and pH monitoring in living cell was further explored.

RESULTS

The dual-emitting Si dots had two emission centers at 427 nm and 500 nm. The emission at 427 nm showed a fluorescence enhancement and effective quenching in the pH ranges of 3.0-10.0 and 10.0-12.0, respectively. While the emission at 500 nm increased gradually with increasing pH from 3.0 to 12.0. Two linear relationships were obtained between the synchronous fluorescence intensity ratio and pH in the ranges of 7.0-9.5 and 10.0-12.0 with a △pH of 0.1, indicating a broad detection range and high precision. Then the Si dots were used to detect urease activity via urea hydrolysis-mediated pH changes. A linear range of 1-80 U/L was established with a detection limit of 0.28 U/L. Furthermore, the Si dots were used for pH imaging in living HeLa cells. The cells changed from green to blue when the pH of HeLa cells increased from 6.0 to 10.0.

SIGNIFICANCE

These findings collectively suggest that the intrinsic dual-emitting Si dots may offer a simple and versatile platform for developing pH-relevant biosensors and bioimaging applications. Additionally, this approach provides reliable methods for preparing intrinsic dual-emitting probe and constructing fluorescence ratiometrics, which widely used in health status assessment.

Rapid microfluidic perfusion system enables controlling dynamics of intracellular pH regulated by Na+/H+ exchanger NHE1

pH regulation of eukaryotic cells is of crucial importance and influences different mechanisms including chemical kinetics, buffer effects, metabolic activity, membrane transport and cell shape parameters. In this study, we develop a microfluidic system to rapidly and precisely control a continuous flow of ionic chemical species to acutely challenge the intracellular pH regulation mechanisms and confront predictive models. We monitor the intracellular pH dynamics in real-time using pH-sensitive fluorescence imaging and establish a robust mathematical tool to translate the fluorescence signals to pH values. By varying flow rate across the cells and duration for the rinsing process, we manage to tweak the dynamics of intracellular pH from a smooth recovery to either an overshooting state, where the pH goes excitedly to a maximum value before decreasing to a plateau, or an undershooting state, where the pH is unable to recover to ∼7. We believe our findings will provide more insight into intracellular regulatory mechanisms and promote the possibility of exploring cellular behavior in the presence of strong gradients or fast changes in homogeneous conditions.

Topical delivery of siRNA to psoriatic skin model using high molecular weight chitosan derivatives: In vitro and in vivo studies

Psoriasis is a chronic inflammatory skin disease that, like other immune-mediated conditions, may benefit from small interfering RNA (siRNA)-based therapies, which are emerging as a promising alternative by addressing several limitations of current treatments. In this study, topical formulations of chitosan-based vectors were developed to deliver siRNA targeting tumor necrosis factor alpha (TNFα) to inflamed skin. Grafting diisopropylethylamine (DIPEA) and polyethylene glycol (PEG) onto the chitosan backbone enhanced siRNA delivery efficiency under physiological conditions, forming robust polymeric vectors with high structural and colloidal stability. These vectors provided siRNA protection against RNAse degradation and oxidative damage. Additionally, the chitosan derivatives displayed lysozyme-mediated biodegradability comparable to native chitosan, while PEG was released in response to reductive environments, supporting controlled vector disassembly. The PEGylated DIPEA-chitosan/siRNA polyplexes demonstrated positive zeta potentials (up to + 11 mV), particle sizes of 100-200 nm, and very low cytotoxicity in keratinocyte and fibroblast cell lines. In vitro, the polyplexes achieved TNFα knockdown levels (65%) in RAW macrophages, comparable to those obtained with Lipofectamine™. Topical formulations showed enhanced interaction of vectors with skin models (Strat-M® and porcine ear skin) compared to naked siRNA. Furthermore, in vivo studies indicated that hair follicles were a key route for polyplexes to penetrate deeper skin layers. A rodent model of psoriasis induced by imiquimod was treated topically with these vectors, resulting in approximately a 50% reduction in TNFα levels at inflammation sites, decreased immune cell infiltration, and preservation of epidermal structure. These findings collectively underscore the potential of DIPEA-chitosan-based vectors for topical siRNA-based therapies.

Histidine improves flesh quality: An assessment of grass carp (Ctenopharyngodon idella) muscle in terms of texture, nutritional value and flavor

The texture, nutritional value, and flavor quality of muscle significantly contribute to the flesh quality. To investigate the beneficial impacts of histidine on the flesh quality of grass carp (Ctenopharyngodon idella), a 63-day feeding trial was conducted using six diets containing histidine at concentrations of 1.08 (control diet), 2.91, 5.87, 8.83, 11.78, and 14.79 g/kg. The findings indicated that histidine mitigated the rapid decline in pH, potentially correlated with elevated carnosine and expression of H+ transporters. Notably, our study is the first to suggest that histidine supplementation may enhance fish flesh hardness by promoting collagen synthesis and inhibiting collagen degradation. Furthermore, histidine supplementation enhanced the nutritional and flavor quality of flesh by altering the fatty acid and free amino acid profiles. Based on pH24h (muscle pH at 24 h post-slaughter) and shear force, the dietary histidine requirements for adult grass carp were 8.09 and 8.44 g/kg, respectively.

Sodium Proton Exchanger NHE9 pHine-Tunes Exosome Production by Impairing Rab7 Activity

Cell-to-cell communication is mediated by vesicles ranging from 30 to 150 nanometers, known as exosomes. These exosomes shuttle bioactive molecules such as proteins, lipids, and nucleic acids, thus playing crucial roles in both health and disease mechanisms. Exosomes form within the endocytic pathway through the process of inward budding of the endosomal membrane, facilitated by the progressive acidification of the endosomal lumen. Although endosomal pH is known to be critical for exosome production, the precise molecular mechanisms involved remain poorly defined. Maintaining optimal endosomal pH involves meticulous coordination between proton pumping and leakage mechanisms. The sodium-proton exchanger NHE9, located on the endosomal membrane, modulates endosomal pH by transporting protons out of the endosomes in exchange for sodium or potassium ions. Here, we use genetic engineering, biochemistry, and advanced microscopy to demonstrate that the sodium-proton exchanger NHE9 significantly affects exosome production by regulating endosomal pH. NHE9-mediated endosomal alkalization impairs Rab7 activation, thereby disrupting the delivery of multivesicular endosomes (MVEs) to lysosomes. Moreover, luminal alkalization promotes the recruitment of Rab27b. This enhances the targeting of MVEs to the cell periphery, their fusion with the plasma membrane, and subsequent exosome secretion. Our findings reveal the detailed molecular mechanisms through which endosomal pH regulates exosome production. Additionally, we identify NHE9 as a potential target for therapeutic strategies aimed at controlling exosome dynamics.

Spatiotemporal generation of alternating disparate pH domains via audible sound controlled opposing enzymatic reactions

Intracellular spatiotemporal chemical heterogeneities with controlled properties are essential for life. However, creating these heterogeneities artificially is challenging. In this study, we used both acid- and base-producing enzymatic reactions simultaneously and demonstrated that the execution of these reactions in the presence of audible sound can effectively create spatiotemporally ordered pH domains in a solution.

pH-Controlled DNA Switching Circuits with Multi-State Responsiveness for Logic Computation and Control

Dynamic control of DNA circuit functionality is essential for constructing chemical reaction networks (CRNs) that implement complex functions. The triplex has been utilized for dynamically regulating the diverse functionalities of DNA circuits due to its distinctive pH responsiveness. However, it is challenging for triplexes to independently regulate the functionality of DNA circuits, as various triplexes were often required for DNA circuits to function in complex environments, which adds complexity to the design and control of dynamic circuits. Here, we proposed a pH-controlled multi-state DNA switching circuit construction strategy to realize dynamic regulation among three states through conformational transitions of the triplex. In addition, by leveraging the regulatory role of multi-state DNA switching circuits on the toehold-mediated strand displacement reaction, we constructed switchable DNA circuits for logic computation and control of hybridization chain reaction (HCR). We confirmed that the designed DNA switching circuits exhibited multi-state responsiveness, allowing for different logical operations at varying pH levels and programmable control of the diverse reaction pathways in the HCR. Our strategy offers a convenient approach for the intelligent response and dynamic regulation of large-scale CRNs and DNA nanostructure self-assembly. It promises applications in biosensing, disease detection and drug delivery.

Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery

Lipid-mediated delivery of active pharmaceutical ingredients (API) opened new possibilities in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can safely deliver APIs not soluble in water, those with otherwise strong adverse effects, or very fragile ones such as nucleic acids. However, for the rational design of LNCs, a detailed understanding of the composition-structure-function relationships is missing. This review presents currently available computational methods for LNC investigation, screening, and design. The state-of-the-art physics-based approaches are described, with the focus on molecular dynamics simulations in all-atom and coarse-grained resolution. Their strengths and weaknesses are discussed, highlighting the aspects necessary for obtaining reliable results in the simulations. Furthermore, a machine learning, i.e., data-based learning, approach to the design of lipid-mediated API delivery is introduced. The data produced by the experimental and theoretical approaches provide valuable insights. Processing these data can help optimize the design of LNCs for better performance. In the final section of this Review, state-of-the-art of computer simulations of LNCs are reviewed, specifically addressing the compatibility of experimental and computational insights.

NADPH-Independent Fluorescent Probe for Live-Cell Imaging of Heme Oxygenase-1

Heme oxygenase-1 (HO-1) catalyzes heme degradation on the consumption of NADPH and molecular oxygen. As an inducible enzyme, HO-1 is highly induced in various disease states, including cancer. Currently, two fluorescent probes for HO-1 have been designed based on the catalytic activity of HO-1, in which the probes serve as a substrate, so NADPH is required to enable the detection. Probes functioning in a NADPH-dependent way may influence other NADPH-consuming pathways, as all these pathways share a common NADPH pool. Here, we report the peptide-based fluorescent probe NBD-P5 as a simple alternative approach for HO-1 sensing. The designed probe NBD-P5 functions independently of the catalytic activity of HO-1, therefore enabling fast and sensitive detection of HO-1 with no requirements of other substances, including NADPH and biliverdin reductase. Moreover, it overcomes the need for a large substrate amount and long incubation time during the detection. NBD-P5 can be quickly taken up by cells, demonstrates an excellent colocalization with the endoplasmic reticulum (where HO-1 is mainly located), and is shown to be reliable in reporting changes in HO-1 levels in live cells. This work provides a simple alternative approach for designing HO-1 fluorescent probes, and we expect it will act as a practical tool for further studying HO-1 biology.

All-in-One Photoacid Generators with Green/Red-light Responsiveness and Cooperative Functionality

Photoacid generators (PAGs) are invaluable molecular tools that exhibited tremendous potential in emerging interdisciplinary researches of life-science, nanotechnology and smart materials. However, current PAGs are primarily mono-functional in terms of acid generation and rely on UV/deep-blue light excitation, posing a fundamental hurdle to their broader adoption. Developing cooperatively functioned PAGs with long-wavelength light responsiveness presents a formidable challenge due to the absence of suitable molecular scaffolds. Here, we introduce a newly-developed perylene bisimides PAG motif (PBI-PAG) that integrates desired multi-functionality and visible-light photo-reactivity. Taking advantages of characteristic opto-electronic properties of PBI scaffold, PBI-PAGs are capable of quantitative releasing (>99 %) a palette of acids upon green/red light (560-605 nm) excitation. Concurrently, a photo-generated counterpart is functioned as a photo-sensitizer that could perform cooperatively with acid as an anti-metastasis cancer therapy agent. These two processes constitute the first example of a cooperatively functioned PAG operated at substrate-adaptive wavelengths.

Control of biomedical nanoparticle distribution and drug release in vivo by complex particle design strategies

The utilization of targeted nanoparticles as a selective drug delivery system is a powerful tool to increase the amount of active substance reaching the target site. This can increase therapeutic efficacy while reducing adverse drug effects. However, nanoparticles face several challenges: upon injection, the immediate adhesion of plasma proteins may mask targeting ligands, thereby diminishing the target cell selectivity. In addition, opsonization can lead to premature clearance and the widespread presence of receptors or enzymes limits the accuracy of target cell recognition. Nanoparticles may also suffer from endosomal entrapment, and controlled drug release can be hindered by premature burst release or insufficient particle retention at the target site. Various strategies have been developed to address these adverse events, such as the implementation of switchable particle properties, regulating the composition of the formed protein corona, or using click-chemistry based targeting approaches. This has resulted in increasingly complex particle designs, raising the question of whether this development actually improves the therapeutic efficacy in vivo. This review provides an overview of the challenges in targeted drug delivery and explores potential solutions described in the literature. Subsequently, appropriate strategies for the development of nanoparticular drug delivery concepts are discussed.

NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism

Mitochondrial metabolism requires the chaperoned import of disulfide-stabilized proteins via CHCHD4/MIA40 and its enigmatic interaction with oxidoreductase Apoptosis-inducing factor (AIF). By crystallizing human CHCHD4's AIF-interaction domain with an activated AIF dimer, we uncover how NADH allosterically configures AIF to anchor CHCHD4's β-hairpin and histidine-helix motifs to the inner mitochondrial membrane. The structure further reveals a similarity between the AIF-interaction domain and recognition sequences of CHCHD4 substrates. NMR and X-ray scattering (SAXS) solution measurements, mutational analyses, and biochemistry show that the substrate-mimicking AIF-interaction domain shields CHCHD4's redox-sensitive active site. Disrupting this shield critically activates CHCHD4 substrate affinity and chaperone activity. Regulatory-domain sequestration by NADH-activated AIF directly stimulates chaperone binding and folding, revealing how AIF mediates CHCHD4 mitochondrial import. These results establish AIF as an integral component of the metazoan disulfide relay and point to NADH-activated dimeric AIF as an organizational import center for CHCHD4 and its substrates. Importantly, AIF regulation of CHCHD4 directly links AIF's cellular NAD(H) sensing to CHCHD4 chaperone function, suggesting a mechanism to balance tissue-specific oxidative phosphorylation (OXPHOS) capacity with NADH availability.

Aggregation-induced emission-based fluorescent probes for cellular microenvironment detection

The cellular microenvironment exerts a pivotal regulatory influence on cell survival, function, and behavior. Dynamic analysis and detection of the cellular microenvironment can promptly elucidate changes in cellular microenvironmental information, uncover the pathogenesis of diseases associated with aberrant microenvironments, and aid in predicting disease risk and monitoring disease progression. Aggregation-induced emission (AIE) fluorescent molecules possess unique AIE characteristics and offer significant advantages in imaging and sensing cellular microenvironments. In this review, we present a profile of the remarkable progress achieved in utilizing AIE fluorescent molecules for detecting cellular microenvironments in recent years. We particularly focus on AIE fluorescent probes applied in imaging key parameters of the cellular microenvironment, including pH, viscosity, polarity, and temperature, as well as in analyzing critical biological components of the microenvironment, such as gas signal molecules, metal ions, redox state, and proteins. We underscore the design principles, detection mechanisms, sensing performance, and biological applications of these fluorescent probes. Furthermore, we address the current challenges confronting this field and provide prospects for the future development of AIE probes used for microenvironment detection. We trust that this review will inspire researchers to develop more precise and sensitive AIE fluorescent probes for the detection of cellular microenvironments.

Research progress of hydrogen sulfide fluorescent probes targeting organelles

Hydrogen sulfide (H2S) is implicated in numerous physiological and pathological processes in living organisms. Abnormal levels of H2S can result in various physiological disorders, highlighting the crucial need for effective identification and detection of H2S at the organellar level. Although numerous H2S fluorescent probes targeting organelles have been reported, a comprehensive review of these probes is required. This review focuses on the strategic selection of organelle-targeting groups and recognition sites for H2S fluorescent probes. This review examines H2S fluorescent probes that can specifically target lysosomes, mitochondria, endoplasmic reticulum, Golgi apparatus, and lipid droplets. These fluorescent probes have been meticulously classified and summarized based on their distinct targets, emphasizing their chemical structure, reaction mechanisms, and biological applications. We carefully designed fluorescent probes to efficiently enhance their ability to recognize target substances and exhibit significant fluorescence variations. Furthermore, we discuss the challenges inherent in the development of fluorescent probes and outline potential future directions for this exciting field.

Red Emission Carbon Nanoparticles Which Can Simultaneously Responding to Hypochlorite and pH

Multi-targets detection has obtained much attention because this sensing mode can realize the detection of multi-targets simultaneously, which is helpful for biomedical analysis. Carbon nanoparticles have attracted extensive attention due to their superior optical and chemical properties, but there are few reports about red emission carbon nanoparticles for simultaneous detection of multi-targets. In this paper, a red emission fluorescent carbon nanoparticles were prepared by 1, 2, 4-triaminobenzene dihydrochloride at room temperature. The as-prepared red emission fluorescent carbon nanoparticles exhibited strong emission peak located at 635 nm with an absolute quantum yield up to 24%. They showed excellent solubility, high photostability and good biocompatibility. Furthermore, it could sensitively and selectively response to hypochlorite and pH, thus simultaneous detection of hypochlorite and pH was achieved by combining the red emission fluorescent carbon nanoparticles with computational chemistry. The formation mechanisms of red emission fluorescent carbon nanoparticles and their response to hypochlorite and pH were investigated, respectively.

Assessment of Protective Effects of DTPA, NAC, and Taurine on Possible Cytotoxicity Induced by Individual and Combined Zinc Oxide and Copper Oxide Nanoparticles in SH-SY5Y Cells

The present study investigated the cytotoxic effects of ZnO, CuO, and mixed combinations of them on SH-SY5Y cells. For this purpose, the cells were exposed to various concentrations of these NPs alone for 24-96 h and as a mixture for 24 h. Variations in cell viability were noted. MTT results showed that ZnO and/or CuO NPs decreased cell survival by about 59% at 200 (ZnO, at 24 h) and 800 µg/ml (ZnO and/or CuO, at 72 and 96 h). When the NR assay was used, slight decreases were noted with ZnO NPs at 72 and 96 h. With CuO NPs alone and NPs in a mixture, only the highest concentrations caused 40 and 70% decreases in cell survival, respectively. Especially with NR assays, DTPA, NAC, or taurine provided marked protection. ROS levels were increased with the highest concentration of CuO NPs and with all concentrations of the mixture. The highest concentration of ZnO NPs and the lowest concentration of CuO NPs caused slight decreases in mitochondrial membrane potential levels. Additionally, increases were noted in caspase 3/7 levels with ZnO and CuO NPs alone or with a mixture of them. Intracellular calcium levels were decreased in this system. These findings demonstrated that ZnO and CuO NPs, either separately or in combination, had a modest cytotoxic effect on SH-SY5Y cells. Protection obtained with DTPA, NAC, or taurine against the cytotoxicity of these NPs and the ROS-inducing effect of CuO NPs and the NPs' mixture suggests that oxidative stress might be involved in the cytotoxicity mechanisms of these NPs.

Reference-Attached pH Nanosensor for Accurately Monitoring the Rapid Kinetics of Intracellular H+ Oscillations

Intracellular pH (pHi) is an essential indicator of cellular metabolic activity, as its transient or small shift can significantly impact cellular homeostasis and reflect the cellular events. Real-time and precise tracking of these rapid pH changes within a single living cell is therefore important. However, achieving high dynamic response performance (subsecond) pH detection inside a living cell with high accuracy remains a challenge. Here a reference-attached pH nanosensor (R-pH-nanosensor) with fast and precise pHi sensing performance is introduced. The nanosensor comprises a highly conductive H+-sensitive IrRuOx nanowire (SiC@IrRuOx NW) as the intracellular working electrode and a SiC@Ag/AgCl NW as an intracellular reference electrode (RE) to diminish the interferences arising from cell membrane potential fluctuations. This whole-inside-cell detection mode ensures that the entire potential detection circuit is located within the same cell, and the R-pH-nanosensor is able to quantify the mild acidification of cytosol and completely record the fast pH variation within a single cell. It also enables real-time potentiometric monitoring of the pHi oscillations, which synchronize with the glycolysis oscillations in cancer cells. Furthermore, the asymmetry in glycolysis oscillations wave is disclosed and the inhibitory effect of just lactate to glycolysis oscillations is further confirmed.

Impaired hippocampal plasticity associated with loss of recycling endosomal SLC9A6/NHE6 is ameliorated by the TrkB agonist 7,8-dihydroxyflavone

Proper maintenance of intracellular vesicular pH is essential for cargo trafficking during synaptic function and plasticity. Mutations in the SLC9A6 gene encoding the recycling endosomal pH regulator (Na+, K+)/H+ exchanger isoform 6 (NHE6) are causal for Christianson syndrome (CS), a severe form of X-linked intellectual disability. NHE6 expression is also downregulated in other neurodevelopmental and neurodegenerative disorders, such as autism spectrum disorder and Alzheimer's disease, suggesting its dysfunction could contribute more broadly to the pathophysiology of other neurological conditions. To understand how ablation of NHE6 function leads to severe learning impairments, we assessed synaptic structure, function, and cellular mechanisms of learning in a novel line of Nhe6 knockout (KO) mice expressing a plasma membrane-tethered green fluorescent protein within hippocampal neurons. We uncovered significant reductions in dendritic spines density, AMPA receptor (AMPAR) expression, and AMPAR-mediated neurotransmission in CA1 pyramidal neurons. The neurons also failed to undergo functional and structural enhancement during long-term potentiation (LTP). Significantly, the selective TrkB agonist 7,8-dihydroxyflavone restored spine density as well as functional and structural LTP in KO neurons. TrkB activation thus may act as a potential clinical intervention to ameliorate cognitive deficits in CS and other neurodegenerative disorders.

Malate initiates a proton-sensing pathway essential for pH regulation of inflammation

Metabolites can double as a signaling modality that initiates physiological adaptations. Metabolism, a chemical language encoding biological information, has been recognized as a powerful principle directing inflammatory responses. Cytosolic pH is a regulator of inflammatory response in macrophages. Here, we found that L-malate exerts anti-inflammatory effect via BiP-IRF2BP2 signaling, which is a sensor of cytosolic pH in macrophages. First, L-malate, a TCA intermediate upregulated in pro-inflammatory macrophages, was identified as a potent anti-inflammatory metabolite through initial screening. Subsequent screening with DARTS and MS led to the isolation of L-malate-BiP binding. Further screening through protein‒protein interaction microarrays identified a L-malate-restrained coupling of BiP with IRF2BP2, a known anti-inflammatory protein. Interestingly, pH reduction, which promotes carboxyl protonation of L-malate, facilitates L-malate and carboxylate analogues such as succinate to bind BiP, and disrupt BiP-IRF2BP2 interaction in a carboxyl-dependent manner. Both L-malate and acidification inhibit BiP-IRF2BP2 interaction, and protect IRF2BP2 from BiP-driven degradation in macrophages. Furthermore, both in vitro and in vivo, BiP-IRF2BP2 signal is required for effects of both L-malate and pH on inflammatory responses. These findings reveal a previously unrecognized, proton/carboxylate dual sensing pathway wherein pH and L-malate regulate inflammatory responses, indicating the role of certain carboxylate metabolites as adaptors in the proton biosensing by interactions between macromolecules.

Imaging phenotype reveals that disulfirams induce protein insolubility in the mitochondrial matrix

The cell painting assay is useful for understanding cellular phenotypic changes and drug effects. To identify other aspects of well-known chemicals, we screened 258 compounds with the cell painting assay and focused on a mitochondrial punctate phenotype seen with disulfiram. To elucidate the reason for this punctate phenotype, we looked for clues by examining staining steps and gene knockdown as well as examining protein solubility and comparing cell lines. From these results, we found that the punctate phenotype was caused by protein insolubility in the mitochondrial matrix. Interestingly, the punctate phenotype of disulfiram was sensitive to the relative expression of LonP1, a protease in the mitochondrial matrix that regulates proteostasis, suggesting that the punctate phenotype manifests when the protein quality control capacity in the mitochondrial matrix is exceeded. Moreover, we discovered that disulfiram and its derivatives, which have all been reported to increase acetaldehyde in the blood after the in vivo intake of alcohol, induced a punctate phenotype as well. The investigated punctate phenotype not only provides a novel clue for elucidating the common mechanism of action among disulfiram derivatives but is also a novel example of chemical perturbation of proteostasis in the mitochondrial matrix.

Development and characterization of fluorescent cholesteryl probes with enhanced solvatochromic and pH-sensitive properties for live-cell imaging

We present novel fluorescent cholesteryl probes (CNDs) with a modular design based on the solvatochromic 1,8-phthalimide scaffold. We have explored how different modules-linkers and head groups-affect the ability of these probes to integrate into lipid membranes and how they distribute intracellularly in mouse astrocytes and fibroblasts targeting lysosomes and lipid droplets. Each compound was assessed for its solvatochromic behavior in organic solvents and model membranes. Molecular dynamics simulations and lipid partitioning using giant unilamellar vesicles showed how these analogs behave in model membranes compared to cholesterol. Live-cell imaging demonstrated distinct staining patterns and cellular uptake behaviors, further validating the utility of these probes in biological systems. We compared the empirical results with those of BODIPY-cholesterol, a well-regarded fluorescent cholesterol analog. The internalization efficiency of fluorescent CND probes varies in different cell types and is affected mainly by the head groups. Our results demonstrate that the modular design significantly simplifies the creation of fluorescent cholesteryl probes bearing distinct spectral, biophysical, and cellular targeting features. It is a valuable toolkit for imaging in live cells, measuring cellular membrane dynamics, and studying cholesterol-related processes.

Cytoskeletal activation of NHE1 regulates mechanosensitive cell volume adaptation and proliferation

Mammalian cells rapidly respond to environmental changes by altering transmembrane water and ion fluxes, changing cell volume. Contractile forces generated by actomyosin have been proposed to mechanically regulate cell volume. However, our findings reveal a different mechanism in adherent cells, where elevated actomyosin activity increases cell volume in normal-like cells (NIH 3T3 and others) through interaction with the sodium-hydrogen exchanger isoform 1 (NHE1). This leads to a slow secondary volume increase (SVI) following the initial regulatory volume decrease during hypotonic shock. The active cell response is further confirmed by intracellular alkalinization during mechanical stretch. Moreover, cytoskeletal activation of NHE1 during SVI deforms the nucleus, causing immediate transcriptomic changes and ERK-dependent growth inhibition. Notably, SVI and its associated changes are absent in many cancer cell lines or cells on compliant substrates with reduced actomyosin activity. Thus, actomyosin acts as a sensory element rather than a force generator during adaptation to environmental challenges.

Expression of Drosophila melanogaster V-ATPases in Olfactory Sensillum Support Cells

V-ATPases are ubiquitous and evolutionarily conserved rotatory proton pumps, which are crucial for maintaining various biological functions. Previous investigations have shown that a V-ATPase is present in the support cells of moth trichoid sensilla and influences their olfactory sensory neuron performance. Generally, V-ATPases are thought to regulate the pH value within the sensillum lymph, and aid K+ homeostasis within the sensillum. This, in turn, could influence various mechanisms involved within the support cells, like maintaining the receptor membrane potential (receptor current), nutrient and ion transport, odorant solubility, and various signaling mechanisms. In this study, we identify V-ATPase expression and localization in the Drosophila melanogaster antenna using bioinformatics and immunohistochemistry. Elucidating an olfactory V-ATPase function will improve our current understanding of how support cells contribute to Drosophila's sense of smell.

Golgi pH elevation due to loss of V-ATPase subunit V0a2 function correlates with tissue-specific glycosylation changes and globozoospermia

Loss-of-function variants in ATP6V0A2, encoding the trans Golgi V-ATPase subunit V0a2, cause wrinkly skin syndrome (WSS), a connective tissue disorder with glycosylation defects and aberrant cortical neuron migration. We used knock-out (Atp6v0a2-/-) and knock-in (Atp6v0a2RQ/RQ) mice harboring the R755Q missense mutation selectively abolishing V0a2-mediated proton transport to investigate the WSS pathomechanism. Homozygous mutants from both strains displayed a reduction of growth, dermis thickness, and elastic fiber formation compatible with WSS. A hitherto unrecognized male infertility due to globozoospermia was evident in both mouse lines with impaired Golgi-derived acrosome formation and abolished mucin-type O-glycosylation in spermatids. Atp6v0a2-/- mutants showed enhanced fucosylation and glycosaminoglycan modification, but reduced levels of glycanated decorin and sialylation in skin and/or fibroblasts, which were absent or milder in Atp6v0a2RQ/RQ. Atp6v0a2RQ/RQ mutants displayed more abnormal migration of cortical neurons, correlating with seizures and a reduced O-mannosylation of α-dystroglycan. While anterograde transport within the secretory pathway was similarly delayed in both mutants the brefeldin A-induced retrograde fusion of Golgi membranes with the endoplasmic reticulum was less impaired in Atp6v0a2RQ/RQ. Measurement of the pH in the trans Golgi compartment revealed a shift from 5.80 in wildtype to 6.52 in Atp6v0a2-/- and 6.25 in Atp6v0a2RQ/RQ. Our findings suggest that altered O-glycosylation is more relevant for the WSS pathomechanism than N-glycosylation and leads to a secondary dystroglycanopathy. Most phenotypic and cellular properties correlate with the different degrees of trans Golgi pH elevation in both mutants underlining the fundamental relevance of pH regulation in the secretory pathway.

Synthesis, optical properties, and two-photon bioimaging evaluation of novel fluorescent cationic molecules with symmetrical long conjugated all-trans structures

Five novel fluorescent molecules (PPy, BOPPy, CNPPy, BPPy, and BPIm), which possess symmetrical long conjugated all-trans structures and are capped with hydroxyethyl-bonded pyridinium or benzimidazolium cations, were designed, synthesized, and characterized by 1H NMR, 13C NMR, and HRMS. The systematic investigations of their linear and nonlinear optical properties in different solvents indicate that all the target compounds exhibit large Stokes shifts (71-152 nm) and four of them (PPy, CNPPy, BPPy, and BPIm) have satisfactory two-photon action cross-sections (45.2-112.4 GM in DMSO). The fluorescence stability experiments reveal that their fluorescence emission is insensitive within the biologically relevant pH range of 4.0-8.0, which may enable applications in vivo to be possible. Cytotoxicity assessments, together with one- and two-photon excited fluorescence imaging studies in live cells were performed to evaluate their application values in bioimaging. It is found that PPy is not only endowed with low cytotoxicity and good cell membrane permeability, but also shows bright intracellular fluorescence signals. The high comprehensive performance enables PPy to have a promising application prospect in living cell imaging.

Repurposing an epithelial sodium channel inhibitor as a therapy for murine and human skin inflammation

Inflammatory skin disease is characterized by a pathologic interplay between skin cells and immunocytes and can result in disfiguring cutaneous lesions and systemic inflammation. Immunosuppression is commonly used to target the inflammatory component; however, these drugs are often expensive and associated with side effects. To identify previously unidentified targets, we carried out a nonbiased informatics screen to identify drug compounds with an inverse transcriptional signature to keratinocyte inflammatory signals. Using psoriasis, a prototypic inflammatory skin disease, as a model, we used pharmacologic, transcriptomic, and proteomic characterization to find that benzamil, the benzyl derivative of the US Food and Drug Administration-approved diuretic amiloride, effectively reversed keratinocyte-driven inflammatory signaling. Through three independent mouse models of skin inflammation (Rac1G12V transgenic mice, topical imiquimod, and human skin xenografts from patients with psoriasis), we found that benzamil disrupted pathogenic interactions between the small GTPase Rac1 and its adaptor NCK1. This reduced STAT3 and NF-κB signaling and downstream cytokine production in keratinocytes. Genetic knockdown of sodium channels or pharmacological inhibition by benzamil prevented excess Rac1-NCK1 binding and limited proinflammatory signaling pathway activation in patient-derived keratinocytes without systemic immunosuppression. Both systemic and topical applications of benzamil were efficacious, suggesting that it may be a potential therapeutic avenue for treating skin inflammation.

Facile synthesis of long-wavelength emission carbon dots for hypochlorite sensing and intracellular pH imaging

Hypochlorite (ClO-), a typical reactive oxygen species, plays an irreplaceable roles in various biological processes. In this work, long-wavelength emission carbon dots (LW-CDs) were fabricated through one-step hydrothermal method by using l-cysteine (cys) and neutral red (NR) as precursors for monitoring of hypochlorite and intracellular pH. Characterizations of as-prepared LW-CDs showed that they had excellent water solubility, high optical stability and sensitive response behavior. Fluorescence intensity of LW-CDs decayed in the presence of ClO- linearly from 10 to 162.5 μM (LOD = 1.021 μM) based on static quenching effect with ideal selectivity. Besides, LW-CDs revealed a pH responsive behavior in the pH range of 2.0 to 10.0, exhibited dual good linear relationships in the pH ranges of 4.2-5.8 and 5.8-7.4. The LW-CDs can also be utilized as imaging reagents in Hela living cells owing excellent biocompatibility and low cytotoxicity. These results demonstrated that the as-mentioned LW-CDs are expected to serve as excellent long wavelength emitting nanomaterials for fluorescence sensing and monitoring of cell fluctuations.

Dissecting the pH Sensitivity of Kinesin-Driven Transport

Kinesin-1 is a crucial motor protein that drives the microtubule-based movement of organelles, vital for cellular function and health. Mostly studied at pH 6.9, it moves at approximately 800 nm/s, covers about 1 μm before detaching, and hydrolyzes one ATP per 8 nm step. Given that cellular pH is dynamic and alterations in pH have significant implications for disease, understanding how kinesin-1 functions across different pH levels is crucial. To explore this, we executed single-molecule motility assays paired with precise optical trapping techniques over a pH range of 5.5-9.8. Our results show a consistent positive relationship between increasing pH and the enhanced detachment (off rate) and speed of kinesin-1. Measurements of the nucleotide-dependent off rate show that kinesin-1 exhibits the highest rate of ATPase activity at alkaline pH, while it demonstrates the optimal number of ATP turnover and cargo translocation efficiency at the acidic pH. Physiological pH of 6.9 optimally balances the biophysical activity of kinesin-1, potentially allowing it to function effectively across a range of pH levels. These insights emphasize the crucial role of pH homeostasis in cellular function, highlighting its importance for the precise regulation of motor proteins and efficient intracellular transport.

Contrasting species-specific stress response to environmental pH determines the fate of coccolithophores in future oceans

Molecular mechanisms driving species-specific environmental sensitivity in coccolithophores are unclear but crucial in understanding species selection and adaptation to environmental change. This study examined proteomic and physiological changes in three species under varying pH conditions. We showed that changing pH drives intracellular oxidative stress and changes membrane potential. Upregulation in antioxidant, DNA repair and cell cycle-related protein-groups indicated oxidative damage across high (pH 8.8) and low pH (pH 7.6) compared to control pH (pH 8.2), and correlated with reduced growth rates. Upregulation of mitochondrial proteins suggested higher metabolite demand for restoring cellular homeostasis under pH-induced stress. Photosynthetic rates generally correlated with CO2 availability, driving higher net carbon fixation rates at low pH. The intracellular pH-buffering capacity of the coastal Chrysotila carterae and high metabolic adaptability in the bloom-forming Gephyrocapsa huxleyi will likely facilitate their adaptation to ocean acidification or artificial ocean alkalinisation. However, the pH sensitivity of the ancient open-ocean Coccolithus braarudii will possibly result in reduced growth and shrinking of its ecological niche.

Phosphorylation of cytochrome c at tyrosine 48 finely regulates its binding to the histone chaperone SET/TAF-Iβ in the nucleus

Post-translational modifications (PTMs) of proteins are ubiquitous processes present in all life kingdoms, involved in the regulation of protein stability, subcellular location and activity. In this context, cytochrome c (Cc) is an excellent case study to analyze the structural and functional changes induced by PTMS as Cc is a small, moonlighting protein playing different roles in different cell compartments at different cell-cycle stages. Cc is actually a key component of the mitochondrial electron transport chain (ETC) under homeostatic conditions but is translocated to the cytoplasm and even the nucleus under apoptotic conditions and/or DNA damage. Phosphorylation does specifically alter the Cc redox activity in the mitochondria and the Cc non-redox interaction with apoptosis-related targets in the cytoplasm. However, little is known on how phosphorylation alters the interaction of Cc with histone chaperones in the nucleus. Here, we report the effect of Cc Tyr48 phosphorylation by examining the protein interaction with SET/TAF-Iβ in the nuclear compartment using a combination of molecular dynamics simulations, biophysical and structural approaches such as isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR) and in cell proximity ligation assays. From these experiments, we infer that Tyr48 phosphorylation allows a fine-tuning of the Cc-mediated inhibition of SET/TAF-Iβ histone chaperone activity in vitro. Our findings likewise reveal that phosphorylation impacts the nuclear, stress-responsive functions of Cc, and provide an experimental framework to explore novel aspects of Cc post-translational regulation in the nucleus.

Unlocking Intracellular Protein Delivery by Harnessing Polymersomes Synthesized at Microliter Volumes using Photo-PISA

Efficient delivery of therapeutic proteins and vaccine antigens to intracellular targets is challenging due to generally poor cell membrane permeation and endolysosomal entrapment causing degradation. Herein, these challenges are addressed by developing an oxygen-tolerant photoinitiated polymerization-induced self-assembly (Photo-PISA) process, allowing for the microliter-scale (10 µL) synthesis of protein-loaded polymersomes directly in 1536-well plates. High-resolution techniques capable of analysis at a single particle level are employed to analyze protein encapsulation and release mechanisms. Using confocal microscopy and super-resolution stochastic optical reconstruction microscopy (STORM) imaging, their ability to deliver proteins into the cytosol following endosomal escape is subsequently visualized. Lastly, the adaptability of these polymersomes is exploited to encapsulate and deliver a prototype vaccine antigen, demonstrating its ability to activate antigen-presenting cells and support antigen cross-presentation for applications in subunit vaccines and cancer immunotherapy. This combination of ultralow volume synthesis and efficient intracellular delivery holds significant promise for unlocking the high throughput screening of a broad range of otherwise cost-prohibitive or early-stage therapeutic protein and vaccine antigen candidates that can be difficult to obtain in large quantities. The versatility of this platform for rapid screening of intracellular protein delivery can result in significant advancements across the fields of nanomedicine and biomedical engineering.

Measuring cerebral enzymatic activity, brain pH and extracranial muscle metabolism with hyperpolarized 13C-pyruvate

Hyperpolarized carbon-13 (13C) magnetic resonance imaging (MRI) has shown promise for non-invasive assessment of the cerebral metabolism of [1-13C]pyruvate in both healthy volunteers and patients. The exchange of pyruvate to lactate catalysed by lactate dehydrogenase (LDH) and that of pyruvate flux to bicarbonate through pyruvate dehydrogenase (PDH) are the most widely studied reactions in vivo. Here we show the potential of the technique to probe additional enzymatic activity within the brain. Approximately 50 s after intravenous injection of hyperpolarized pyruvate, high-flip-angle pulses were used to detect cerebral 13C-labelled carbon dioxide (13CO2), in addition to the 13C-bicarbonate (H13CO3 -) subsequently formed by carbonic anhydrase (CA). Brain pH measurements, which were weighted towards the extracellular compartment, were calculated from the ratio of H13CO3 - to 13CO2 in seven volunteers using the Henderson-Hasselbalch equation, demonstrating an average pH ± SD of 7.40 ± 0.02, with inter-observer reproducibility of 0.04. In addition, hyperpolarized [1-13C]aspartate was also detected, demonstrating irreversible pyruvate carboxylation to oxaloacetate by pyruvate carboxylase (PC) and subsequent transamination by aspartate aminotransferase (AST), with the average flux being on average 11% ± 3% of that through PDH. A hyperpolarized [1-13C]alanine signal was also detected, but this was localized to extracranial muscle tissue in keeping with skeletal alanine aminotransferase (ALT) activity. The results demonstrate the potential of hyperpolarized 13C-MRI to assess cerebral and extracerebral [1-13C]pyruvate metabolism in addition to LDH and PDH activity. Non-invasive measurements of brain pH could be particularly important in assessing cerebral pathology given the wide range of disease processes that alter acid-base balance.

The role of ATP6V0D2 in breast cancer: associations with prognosis, immune characteristics, and TNBC progression

Objective

Researches have identified ATPase H+ transporting V0 subunit d2 (ATP6V0D2) as a significant factor in various cancers. However, its prognostic value in breast cancer (BRCA) and its biological role in BRCA cells remain unclear.

Methods

In this research, we examined the varying expression levels of ATP6V0D2 in both BRCA and normal breast tissue by utilizing information derived from databases including the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO), along with clinical samples. Survival studies were carried out to investigate the link between ATP6V0D2 levels and prognosis in BRCA patients. A series of enrichment analyses identified possible pathways associated with the differentially expressed genes in BRCA. The relationships among ATP6V0D2 expression, immune characteristics, and gene mutation were evaluated using Spearman's test. Finally, the expression of ATP6V0D2 was identified by quantitative real-time polymerase chain reaction (RT-qPCR) alongside western blot analysis. Additionally, Cell Counting kit-8 (CCK-8), Colony formation, Transwell, Scratch healing, and Mouse xenograft tumor assays were conducted to assessed the impact of ATP6V0D2 knockdown on the biological functions in TNBC.

Results

ATP6V0D2 exhibited high expression in a range of cancers and correlated with unfavorable prognosis in BRCA. Functional enrichment analyses revealed enrichment of extracellular matrix-receptor interaction, focal adhesion, and the signaling pathway of tumor growth factor-beta in the high ATP6V0D2 expression group. Additionally, ATP6V0D2 was closely associated with immune checkpoints. Its expression positively associated with the infiltration levels of macrophage and neutrophil, but inversely with CD8+ T and plasmacytoid dendritic cells. Mutation analysis revealed that PIK3CA, linked to decreased OS, exhibited a higher mutation rate in the ATP6V0D2 high expression group. Furthermore, ATP6V0D2 knockdown inhibited TNBC cells invasion, migration, and proliferation abilities.

Conclusion

ATP6V0D2 acts as a promising indicator for both diagnosis and prediction of outcomes in breast cancer and could potentially be a novel therapeutic target for BRCA.

GPR180 is a new member of the Golgi-dynamics domain seven-transmembrane helix protein family

GOLD domain seven-transmembrane helix (GOST) proteins form a new protein family involved in trafficking of membrane-associated cargo. They share a characteristic extracellular/luminal Golgi-dynamics (GOLD) domain, possibly responsible for ligand recognition. Based on structural homology, GPR180 is a new member of this protein family, but little is known about the cellular role of GPR180. Here we show the X-ray structure of the N-terminal domain of GPR180 (1.9 Å) and can confirm the homology to GOLD domains. Using cellular imaging we show the localization of GPR180 in intracellular vesicular structures implying its exposure to acidic pH environments. With Hydrogen/Deuterium Exchange-Mass Spectrometry (HDX-MS) we identify pH-dependent conformational changes, which can be mapped to a putative ligand binding site in the transmembrane region. The results reveal GPR180's role in intracellular vesicles and offer insights into the pH-dependent function of this conserved GOST protein.

Excitation-Dependent pKa Extends the Sensing Range of Fluorescence Lifetime pH Sensors

Biological activity is strongly dependent on pH, which fluctuates within a variety of neutral, alkaline, and acidic local environments. The heterogeneity of tissue and subcellular pH has driven the development of sensors with different pKa values, and a huge assortment of fluorescent sensors have been created to measure and visualize pH in living cells and tissues. In particular, sensors that report based on fluorescence lifetime are advantageous for quantitation. Here, we apply a theoretical framework to derive how the apparent pKa of lifetime-based pH sensors depends on fluorescence excitation wavelength. We demonstrate that theory predicts the behavior of two different fluorescent protein-based pH sensors in solution as proofs-of-concept. Furthermore, we show that this behavior has great practical value in living cells because it extends the sensing range of a single sensor by simply choosing appropriate detection parameters to match the physiological pH range of interest. More broadly, our results show that the versatility of a single lifetime-based sensor has been significantly underappreciated, and our approach provides a means to use a single sensor across a range of pH environments.

Construction of a Dataset for All Expressed Transcripts for Alzheimer's Disease Research

Accurate identification and functional annotation of splicing isoforms and non-coding RNAs (lncRNAs), alongside full-length protein-encoding transcripts, are critical for understanding gene (mis)regulation and metabolic reprogramming in Alzheimer's disease (AD). This study aims to provide a comprehensive and accurate transcriptome resource to improve existing AD transcript databases. Background/Objectives: Gene mis-regulation and metabolic reprogramming play a key role in AD, yet existing transcript databases lack accurate and comprehensive identification of splicing isoforms and lncRNAs. This study aims to generate a refined transcriptome dataset, expanding the understanding of AD onset and progression. Methods: Publicly available RNA-seq data from pre-AD and AD tissues were utilized. Advanced bioinformatics tools were applied to assemble and annotate full-length transcripts, including splicing isoforms and lncRNAs, with an emphasis on correcting errors and enhancing annotation accuracy. Results: A significantly improved transcriptome dataset was generated, which includes detailed annotations of splicing isoforms and lncRNAs. This dataset expands the scope of existing AD transcript databases and provides new insights into the molecular mechanisms underlying AD. The findings demonstrate that the refined dataset captures more relevant details about AD progression compared to publicly available data. Conclusions: The newly developed transcriptome resource and the associated analysis tools offer a valuable contribution to AD research, providing deeper insights into the disease's molecular mechanisms. This work supports future research into gene regulation and metabolic reprogramming in AD and serves as a foundation for exploring novel therapeutic targets.

Harnessing microbial heterogeneity for improved biosynthesis fueled by synthetic biology

Metabolic engineering-driven microbial cell factories have made great progress in the efficient bioproduction of biochemical and recombinant proteins. However, the low efficiency and robustness of microbial cell factories limit their industrial applications. Harnessing microbial heterogeneity contributes to solving this. In this review, the origins of microbial heterogeneity and its effects on biosynthesis are first summarized. Synthetic biology-driven tools and strategies that can be used to improve biosynthesis by increasing and reducing microbial heterogeneity are then systematically summarized. Next, novel single-cell technologies available for unraveling microbial heterogeneity and facilitating heterogeneity regulation are discussed. Furthermore, a combined workflow of increasing genetic heterogeneity in the strain-building step to help in screening highly productive strains - reducing heterogeneity in the production process to obtain highly robust strains (IHP-RHR) facilitated by single-cell technologies was proposed to obtain highly productive and robust strains by harnessing microbial heterogeneity. Finally, the prospects and future challenges are discussed.

Arginine Accelerates Sulfur Fluoride Exchange and Phosphorus Fluoride Exchange Reactions between Proteins

Sulfur fluoride exchange (SuFEx) and phosphorus fluoride exchange (PFEx) click chemistries are advancing research across multiple disciplines. By genetically incorporating latent bioreactive unnatural amino acids (Uaas), these chemistries have been integrated into proteins, enabling precise covalent linkages with biological macromolecules and paving the way for new applications. However, their suboptimal reaction rates in proteins limit effectiveness, and traditional catalytic methods for small molecules are often incompatible with biological systems or in vivo applications. We demonstrated that introducing an arginine adjacent to the latent bioreactive Uaa significantly boosts SuFEx and PFEx reaction rates between proteins. This method is effective across various Uaas, target residues, and protein environments. Notably, it also enables efficient SuFEx reactions in acidic conditions, common in certain cellular compartments and tumor microenvironments, which typically hinder SuFEx reactions. Furthermore, we developed the first covalent cell engager that substantially enhances natural killer cell activation through improved covalent interaction facilitated by arginine. These findings provide mechanistic insights and offer a biocompatible strategy to harness these robust chemistries for advancing biological research and developing new biotherapeutics.

Mapping Endocytic Vesicular Acidification with a pH-Responsive DNA Nanomachine

Mapping the endocytic vesicular acidification process is of prior importance to better understand the health and pathological processes of cells. Herein, by integrating a pH-sensitive i-motif and a pair of fluorescence resonance energy transfer (FRET) into a tetrahedral DNA framework (TDF), we develop a pH-responsive DNA nanomachine, allowing for efficient sensing of pH from 7.0 to 5.5 via the pH-triggered spatial proximity modulation of FRET. The inheriting endo-lysosome-targeting ability of TDF enables spatiotemporal tracking of endocytic vesicle acidification during the endosomal maturation process. Analysis of pH-dependent FRET response at single fluorescent spot level reveals the significant difference of endocytic vesicular acidification between normal and cancer cells. The performance of pH-responsive DNA nanomachine underlines its potential for studies on vesicle acidification-related pathologies as a universal platform.

pH Sensitivity of YFPs is Reduced Upon AlphaRep Binding: Proof of Concept in Vitro and in Living Cells

Yellow fluorescent proteins (YFPs) are commonly used in biology to track cellular processes, particularly as acceptors in experiments using the Förster Resonant Energy Transfer (FRET) phenomenon. However, their fluorescence intensity is strongly pH-dependent, limiting their utility in acidic environments. Here, we explore the pH sensitivity of YFPs upon binding with an artificial repeat protein (αRep) both in vitro and in living cells. We show that αRep binds to Citrine, with high affinity in the nanomolar range at physiological and acidic pHs, leading to increased thermal stability of the complex. Moreover, αRep binding reduces Citrine's pKa by 0.75 pH units, leading to a decreased sensitivity to pH fluctuations. This effect can be generalized to other YFPs as Venus and EYFP in vitro. An efficient binding of αRep to Citrine has also been observed in living cells both at pH 7.4 and pH 6. This interaction leads to reduced variations of Citrine fluorescence intensity in response to pH variations in cells. Overall, the study highlights the potential of αReps as a tool to modulate the pH sensitivity of YFPs, paving the way for future exploration of biological events in acidic environments by FRET in combination with a pH-insensitive cyan donor.

Acidic proteomes are linked to microbial alkaline preference in African lakes

Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphiles. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies for environmental adaptation.

The vacuolar K+/H+ exchangers and calmodulin-like CML18 constitute a pH-sensing module that regulates K+ status in Arabidopsis

Shifts in cytosolic pH have been recognized as key signaling events and mounting evidence supports the interdependence between H+ and Ca2+ signaling in eukaryotic cells. Among the cellular pH-stats, K+/H+ exchange at various membranes is paramount in plant cells. Vacuolar K+/H+ exchangers of the NHX (Na+,K+/H+ exchanger) family control luminal pH and, together with K+ and H+ transporters at the plasma membrane, have been suggested to also regulate cytoplasmic pH. We show the regulation of vacuolar K+/H+ exchange by cytoplasmic pH and the calmodulin-like protein CML18 in Arabidopsis. The crystal structure and physicochemical properties of CML18 indicate that this protein senses pH shifts. Interaction of CML18 with tonoplast exchangers NHX1 and NHX2 was favored at acidic pH, a physiological condition elicited by K+ starvation in Arabidopsis roots, whereas excess K+ produced cytoplasmic alkalinization and CML18 dissociation. These results imply that the pH-responsive NHX-CML18 module is an essential component of the cellular K+- and pH-stats.

Rapid intracellular pH measurement based on electroporation- surface-enhanced Raman scattering

In this study, electroporation-surface-enhanced Raman scattering (SERS) was applied to rapidly measure intracellular pH. The generation of a sensitive SERS probe for measuring pH in the range of 6.0-8.0 was accomplished through the conjugation of the pH-sensitive molecule 4-mercaptobenzoic acid (4-MBA) to the surface of gold nanoparticles (Au NPs) through its thiol functional group. This bioprobe was then rapidly introduced into nasopharyngeal carcinoma CNE-1 cells by electroporation, followed by SERS scanning and the fitting of intensity ratios of each detection point's Raman peaks at 1423 cm-1 and 1072 cm-1, to create the pH distribution map of CNE-1 cells. The electroporation-SERS assay introduces pH bioprobes into a living cell in a very short time and disperses the nanoprobe throughout the cytoplasm, ultimately enabling rapid and comprehensive pH analysis of the entire cell. Our work demonstrates the potential of electroporation-SERS for the biochemical analysis of live cells.

Biomimetic Synthesis of the Marine-Derived Thioalkaloids Dassonmycins A and B

A biomimetic synthesis of the marine thioalkaloids dassonmycins A and B is reported. The synthesis features a chemoselective reduction of a diketopiperazine to form a 2-piperazinone, which undergoes heteroannulation with naphthoquinone to yield dassonmycin A. Dassonmycin A undergoes slow cyclization to form dassonmycin B at physiological pH, supporting a biosynthesis hypothesis that this reaction could occur in the cytosol of the bacterial host species.

Disruption of the Physical Interaction Between Carbonic Anhydrase IX and the Monocarboxylate Transporter 4 Impacts Lactate Transport in Breast Cancer Cells

It has been previously established that breast cancer cells exhibit high expression of the monocarboxylate (lactate) transporters (MCT1 and/or MCT4) and carbonic anhydrase IX (CAIX) and form a functional metabolon for proton-coupled lactate export, thereby stabilizing intracellular pH. CD147 is the MCT accessory protein that facilitates the creation of the MCT/CAIX complex. This study describes how the small molecule Beta-Galactose 2C (BGal2C) blocks the physical and functional interaction between CAIX and either MCT1 or MCT4 in Xenopus oocytes, which reduces the rate of proton and lactate flux with an IC50 of ~90 nM. This value is similar to the Ki for inhibition of CAIX activity. Furthermore, it is shown that BGal2C blocks hypoxia-induced lactate transport in MDA-MB-231 and MCF-7 breast cancer cells, both of which express CAIX. As in oocytes, BGal2C interferes with the physical interaction between CAIX and MCTs in both cell types. Finally, X-ray crystallographic studies highlight unique interactions between BGal2C and a CAIX-mimic that are not observed within the CAII active site and which may underlie the strong specificity of BGal2C for CAIX. These studies demonstrate the utility of a novel sulfonamide in interfering with elevated proton and lactate flux, a hallmark of many solid tumors.

Advances in mRNA LNP-Based Cancer Vaccines: Mechanisms, Formulation Aspects, Challenges, and Future Directions

After the COVID-19 pandemic, mRNA-based vaccines have emerged as a revolutionary technology in immunization and vaccination. These vaccines have shown remarkable efficacy against the virus and opened up avenues for their possible application in other diseases. This has renewed interest and investment in mRNA vaccine research and development, attracting the scientific community to explore all its other applications beyond infectious diseases. Recently, researchers have focused on the possibility of adapting this vaccination approach to cancer immunotherapy. While there is a huge potential, challenges still remain in the design and optimization of the synthetic mRNA molecules and the lipid nanoparticle delivery system required to ensure the adequate elicitation of the immune response and the successful eradication of tumors. This review points out the basic mechanisms of mRNA-LNP vaccines in cancer immunotherapy and recent approaches in mRNA vaccine design. This review displays the current mRNA modifications and lipid nanoparticle components and how these factors affect vaccine efficacy. Furthermore, this review discusses the future directions and clinical applications of mRNA-LNP vaccines in cancer treatment.

Naphthalimide-Based, Single-Chromophore, Emission Ratiometric Fluorescent Sensor for Tracking Intracellular pH

We report a novel, reversible, cell-permeable, pH-sensor, TRapH. TRapH afforded a pH-sensitive ratiometric emission response in the pH range ~3-6, enabling imaging and quantification of pH in living cells. The biological-applicability of TRapH was illustrated via live-tracking of intracellular pH dynamics in living mammalian cells induced by a synthetic H+-transporter.

Deregulation of lactate permeability using a small-molecule transporter (Lactrans-1) disturbs intracellular pH and triggers cancer cell death

Due to the relevance of lactic acidosis in cancer, several therapeutic strategies have been developed targeting its production and/or regulation. In this matter, inhibition approaches of key proteins such as lactate dehydrogenase or monocarboxylate transporters have showed promising results, however, metabolic plasticity and tumor heterogeneity limits their efficacy. In this study, we explored the anticancer potential of a new strategy based on disturbing lactate permeability independently of monocarboxylate transporters activity using a small molecule ionophore named Lactrans-1. Derived from click-tambjamines, Lactrans-1 facilitates transmembrane lactate transportation in liposome models and reduces cancer cell viability. The results showed that Lactrans-1 triggered both apoptosis and necrosis depending on the cell line tested, displaying a synergistic effect in combination with first-line standard chemotherapeutic cisplatin. The ability of this compound to transport outward lactate anions was confirmed in A549 and HeLa cells, two cancer cell lines having distinct rates of lactate production. In addition, through cell viability reversion experiments it was possible to establish a correlation between the amount of lactate transported and the cytotoxic effect exhibited. The movement of lactate anions was accompanied with intracellular pH disturbances that included basification of lysosomes and acidification of the cytosol and mitochondria. We also observed mitochondrial swelling, increased ROS production and activation of oxidative stress signaling pathways p38-MAPK and JNK/SAPK. Our findings provide evidence that enhancement of lactate permeability is critical for cellular pH homeostasis and effective to trigger cancer cell death, suggesting that Lactrans-1 may be a promising anticancer therapy.

Dominant and genome-wide formation of DNA:RNA hybrid G-quadruplexes in living yeast cells

Guanine-rich DNA forms G-quadruplexes (G4s) that play a critical role in essential cellular processes. Previous studies have mostly focused on intramolecular G4s composed of four consecutive guanine tracts (G-tracts) from a single strand. However, this structural form has not been strictly confirmed in the genome of living eukaryotic cells. Here, we report the formation of hybrid G4s (hG4s), consisting of G-tracts from both DNA and RNA, in the genome of living yeast cells. Analysis of Okazaki fragment syntheses and two other independent G4-specific detections reveal that hG4s can efficiently form with as few as a single DNA guanine-guanine (GG) tract due to the participation of G-tracts from RNA. This finding increases the number of potential G4-forming sites in the yeast genome from 38 to 587,694, a more than 15,000-fold increase. Interestingly, hG4s readily form and even dominate at G4 sites that are theoretically capable of forming the intramolecular DNA G4s (dG4s) by themselves. Compared to dG4s, hG4s exhibit broader kinetics, higher prevalence, and greater structural diversity and stability. Most importantly, hG4 formation is tightly coupled to transcription through the involvement of RNA, allowing it to function in a transcription-dependent manner. Overall, our study establishes hG4s as the overwhelmingly dominant G4 species in the yeast genome and emphasizes a renewal of the current perception of the structural form, formation mechanism, prevalence, and functional role of G4s in eukaryotic genomes. It also establishes a sensitive and currently the only method for detecting the structural form of G4s in living cells.