Organelle acidification and disease

Design strategies for organelle-selective fluorescent probes: where to start?

Monitoring physiological changes within cells is crucial for understanding their biological aspects and pathological activities. Fluorescent probes serve as powerful tools for this purpose, offering advantageous characteristics over genetically encoded probes. While numerous organelle-selective probes have been developed in the past decades, several challenges persist. This review explores the strategies and key factors contributing to the successful rationale design of these probes. We systematically discuss the typical mode of cellular uptake generally adopted by fluorescent probes and provide a detailed examination of the key factors to consider in design rationale from two perspectives: the properties of the target organelle and the physicochemical properties of the probe itself. Additionally, recent examples of organelle-targeted probes are presented, along with a discussion of the current challenges faced by fluorescent probes in the field.

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.

Golgi pH homeostasis stabilizes the lysosomal membrane through N-glycosylation of membrane proteins

Protein glycosylation plays a vital role in various cellular functions, many of which occur within the Golgi apparatus. The Golgi pH regulator (GPHR) is essential for the proper functioning of the Golgi apparatus. The lysosomal membrane contains highly glycosylated membrane proteins in abundance. This study investigated the role of the Golgi luminal pH in N-glycosylation of lysosomal membrane proteins and the effect of this protein modification on membrane stability using Gphr-deficient MEFs. We showed that Gphr deficiency causes an imbalance in the Golgi luminal pH, resulting in abnormal protein N-glycosylation, indicated by a reduction in sialylated glycans and markedly reduced molecular weight of glycoproteins. Further experiments using FRAP and PLA revealed that Gphr deficiency prevented the trafficking dynamics and proximity condition of glycosyltransferases in the Golgi apparatus. In addition, incomplete N-glycosylation of lysosomal membrane proteins affected lysosomal membrane stability, as demonstrated by the increased susceptibility to lysosomal damage. Thus, this study highlights the critical role of Golgi pH regulation in controlling protein glycosylation and the impact of Golgi dysfunction on lysosomal membrane stability.

Subcellular Drug Distribution: Exploring Organelle-Specific Characteristics for Enhanced Therapeutic Efficacy

The efficacy and potential toxicity of drug treatments depends on the drug concentration at its site of action, intricately linked to its distribution within diverse organelles of mammalian cells. These organelles, including the nucleus, endosome, lysosome, mitochondria, endoplasmic reticulum, Golgi apparatus, lipid droplets, exosomes, and membrane-less structures, create distinct sub-compartments within the cell, each with unique biological features. Certain structures within these sub-compartments possess the ability to selectively accumulate or exclude drugs based on their physicochemical attributes, directly impacting drug efficacy. Under pathological conditions, such as cancer, many cells undergo dynamic alterations in subcellular organelles, leading to changes in the active concentration of drugs. A mechanistic and quantitative understanding of how organelle characteristics and abundance alter drug partition coefficients is crucial. This review explores biological factors and physicochemical properties influencing subcellular drug distribution, alongside strategies for modulation to enhance efficacy. Additionally, we discuss physiologically based computational models for subcellular drug distribution, providing a quantifiable means to simulate and predict drug distribution at the subcellular level, with the potential to optimize drug development strategies.

Amifostine loaded lipid-calcium carbonate nanoparticles as an oral drug delivery system for radiation protection

Amifostine (AMF) as the first-line radiation protection drug, usually suffered from low compliance and short half-life upon clinical applications. The development of oral drug delivery system (DDS) for AMF is a promising solution. However, the inherent shortages of AMF present significant challenges in the design of suitable oral DDS. Here in this study, we utilized the ability of calcium ions to bind with AMF and prepared AMF loaded calcium carbonate (CC) core, CC/AMF, using phase transferred coprecipitation method. We further modified the CC/AMF using phospholipids to prepare AMF loaded lipid-calcium carbonate (LCC) hybrid nanoparticles (LCC/AMF) via a thin-film dispersion method. LCC/AMF combines the oral advantages of lipid nanoparticles with the drug-loading capabilities of CC, which was shown as uniform nano-sized formulation with decent stability in aqueous solution. With favorable intestinal transport and absorption effects, it effectively enhances the in vivo radiation protection efficacy of AMF through oral administration. More importantly, we further investigated the cellular accumulation profile and intracellular transport mechanism of LCC/AMF using MDCK and Caco-2 cell lines as models. This research not only alters the current administration method of AMF to enhance its convenience and compliance, but also provides insights and guidance for the development of more suitable oral DDS for AMF in the future.

An Insulin-Modified pH-Responsive Nanopipette Based on Ion Current Rectification

The properties of nanopipettes largely rely on the materials introduced onto their inner walls, which allow for a vast extension of their sensing capabilities. The challenge of simultaneously enhancing the sensitivity and selectivity of nanopipettes for pH sensing remains, hindering their practical applications. Herein, we report insulin-modified nanopipettes with excellent pH response performances, which were prepared by introducing insulin onto their inner walls via a two-step reaction involving silanization and amidation. The pH response intensity based on ion current rectification was significantly enhanced by approximately 4.29 times when utilizing insulin-modified nanopipettes compared with bare ones, demonstrating a linear response within the pH range of 2.50 to 7.80. In addition, insulin-modified nanopipettes featured good reversibility and selectivity. The modification processes were monitored using the I-V curves, and the relevant mechanisms were discussed. The effects of solution pH and insulin concentration on the modification results were investigated to achieve optimal insulin introduction. This study showed that the pH response behavior of nanopipettes can be greatly improved by introducing versatile molecules onto the inner walls, thereby contributing to the development and utilization of pH-responsive nanopipettes.

Salinomycin disturbs Golgi function and specifically affects cells in epithelial-to-mesenchymal transition

Epithelial-to-mesenchymal transition (EMT) gives rise to cells with properties similar to cancer stem cells (CSCs). Targeting the EMT program to selectively eliminate CSCs is a promising way to improve cancer therapy. Salinomycin (Sal), a K+/H+ ionophore, was identified as highly selective towards CSC-like cells, but its mechanism of action and selectivity remains elusive. Here, we show that Sal, similar to monensin and nigericin, disturbs the function of the Golgi. Sal alters the expression of Golgi-related genes and leads to marked changes in Golgi morphology, particularly in cells that have undergone EMT. Moreover, Golgi-disturbing agents severely affect post-translational modifications of proteins, including protein processing, glycosylation and secretion. We discover that the alterations induced by Golgi-disturbing agents specifically affect the viability of EMT cells. Collectively, our work reveals a novel vulnerability related to the EMT, suggesting an important role for the Golgi in the EMT and that targeting the Golgi could represent a novel therapeutic approach against CSCs.

17⍺-Estradiol Protects against HIV-1 Tat-Induced Endolysosome Dysfunction and Dendritic Impairments in Neurons

HIV-1 Tat continues to play an important role in the development of HIV-associated neurocognitive disorders (HAND), which persist in 15-55% of people living with HIV even with virological control. In the brain, Tat is present on neurons, where Tat exerts direct neuronal damaging effects by, at least in part, disrupting endolysosome functions, a pathological feature present in HAND. In this study, we determined the protective effects of 17α-estradiol (17αE2), the predominant form of estrogen in the brain, against Tat-induced endolysosome dysfunction and dendritic impairment in primary cultured hippocampal neurons. We demonstrated that pre-treatment with 17αE2 protected against Tat-induced endolysosome dysfunction and reduction in dendritic spine density. Estrogen receptor alpha (ERα) knockdown impairs the ability of 17αE2 to protect against Tat-induced endolysosome dysfunction and reduction in dendritic spine density. Furthermore, over-expressing an ERα mutant that fails to localize on endolysosomes impairs 17αE2's protective effects against Tat-induced endolysosome dysfunction and reduction in dendritic spine density. Our findings demonstrate that 17αE2 protects against Tat-induced neuronal injury via a novel ERα-mediated and endolysosome-dependent pathway, and such a finding might lead to the development of novel adjunct therapeutics against HAND.

Golgi-Targeted Fluorescent Probe for Imaging NO in Alzheimer's Disease

Nitric oxide (NO) is a crucial neurotransmitter participating in many biological processes via nitrosylation reaction. NO produced in diverse subcellular regions also regulates the function of cells in different manners. A Golgi apparatus is rich in nitric oxide synthase and may serve as a potential therapeutic target for Alzheimer's disease (AD). However, due to the lack of an effective tool, it is difficult to reveal the relationship between Golgi-NO and AD. Herein, we report Golgi-NO as the first Golgi-targeted fluorescent probe for sensing and imaging NO in the Golgi apparatus. The probe is designed and synthesized by incorporating 4-sulfamoylphenylamide as a Golgi-targeted moiety to 6-carboxyrhodamine B, generating a fluorophore of Golgi-RhB with modifiable carboxyl, which is then combined with the NO recognition moiety of o-diaminobenzene. The probe shows superior analytical performance including accurate Golgi-targeted ability and high selectivity for NO. Moreover, using the probe, we disclose a significant increase of NO in Golgi apparatus in the AD model. This study provides a competent tool for studying the function and nitrosylation of NO in the Golgi apparatus in related diseases.

Strategies for organelle targeting of fluorescent probes

Fluorescent tools have emerged as an important tool for studying the distinct chemical microenvironments of organelles, due to their high specificity and ability to be used in non-destructive, live cellular studies. These tools fall largely in two categories: exogenous fluorescent dyes, or endogenous labels such as genetically encoded fluorescent proteins. In both cases, the probe must be targeted to the organelle of interest. To date, many organelle-targeted fluorescent tools have been reported and used to uncover new information about processes that underpin health and disease. However, the majority of these tools only apply a handful of targeting groups, and less-studied organelles have few robust targeting strategies. While the development of new, robust strategies is difficult, it is essential to develop such strategies to allow for the development of new tools and broadening the effective study of organelles. This review aims to provide a comprehensive overview of the major targeting strategies for both endogenous and exogenous fluorescent cargo, outlining the specific challenges for targeting each organelle type and as well as new developments in the field.

Enhanced-contrast two-photon optogenetic pH sensing and pH-resolved brain imaging

We present experiments on cell cultures and brain slices that demonstrate two-photon optogenetic pH sensing and pH-resolved brain imaging using a laser driver whose spectrum is carefully tailored to provide the maximum contrast of a ratiometric two-photon fluorescence readout from a high-brightness genetically encoded yellow-fluorescent-protein-based sensor, SypHer3s. Two spectrally isolated components of this laser field are set to induce two-photon-excited fluorescence (2PEF) by driving SypHer3s through one of two excitation pathways-via either the protonated or deprotonated states of its chromophore. With the spectrum of the laser field accurately adjusted for a maximum contrast of these two 2PEF signals, the ratio of their intensities is shown to provide a remarkably broad dynamic range for pH measurements, enabling high-contrast optogenetic deep-brain pH sensing and pH-resolved 2PEF imaging within a vast class of biological systems, ranging from cell cultures to the living brain.

Emerging links between endosomal pH and cancer

Extracellular acidification is a well-known driver of tumorigenesis that has been extensively studied. In contrast, the role of endosomal pH is novel and relatively unexplored. There is emerging evidence from a growing number of studies showing that the pH of endosomal compartments controls proliferation, migration, stemness, and sensitivity to chemoradiation therapy in a variety of tumors. Endosomes are a crucial hub, mediating cellular communication with the external environment. By finely regulating the sorting and trafficking of vesicular cargo for degradation or recycling, endosomal pH determines the fate of plasma membrane proteins, lipids, and extracellular signals including growth factor receptors and their ligands. Several critical regulators of endosomal pH have been identified, including multiple isoforms of the family of electroneutral Na⁺/H⁺ exchangers (NHE) such as NHE6 and NHE9. Recent studies have shed light on molecular mechanisms linking endosomal pH to cancer malignancy. Manipulating endosomal pH by epigenetic reprogramming, small molecules, or nanoparticles may offer promising new options in cancer therapy. In this review, we summarize evidence linking endosomal pH to cancer, with a focus on the role of endosomal Na⁺/H⁺ exchangers and how they affect the prognosis of cancer patients, and also suggest how regulation of endosomal pH may be exploited to develop new cancer therapies.

Emerging insights on the role of V-ATPase in human diseases: Therapeutic challenges and opportunities

The control of the intracellular pH is vital for the survival of all organisms. Membrane transporters, both at the plasma and intracellular membranes, are key players in maintaining a finely tuned pH balance between intra- and extracellular spaces, and therefore in cellular homeostasis. V-ATPase is a housekeeping ATP-driven proton pump highly conserved among prokaryotes and eukaryotes. This proton pump, which exhibits a complex multisubunit structure based on cell type-specific isoforms, is essential for pH regulation and for a multitude of ubiquitous and specialized functions. Thus, it is not surprising that V-ATPase aberrant overexpression, mislocalization, and mutations in V-ATPase subunit-encoding genes have been associated with several human diseases. However, the ubiquitous expression of this transporter and the high toxicity driven by its off-target inhibition, renders V-ATPase-directed therapies very challenging and increases the need for selective strategies. Here we review emerging evidence linking V-ATPase and both inherited and acquired human diseases, explore the therapeutic challenges and opportunities envisaged from recent data, and advance future research avenues. We highlight the importance of V-ATPases with unique subunit isoform molecular signatures and disease-associated isoforms to design selective V-ATPase-directed therapies. We also discuss the rational design of drug development pipelines and cutting-edge methodological approaches toward V-ATPase-centered drug discovery. Diseases like cancer, osteoporosis, and even fungal infections can benefit from V-ATPase-directed therapies.

Recent Progress in the Development of Multifunctional Nanoplatform for Precise Tumor Phototherapy

Phototherapy, including photodynamic therapy and photothermal therapy, mainly relies on phototherapeutic agents (PAs) to produce heat or toxic reactive oxygen species (ROS) to kill tumors. It has attracted wide attention due to its merits of noninvasive properties and negligible drug resistance. However, the phototoxicity of conventional PAs is one of the main challenges for its potential clinical application. This is mainly caused by the uncontrolled distribution of PA in vivo, as well as the inevitable damage to healthy cells along the light path. Ensuring the generation of ROS or heat specific at tumor site is the key for precise tumor phototherapy. In this review, the progress of targeted delivery of PA and activatable phototherapy strategies based on nanocarriers for precise tumor therapy is summarized. The research progress of passive targeting, active targeting, and activatable targeting strategies in the delivery of PA is also described. Then, the switchable nanosystems for tumor precise phototherapy in response to tumor microenvironment, including pH, glutathione (GSH), protein, and nucleic acid, are highlighted. Finally, the challenges and opportunities of nanocarrier-based precise phototherapy are discussed for clinical application in the future.

Label-Free in Situ pH Monitoring in a Single Living Cell Using an Optical Nanoprobe

Intracellular pH plays critical roles in cell and tissue functions during processes such as metabolism, proliferation, apoptosis, ion transportation, endocytosis, muscle contraction and so on. It is thus an important biomarker that can readily be used to monitor the physiological status of a cell. Thus, disrupted intracellular pH may serve as an early indicator of cell dysfunction and deterioration. Various methods have been developed to detect cellular pH, such as pH-sensitive labeling reagents with fluorescent or Raman signals. However, excessive cellular uptake of these reagents will not only disrupt cell viability but also compromise effective long-term monitoring. Here, we present a novel fiber-optic fluorescent nanoprobe with a high spatial resolution for label-free, subcellular pH sensing. The probe has a fast response time (~20 seconds) with minimum invasiveness and excellent pH resolution (0.02 pH units) within a biologically relevant pH environment ranging from 6.17 to 8.11. Its applicability was demonstrated on cultured A549 lung cancer cells, and its efficacy was further testified in two typical cytotoxic cases using carbonylcyanide 3-chlorophenyl hydrazine, titanium dioxide, and nanoparticles. The probe can readily detect the pH variations among cells under toxin/nanoparticles administration, enabling direct monitoring of the early onset of physiological or pathological events with high spatiotemporal resolution. This platform has excellent promise as a minimum invasive diagnostic tool for pH-related cellular mechanism studies, such as inflammation, cytotoxicity, drug resistance, carcinogenesis, stem cell differentiation and so on.

Janus sword actions of chloroquine and hydroxychloroquine against COVID-19

Chloroquine (CQ) and its analogue hydroxychloroquine (HCQ) have been thrust into our everyday vernacular because some believe, based on very limited basic and clinical data, that they might be helpful in preventing and/or lessening the severity of the pandemic coronavirus disease 2019 (COVID-19). However, lacking is a temperance in enthusiasm for their possible use as well as sufficient perspective on their effects and side-effects. CQ and HCQ have well-known properties of being diprotic weak bases that preferentially accumulate in acidic organelles (endolysosomes and Golgi apparatus) and neutralize luminal pH of acidic organelles. These primary actions of CQ and HCQ are responsible for their anti-malarial effects; malaria parasites rely on acidic digestive vacuoles for survival. Similarly, de-acidification of endolysosomes and Golgi by CQ and HCQ may block severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) integration into host cells because SARS-CoV-2 may require an acidic environment for its entry and for its ability to bud and infect bystander cells. Further, de-acidification of endolysosomes and Golgi may underly the immunosuppressive effects of these two drugs. However, modern cell biology studies have shown clearly that de-acidification results in profound changes in the structure, function and cellular positioning of endolysosomes and Golgi, in signaling between these organelles and other subcellular organelles, and in fundamental cellular functions. Thus, studying the possible therapeutic effects of CQ and HCQ against COVID-19 must occur concurrent with studies of the extent to which these drugs affect organellar and cell biology. When comprehensively examined, a better understanding of the Janus sword actions of these and other drugs might yield better decisions and better outcomes.

What biologists want from their chloride reporters – a conversation between chemists and biologists

Impaired chloride transport affects diverse processes ranging from neuron excitability to water secretion, which underlie epilepsy and cystic fibrosis, respectively. The ability to image chloride fluxes with fluorescent probes has been essential for the investigation of the roles of chloride channels and transporters in health and disease. Therefore, developing effective fluorescent chloride reporters is critical to characterizing chloride transporters and discovering new ones. However, each chloride channel or transporter has a unique functional context that demands a suite of chloride probes with appropriate sensing characteristics. This Review seeks to juxtapose the biology of chloride transport with the chemistries underlying chloride sensors by exploring the various biological roles of chloride and highlighting the insights delivered by studies using chloride reporters. We then delineate the evolution of small-molecule sensors and genetically encoded chloride reporters. Finally, we analyze discussions with chloride biologists to identify the advantages and limitations of sensors in each biological context, as well as to recognize the key design challenges that must be overcome for developing the next generation of chloride sensors.

Cysteine reactivity across the subcellular universe

Cysteine residues are concentrated at key functional sites within proteins, performing diverse roles in metal binding, catalysis, and redox chemistry. Chemoproteomic platforms to interrogate the reactive cysteinome have developed significantly over the past 10 years, resulting in a greater understanding of cysteine functionality, modification, and druggability. Recently, chemoproteomic methods to examine reactive cysteine residues from specific subcellular organelles have provided significantly improved proteome coverage and highlights the unique functionalities of cysteine residues mediated by cellular localization. Here, the diverse physicochemical properties of the mammalian subcellular organelles are explored in the context of their effects on cysteine reactivity. The unique functions of cysteine residues found in the mitochondria and endoplasmic reticulum are highlighted, together with an overview into chemoproteomic platforms employed to investigate cysteine reactivity in subcellular organelles.

Redox proteomic insights into involvement of clathrin-mediated endocytosis in silver nanoparticles toxicity to Mytilus galloprovincialis

Clathrin-mediated endocytosis is a major mode of nanoparticle (NP) internalization into cells. However, influence of internalization routes on nanoparticle toxicity is poorly understood. Here, we assess the impact of blocking clathrin-mediated endocytosis upon silver NP (AgNP) toxicity to gills and digestive glands of the mussel Mytilusgalloprovincialisusing the uptake inhibitor, amantadine. Animals were exposed for 12h to AgNP (< 50 nm) in the presence and absence of amantadine. Labeling of oxidative protein modifications, either thiol oxidation, carbonyl formation or both in two-dimensional electrophoresis separations revealed 16 differentially affected abundance spots. Amongst these, twelve hypothetical proteins were successfully identified by peptide mass fingerprinting (MALDI TOF-MS/MS). The proteins identified are involved in buffering redox status or in cytoprotection. We conclude that blockade of clathrin-mediated endocytosis protected against NP toxicity, suggesting this uptake pathway facilitates toxicity. Lysosomal degradation and autophagy are major mechanisms that might be induced to mitigate NP toxicity.

A naphthalene-based fluorescent probe with a large Stokes shift for mitochondrial pH imaging

A naphthalene-based fluorescent pH probe with a pK_a of 8.8 for imaging mitochondrial pH changes in live cells.

Chiral-aminoquinoline-based fluorescent pH probe with large stokes shift for bioimaging

The aminoquinoline derivatives, (R)- and (S)-2-phenyl-2-(quinolin-6-ylamino)ethan-1-ol (R-PEO and S-PEO), were synthesized by a tandem one-pot three-step CN coupling method where Smiles rearrangement was the key procedure. The selected compound R-PEO showed a significant fluorescence enhancement with a turn-on ratio over 98-fold and enabled the real time determination of proton concentration in acidic solution. The fluorescence intensity of R-PEO exhibited strong pH-dependent performance with a large Stokes shift (115nm) and responded linearly to minor pH change within the range of 3.8-6.0. With the help of ¹H NMR spectrum, we also confirmed the protonation of the quinoline unit should be the proposed reaction. Compared with the conjugated acid of N-hexylquinolin-6-amine (NQA), the conjugated acid of R-PEO shows significant planar intramolecular charge transfer (PICT) character. Furthermore, biological imaging proved that R-PEO probe can be used to monitor the pH change of S. cerevisiae in vivo.

Hepatocyte growth factor secreted by bone marrow stem cell reduce ER stress and improves repair in alveolar epithelial II cells

Idiopathic Pulmonary Fibrosis (IPF) is a progressive, irreversible lung disease with complex pathophysiology. Evidence of endoplasmic reticulum (ER) stress has been reported in alveolar epithelial cells (AEC) in IPF patients. Secreted mediators from bone marrow stem cells (BMSC-cm) have regenerative properties. In this study we investigate the beneficial effects of BMSC-cm on ER stress response in primary AEC and ER stressed A549 cells. We hypothesize that BMSC-cm reduces ER stress. Primary AEC isolated from IPF patients were treated with BMSC-cm. To induce ER stress A549 cells were incubated with Tunicamycin or Thapsigargin and treated with BMSC-cm, or control media. Primary IPF-AEC had high Grp78 and CHOP gene expression, which was lowered after BMSC-cm treatment. Similar results were observed in ER stressed A549 cells. Alveolar epithelial repair increased in presence of BMSC-cm in ER stressed A549 cells. Hepatocyte growth factor (HGF) was detected in biologically relevant levels in BMSC-cm. Neutralization of HGF in BMSC-cm attenuated the beneficial effects of BMSC-cm including synthesis of surfactant protein C (SP-C) in primary AEC, indicating a crucial role of HGF in ER homeostasis and alveolar epithelial repair. Our data suggest that BMSC-cm may be a potential therapeutic option for treating pulmonary fibrosis.

A smart drug: a pH-responsive photothermal ablation agent for Golgi apparatus activated cancer therapy

A pH-responsive photothermal ablation agent for Golgi apparatus activated cancer therapy with NIR excitation was developed.

Biochemical and biophysical approaches to study the structure and function of the chloride channel (ClC) family of proteins

The chloride channel (ClC) protein family comprises both chloride (Cl(-)) channels and chloride/proton (Cl(-)/H(+)) antiporters. In prokaryotes and eukaryotes, these proteins mediate the movement of Cl(-) ions across the membrane. In eukaryotes, ClC proteins play a role in the stabilization of membrane potential, epithelial ion transport, hippocampal neuroprotection, cardiac pacemaker activity and vesicular acidification. Moreover, mutations in the genes encoding ClC proteins can cause genetic disease in humans. In prokaryotes, the Cl(-)/H(+) antiporters, such as ClC-ec1 found in Escherichia coli promote proton expulsion in the extreme acid-resistance response common to enteric bacteria. To date, structural and functional studies of the prokaryotic protein have revealed unique structural features, including complicated transmembrane topology with 18 α-helices in each subunit and an anion-coordinating region in each subunit. Several different approaches such as X-ray crystallography, NMR, biochemical studies, and molecular dynamics simulations have been applied to the study of ClC proteins. Continued study of the unique structure and function of this diverse family of proteins has the potential to lead to the development of novel therapeutic targets for neuronal, renal, bone, and food-borne diseases.

Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter

Chloride plays a major role in cellular homeostasis by regulating the lumenal pH of intracellular organelles. We have described a pH-independent, fluorescent chloride reporter called Clensor that has successfully measured resting chloride in organelles of living cells. Here, we describe the rational design of Clensor. Clensor integrates a chloride sensitive fluorophore called 10,10'-bis[3-carboxypropyl]-9,9'-biacridinium dinitrate (BAC) with the programmability, modularity and targetability available to nucleic acid scaffolds. We show that simple conjugation of BAC to a DNA backbone fails to yield a viable chloride-sensitive reporter. Fluorescence intensity and lifetime investigations on a series of BAC-functionalized structural variants yielded molecular insights that guided the rational design and successful realization of the chloride sensitive fluorescent reporter, Clensor. This study provides some general design principles that would aid the realization of diverse ion-sensitive nucleic acid reporters based on the sensing strategy of Clensor.

Actin Filaments Are Involved in the Coupling of V0-V1 Domains of Vacuolar H+-ATPase at the Golgi Complex

We previously reported that actin-depolymerizing agents promote the alkalization of the Golgi stack and thetrans-Golgi network. The main determinant of acidic pH at the Golgi is the vacuolar-type H(+)-translocating ATPase (V-ATPase), whose V1domain subunitsBandCbind actin. We have generated a GFP-tagged subunitB2construct (GFP-B2) that is incorporated into the V1domain, which in turn is coupled to the V0sector. GFP-B2 subunit is enriched at distal Golgi compartments in HeLa cells. Subcellular fractionation, immunoprecipitation, and inversal FRAP experiments show that the actin depolymerization promotes the dissociation of V1-V0domains, which entails subunitB2translocation from Golgi membranes to the cytosol. Moreover, molecular interaction between subunitsB2andC1and actin were detected. In addition, Golgi membrane lipid order disruption byd-ceramide-C6 causes Golgi pH alkalization. We conclude that actin regulates the Golgi pH homeostasis maintaining the coupling of V1-V0domains of V-ATPase through the binding of microfilaments to subunitsBandCand preserving the integrity of detergent-resistant membrane organization. These results establish the Golgi-associated V-ATPase activity as the molecular link between actin and the Golgi pH.

Optogenetic acidification of synaptic vesicles and lysosomes

Acidification is required for the function of many intracellular organelles, but methods to acutely manipulate their intraluminal pH have not been available. Here we present a targeting strategy to selectively express the light-driven proton pump Arch3 on synaptic vesicles. Our new tool, pHoenix, can functionally replace endogenous proton pumps, enabling optogenetic control of vesicular acidification and neurotransmitter accumulation. Under physiological conditions, glutamatergic vesicles are nearly full, as additional vesicle acidification with pHoenix only slightly increased the quantal size. By contrast, we found that incompletely filled vesicles exhibited a lower release probability than full vesicles, suggesting preferential exocytosis of vesicles with high transmitter content. Our subcellular targeting approach can be transferred to other organelles, as demonstrated for a pHoenix variant that allows light-activated acidification of lysosomes.

Mechanism of Fine-tuning pH Sensors in Proprotein Convertases: IDENTIFICATION OF A pH-SENSING HISTIDINE PAIR IN THE PROPEPTIDE OF PROPROTEIN CONVERTASE 1/3

The propeptides of proprotein convertases (PCs) regulate activation of cognate protease domains by sensing pH of their organellar compartments as they transit the secretory pathway. Earlier experimental work identified a conserved histidine-encoded pH sensor within the propeptide of the canonical PC, furin. To date, whether protonation of this conserved histidine is solely responsible for PC activation has remained unclear because of the observation that various PC paralogues are activated at different organellar pH values. To ascertain additional determinants of PC activation, we analyzed PC1/3, a paralogue of furin that is activated at a pH of ∼5.4. Using biophysical, biochemical, and cell-based methods, we mimicked the protonation status of various histidines within the propeptide of PC1/3 and examined how such alterations can modulate pH-dependent protease activation. Our results indicate that whereas the conserved histidine plays a crucial role in pH sensing and activation of this protease an additional histidine acts as a "gatekeeper" that fine-tunes the sensitivity of the PC1/3 propeptide to facilitate the release inhibition at higher proton concentrations when compared with furin. Coupled with earlier analyses that highlighted the enrichment of the amino acid histidine within propeptides of secreted eukaryotic proteases, our work elucidates how secreted proteases have evolved to exploit the pH of the secretory pathway by altering the spatial juxtaposition of titratable groups to regulate their activity in a spatiotemporal fashion.

Bioresponsive polymer-based nucleic acid carriers

Nucleic acid carriers need to possess multifunctionality for overcoming biological barriers, such as the stable encapsulation of nucleic acids in extracellular milieu, internalization by target cells, controlled intracellular distribution, and release of nucleic acids at the target site of action. To fulfill these stepwise functionalities, "bioresponsive" polymers that can alter their structure responding to site-specific biological signals are highly useful. Notably, pH, redox potential, and enzymatic activities vary along with microenvironments in the body, and thus, the responsiveness to these signals enables to construct nucleic acid carriers with programmed functionalities. This chapter describes the design of bioresponsive polymers that respond to various biological microenvironments for smart nucleic acids delivery.

Advances in Use of Capsule-Based Fluorescent Sensors for Measuring Acidification of Endocytic Compartments in Cells with Altered Expression of V-ATPase Subunit V1G1

Acidification of eukaryotic cell compartments is accomplished by vacuolar H+-ATPases (V-ATPases), large multisubunit complexes able to pump protons into the lumen of organelles or in the extracellular medium. V-ATPases are involved in a number of physiological cellular processes, and thus regulation of V-ATPase activity is of crucial importance for the cell. Indeed, dysfunction of V-ATPase or alterations of acidification have been recently recognized as key factors in a variety of human diseases. In this study, we applied capsule-based pH sensors and a real-time tracking method for investigating the role of the V1G1 subunit of V-ATPases in regulating the activity of the proton pump. We first constructed stable cell lines overexpressing or silencing the subunit V1G1. Second, we used fluorescent capsule-based pH sensors to monitor acidification before and during internalization by modified and control living cells. By using a simple real-time method for tracking capsule internalization, we were able to identify different capsule acidification levels with respect to each analyzed cell and to establish the kinetics for each. The intracellular pH measurements indicate a delay in acidification in either V1G1-overexpressing or V1G1-silenced cells compared to controls. Finally, in an independent set of experiments, we applied transmission electron microscopy and confocal fluorescence microscopy to further investigate the internalization of the capsules. Both analyses confirm that capsules are engulfed in acidic vesicular structures in modified and control cell lines. The use of capsule-based pH sensors allowed demonstration of the importance of the V1G1 subunit in V-ATPase activity concerning intravesicular acidification. We believe that the combined use of these pH-sensor system and such a real-time method for tracking their internalization path would contribute to systematically measure the proton concentration changes inside the endocytic compartments in various cell systems. This approach would provide fundamental information regarding molecular mechanisms and factors that regulate intracellular acidification, vesicular trafficking, and cytoskeletal reorganizations.

Single-cell intracellular nano-pH probes

Within a large clonal population, such as cancerous tumor entities, cells are not identical, and the differences between intracellular pH levels of individual cells may be important indicators of heterogeneity that could be relevant in clinical practice, especially in personalized medicine. Therefore, the detection of the intracellular pH at the single-cell level is of great importance to identify and study outlier cells. However, quantitative and real-time measurements of the intracellular pH of individual cells within a cell population is challenging with existing technologies, and there is a need to engineer new methodologies. In this paper, we discuss the use of nanopipette technology to overcome the limitations of intracellular pH measurements at the single-cell level. We have developed a nano-pH probe through physisorption of chitosan onto hydroxylated quartz nanopipettes with extremely small pore sizes (~100 nm). The dynamic pH range of the nano-pH probe was from 2.6 to 10.7 with a sensitivity of 0.09 units. We have performed single-cell intracellular pH measurements using non-cancerous and cancerous cell lines, including human fibroblasts, HeLa, MDA-MB-231 and MCF-7, with the pH nanoprobe. We have further demonstrated the real-time continuous single-cell pH measurement capability of the sensor, showing the cellular pH response to pharmaceutical manipulations. These findings suggest that the chitosan-functionalized nanopore is a powerful nano-tool for pH sensing at the single-cell level with high temporal and spatial resolution.

NHE8 is essential for RPE cell polarity and photoreceptor survival

A new N-ethyl-N-nitrosourea (ENU)-induced mouse recessive mutation, identified by fundus examination of the eye, develops depigmented patches, indicating retinal disorder. Histology data show aberrant retinal pigment epithelium (RPE) and late-onset photoreceptor cell loss in the mutant retina. Chromosomal mapping and DNA sequencing reveal a point mutation (T to A) of the Slc9a8 gene, resulting in mutant sodium/proton exchanger 8 (NHE8)-M120K protein. The lysine substitution decreases the probability of forming the 3(rd) transmembrane helix, which impairs the pore structure of the Na(+)/H(+) exchanger. Various RPE defects, including mislocalization of the apical marker ezrin, and disrupted apical microvilli and basal infoldings are observed in mutant mice. We have further generated NHE8 knockout mice and confirmed similar phenotypes, including abnormal RPE cells and late-onset photoreceptor cell loss. Both in vivo and in vitro data indicate that NHE8 co-localizes with ER, Golgi and intracellular vesicles in RPE cells. Thus, NHE8 function is necessary for the survival of photoreceptor cells and NHE8 is important for RPE cell polarity and function. Dysfunctional RPE may ultimately lead to photoreceptor cell death in the NHE8 mutants. Further studies will be needed to elucidate whether or not NHE8 regulates pH homeostasis in the protein secretory pathways of RPE.

Silencing bcl-2 expression in epithelial cancer cells using "smart" particles

Short interfering RNA (siRNA) targeted against anti-apoptotic Bcl-2 protein proved to knockdown its expression and trigger cancer cell death. We used degradable, pH-sensitive, comb-like [P(EAA-co-BMA)-b-PNASI-g-P(HMA-co-TMAEMA)] polymer to condense anti-Bcl-2 siRNA into "smart" particles, which proved to shuttle their cargo past the endosomal membrane and into the cytoplasm of HeLa and UM-SCC-17B cancer cells. HeLa and UM-SCC-17B cancer cells were treated with anti-Bcl-2 particles followed by quantifying Bcl-2 mRNA and protein levels using qRT-PCR and western blotting, respectively. "Smart" anti-Bcl-2 particles selectively suppress Bcl-2 mRNA and protein levels in HeLa cells by 50%-60% and 79%-81%, respectively. Similarly, "smart" anti-Bcl-2 particles inhibited Bcl-2 mRNA levels by 30%, 40%, and 20% upon incubation with UM-SCC-17B cancer cells for 48, 72, and 96 h, respectively. Bcl-2 protein expression in UM-SCC-17B cancer cells was inhibited by 30% after treatment for 72 h. Results show that pH-sensitive comb-like polymer complex anti-Bcl-2 siRNA forming "smart" nanoparticles that deliver their cargo into the cytoplasm of HeLa and UM-SCC-17B cancer cells causing Bcl-2 knockdown at the mRNA and protein levels.

Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways

DNA has been used to build nanomachines with potential in cellulo and in vivo applications. However their different in cellulo applications are limited by the lack of generalizable strategies to deliver them to precise intracellular locations. Here we describe a new molecular design of DNA pH sensors with response times that are nearly 20 fold faster. Further, by changing the sequence of the pH sensitive domain of the DNA sensor, we have been able to tune their pH sensitive regimes and create a family of DNA sensors spanning ranges from pH 4 to 7.6. To enable a generalizable targeting methodology, this new sensor design also incorporates a 'handle' domain. We have identified, using a phage display screen, a set of three recombinant antibodies (scFv) that bind sequence specifically to the handle domain. Sequence analysis of these antibodies revealed several conserved residues that mediate specific interactions with the cognate DNA duplex. We also found that all three scFvs clustered into different branches indicating that their specificity arises from mutations in key residues. When one of these scFvs is fused to a membrane protein (furin) that traffics via the cell surface, the scFv-furin chimera binds the 'handle' and ferries a family of DNA pH sensors along the furin endocytic pathway. Post endocytosis, all DNA nanodevices retain their functionality in cellulo and provide spatiotemporal pH maps of retrogradely trafficking furin inside living cells. This new molecular technology of DNA-scFv-protein chimeras can be used to site-specifically complex DNA nanostructures for bioanalytical applications.

Mutations in the Drosophila ortholog of the vertebrate Golgi pH regulator (GPHR) protein disturb endoplasmic reticulum and Golgi organization and affect systemic growth

Sorting of secretory cargo and retrieval of components of the biosynthetic pathway occur in organelles such as the Golgi apparatus, the endoplasmic reticulum and the endosomes. In order to perform their functions in protein sorting, these organelles require a weakly acidified lumen. In vitro data have shown that Golgi luminal pH is in part regulated by an anion channel called Golgi pH Regulator (GPHR). Mammalian cells carrying a mutated GPHR version present an increased luminal pH leading to delayed protein transport, impaired glycosylation and Golgi disorganization. Using Drosophila as a model system, we present here the first phenotypic consequences, at the organism level, of a complete lack of GPHR function. We show that, although all individuals carrying complete loss-of-function mutations in the dGPHR gene can go through embryonic development, most of them die at late larval stages. The dGPHR mutations are, however, sublethal and can therefore generate escapers that are smaller than controls. Using cellular and molecular readouts, we demonstrate that the effects of dGPHR mutation on larval growth are not due to Insulin signaling pathway impairment and can be rescued by providing dGPHR in only some of the larval tissues. We reveal that, although functionally exchangeable, the invertebrate and vertebrate GPHRs display not completely overlapping sub-cellular localization. Whereas the mammalian GPHR is a Golgi-only associated protein whose inactivation disturbs the Golgi apparatus, our data suggest that dGPHR is expressed in both the ER and the Golgi and that dGPHR mutant flies have defects in both organelles that lead to a defective secretory pathway.

Chemical, biochemical, and biological behaviors of vanadate and its oligomers

Vanadate is widely used as an inhibitor of protein tyrosine phosphatases (PTPase) and is routinely applied in cell lysis buffers or immunoprecipitations of phosphotyrosyl proteins. Additionally, vanadate has been extensively studied for its antidiabetic and anticancer effects. In most studies, orthovanadate or metavanadate was used as the starting compound, whereas these "vanadate" solutions may contain more or less oligomerized species. Whether and how different species of vanadium compounds formed in the biological media exert specific biological effect is still a mystery. In the present commentary, we focus on the chemical, biochemical, and biological behaviors of vanadate. On the basis of species formation of vanadate in chemical and biological systems, we compared the biological effects and working mechanism of monovanadate with that of its oligomers, especially the decamer. We propose that different oligomers may exert a specific biological effect, which depends on their structures and the context of the cell types, by different modes of action.

Fabrication of triple-labeled polyelectrolyte microcapsules for localized ratiometric pH sensing

Encapsulation of pH sensitive fluorophores as reporting molecules provides a powerful approach to visualize the transportation of multilayer capsules. In this study, two pH sensitive dyes (fluorescein and oregon green) and one pH insensitive dye (rhodamine B) were simultaneously labeled on the microcapsules to fabricate ratiometric pH sensors. The fluorescence of the triple-labeled microcapsule sensors was robust and nearly independent of other intracellular species. With a dynamic pH measurement range of 3.3-6.5, the microcapsules can report their localized pH at a real time. Cell culture experiments showed that the microcapsules could be internalized by RAW 246.7 cells naturally and finally accumulated in acidic organelles with a pH value of 5.08 ± 0.59 (mean ± s.d.; n=162).

Functional vacuolar ATPase (V-ATPase) proton pumps traffic to the enterocyte brush border membrane and require CFTR

Vacuolar ATPases (V-ATPases) are highly conserved proton pumps that regulate organelle pH. Epithelial luminal pH is also regulated by cAMP-dependent traffic of specific subunits of the V-ATPase complex from endosomes into the apical membrane. In the intestine, cAMP-dependent traffic of cystic fibrosis transmembrane conductance regulator (CFTR) channels and the sodium hydrogen exchanger (NHE3) in the brush border regulate luminal pH. V-ATPase was found to colocalize with CFTR in intestinal CFTR high expresser (CHE) cells recently. Moreover, apical traffic of V-ATPase and CFTR in rat Brunner's glands was shown to be dependent on cAMP/PKA. These observations support a functional relationship between V-ATPase and CFTR in the intestine. The current study examined V-ATPase and CFTR distribution in intestines from wild-type, CFTR(-/-) mice and polarized intestinal CaCo-2BBe cells following cAMP stimulation and inhibition of CFTR/V-ATPase function. Coimmunoprecipitation studies examined V-ATPase interaction with CFTR. The pH-sensitive dye BCECF determined proton efflux and its dependence on V-ATPase/CFTR in intestinal cells. cAMP increased V-ATPase/CFTR colocalization in the apical domain of intestinal cells and redistributed the V-ATPase Voa1 and Voa2 trafficking subunits from the basolateral membrane to the brush border membrane. Voa1 and Voa2 subunits were localized to endosomes beneath the terminal web in untreated CFTR(-/-) intestine but redistributed to the subapical cytoplasm following cAMP treatment. Inhibition of CFTR or V-ATPase significantly decreased pHi in cells, confirming their functional interdependence. These data establish that V-ATPase traffics into the brush border membrane to regulate proton efflux and this activity is dependent on CFTR in the intestine.

Sequestration of AS-DACA into acidic compartments of the membrane trafficking system as a mechanism of drug resistance in rhabdomyosarcoma

The accumulation of weakly basic drugs into acidic organelles has recently been described as a contributor to resistance in childhood cancer rhabdomyosarcoma (RMS) cell lines with differential sensitivity to a novel topoisomerase II inhibitor, AS-DACA. The current study aims to explore the contribution of the endocytic pathway to AS-DACA sequestration in RMS cell lines. A 24-fold differential in AS-DACA cytotoxicity was detected between the RMS lines RD and Rh30. The effect of inhibitors of the endocytic pathway on AS-DACA sensitivity in RMS cell lines, coupled with the variations of endosomal marker expression, indicated the late endosomal/lysosomal compartment was implicated by confounding lines of evidence. Higher expression levels of Lysosomal-Associated Membrane Protein-1 (LAMP1) in the resistant RMS cell line, RD, provided correlations between the increased amount and activity of these compartments to AS-DACA resistance. The late endosomal inhibitor 3-methyladenine increased AS-DACA sensitivity solely in RD leading to the reduction of AS-DACA in membrane trafficking organelles. Acidification inhibitors did not produce an increase in AS-DACA sensitivity nor reduce its sequestration, indicating that the pH partitioning of weakly basic drugs into acidic compartments does not likely contribute to the AS-DACA sequestering resistance mechanism evident in RMS cells.

Enhanced recruitment of endosomal Na+/H+ exchanger NHE6 into Dendritic spines of hippocampal pyramidal neurons during NMDA receptor-dependent long-term potentiation

Postsynaptic endosomal trafficking has emerged as a principal regulatory mechanism of structural and functional plasticity of glutamatergic synapses. Recycling endosomes perform activity-dependent transport of AMPA receptors (AMPARs) and lipids to the postsynaptic membrane, activities that are known to contribute to long-term synaptic potentiation and hypothesized to subserve learning and memory processes in the brain. Recently, genetic defects in a widely expressed vesicular pH-regulating transporter, the Na(+)/H(+) exchanger NHE6 isoform, have been implicated in neurodevelopmental disorders including severe X-linked mental retardation and autism. However, little information is available regarding the cellular properties of this transporter in the CNS. Here, we show by quantitative light microscopy that the protein abundance of NHE6 is developmentally regulated in area CA1 of the mouse hippocampus. Within pyramidal neurons, NHE6 was found to localize to discrete puncta throughout the soma and neurites, with noticeable accumulation at dendritic spines and presynaptic terminals. Dual immunolabeling of dendritic spines revealed that NHE6 partially colocalizes with typical markers of early and recycling endosomes as well as with the AMPAR subunit GluA1. Significantly, NHE6-containing vesicles exhibited enhanced translocation to dendritic spine heads during NMDA receptor (NMDAR)-dependent long-term potentiation. These data suggest that NHE6 may play a unique, previously unrecognized, role at glutamatergic synapses that are important for learning and memory.

Golgi pH, its regulation and roles in human disease

Most organelles within the exocytic and endocytic pathways typically acidify their interiors, a phenomenon that is known to be crucial for their optimal functioning in eukaryotic cells. This review highlights recent advances in our understanding of how Golgi acidity is maintained and regulated, and how its misregulation contributes to organelle dysfunction and disease. Both its biosynthetic products (glycans) and protein-sorting events are highly sensitive to changes in Golgi luminal pH and are affected in certain human disease states such as cancers and cutis laxa. Other potential disease states that are caused by, or are associated with, Golgi pH misregulation will also be discussed.

Proteoglycan synthesis and Golgi organization in polarized epithelial cells

A large number of complex glycosylation mechanisms take place in the Golgi apparatus. In epithelial cells, glycosylated protein molecules are transported to both the apical and the basolateral surface domains. Although the prevailing view is that the Golgi apparatus provides the same lumenal environment for glycosylation of apical and basolateral cargo proteins, there are indications that proteoglycans destined for the two opposite epithelial surfaces are exposed to different conditions in transit through the Golgi apparatus. We will here review data relating proteoglycan and glycoprotein synthesis to characteristics of the apical and basolateral secretory pathways in epithelial cells.

The intracellular Ca²⁺ channels of membrane traffic

Regulation of organellar fusion and fission by Ca ( 2+) has emerged as a central paradigm in intracellular membrane traffic. Originally formulated for Ca ( 2+) -driven SNARE-mediated exocytosis in the presynaptic terminals, it was later expanded to explain membrane traffic in other exocytic events within the endo-lysosomal system. The list of processes and conditions that depend on the intracellular membrane traffic includes aging, antigen and lipid processing, growth factor signaling and enzyme secretion. Characterization of the ion channels that regulate intracellular membrane fusion and fission promises novel pharmacological approaches in these processes when their function becomes aberrant. The recent identification of Ca ( 2+) permeability through the intracellular ion channels comprising the mucolipin (TRPMLs) and the two-pore channels (TPCs) families pinpoints the candidates for the Ca ( 2+) channel that drive intracellular membrane traffic. The present review summarizes the recent developments and the current questions relevant to this topic.

A weak base-generating system suitable for selective manipulation of lysosomal pH

pH varies widely among the different intracellular compartments. The establishment and maintenance of a particular pH appears to be critical for proper organellar function. This has been deduced from experiments where intraorganellar pH was altered by means of weak acids or bases, ionophores or inhibitors of the vacuolar H(+)-ATPase (V-ATPase). These manipulations, however, are not specific and simultaneously alter the pH of multiple compartments. As a result, it is difficult to assign their effect to a defined organelle. To circumvent this limitation, we designed and implemented a procedure to selectively manipulate the pH of a compartment of choice, using lysosomes as a model organelle. The approach is based on the targeted and continuous enzymatic generation of weak electrolyte, which enabled us to overcome the high buffering capacity of the lysosomal lumen, without altering the pH of other compartments. We targeted jack-bean urease to lysosomes and induced the localized generation of ammonia by providing the membrane-permeant substrate, urea. This resulted in a marked, rapid and fully reversible alkalinization that was restricted to the lysosomal lumen, without measurably affecting the pH of endosomes or of the cytosol. The acute alkalinization induced by urease-urea impaired the activity of pH-dependent lysosomal enzymes, including cathepsins C and L, without altering endosomal function. This approach, which can be extended to other organelles, enables the analysis of the role of pH in selected compartments, without the confounding effects of global disturbances in pH or vesicular traffic.

The mechanism of selective transfection mediated by pentablock copolymers; part II: nuclear entry and endosomal escape

Transfection efficiencies of non-viral gene delivery vectors commonly vary with cell type, owing to differences in proliferation rates and intracellular characteristics. Previous work demonstrated that the poly(diethylaminoethylmethacrylate) (PDEAEM)/Pluronic F127 pentablock copolymers exhibit transfection in vitro selectively in cancer cell lines as opposed to non-cancerous cell lines. This study continues the investigation of intracellular barriers to transfection using this vector in "normal" and cancer cell lines to understand the underlying mechanisms of the selectivity. Results from Part I of this investigation showed, using conjugated epidermal growth factor, that cellular uptake of these polyplexes is not a major barrier in these systems. Part II of this work continues the investigation into the other potential intracellular barriers, endosomal escape and nuclear entry, using a lysosomotropic agent chloroquine (CLQ), and a nuclear localization signal (NLS) SV40, respectively. Lack of effectiveness of NLS peptide in improving the transfection efficiency suggests that nuclear uptake might not be the major intracellular barrier using the pentablock copolymer vectors, or that the nuclear transport might not be primarily achieved through nuclear pores. However, inclusion of CLQ led to a dramatic enhancement in the level of gene expression, with an almost two orders of magnitude increase in expression seen in normal cell lines, compared with that the increase observed in cancer cell lines. The different lysosomal pH values in normal vs cancer cells was believed to cause the pentablock copolymer vectors to behave distinctly during transport through endocytic pathways, with greater loss of functional DNA occurring in normal cells containing more acidic endocytic vesicles in contrast to cancer cells with less acidic vesicles. Interestingly, CLQ introduced almost no enhancement in the transfection with the control vector ExGen which lacked selectivity of transfection. Exploiting intracellular differences between normal and cancer cells for gene delivery vector design offers a new paradigm to achieve transfection selectivity based on intracellular differences rather than conventional approaches involving vector modification using specific ligands for targeted delivery.

Genome-wide analysis reveals the vacuolar pH-stat of Saccharomyces cerevisiae

Protons, the smallest and most ubiquitous of ions, are central to physiological processes. Transmembrane proton gradients drive ATP synthesis, metabolite transport, receptor recycling and vesicle trafficking, while compartmental pH controls enzyme function. Despite this fundamental importance, the mechanisms underlying pH homeostasis are not entirely accounted for in any organelle or organism. We undertook a genome-wide survey of vacuole pH (pH_v) in 4,606 single-gene deletion mutants of Saccharomyces cerevisiae under control, acid and alkali stress conditions to reveal the vacuolar pH-stat. Median pH_v (5.27±0.13) was resistant to acid stress (5.28±0.14) but shifted significantly in response to alkali stress (5.83±0.13). Of 107 mutants that displayed aberrant pH_v under more than one external pH condition, functional categories of transporters, membrane biogenesis and trafficking machinery were significantly enriched. Phospholipid flippases, encoded by the family of P4-type ATPases, emerged as pH regulators, as did the yeast ortholog of Niemann Pick Type C protein, implicated in sterol trafficking. An independent genetic screen revealed that correction of pH_v dysregulation in a neo1^ts mutant restored viability whereas cholesterol accumulation in human NPC1^−/− fibroblasts diminished upon treatment with a proton ionophore. Furthermore, while it is established that lumenal pH affects trafficking, this study revealed a reciprocal link with many mutants defective in anterograde pathways being hyperacidic and retrograde pathway mutants with alkaline vacuoles. In these and other examples, pH perturbations emerge as a hitherto unrecognized phenotype that may contribute to the cellular basis of disease and offer potential therapeutic intervention through pH modulation.

Insights from bacterial subtilases into the mechanisms of intramolecular chaperone-mediated activation of furin

Prokaryotic subtilisins and eukaryotic proprotein convertases (PCs) are two homologous protease subfamilies that belong to the larger ubiquitous super-family called subtilases. Members of the subtilase super-family are produced as zymogens wherein their propeptide domains function as dedicated intramolecular chaperones (IMCs) that facilitate correct folding and regulate precise activation of their cognate catalytic domains. The molecular and cellular determinants that modulate IMC-dependent folding and activation of PCs are poorly understood. In this chapter we review what we have learned from the folding and activation of prokaryotic subtilisin, discuss how this has molded our understanding of furin maturation, and foray into the concept of pH sensors, which may represent a paradigm that PCs (and possibly other IMC-dependent eukaryotic proteins) follow for regulating their biological functions using the pH gradient in the secretory pathway.