1
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Gui R, Jin H. Organic fluorophores-based molecular probes with dual-fluorescence ratiometric responses to in-vitro/in-vivo pH for biosensing, bioimaging and biotherapeutics applications. Talanta 2024; 275:126171. [PMID: 38703479 DOI: 10.1016/j.talanta.2024.126171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
In recent years, organic fluorophores-based molecular probes with dual-fluorescence ratiometric responses to in-vitro/in-vivo pH (DFR-MPs-pH) have been attracting much interest in fundamental application research fields. More and more scientific publications have reported the exploration of various DFR-MPs-pH systems that have unique dual-fluorescence ratiometry as the signal output, in-built and signal self-calibration functions to improve precise detection of targets. DFR-MPs-pH systems possess high-performance applications in biosensing, bioimaging and biomedicine fields. This review has comprehensively summarized recent advances of DFR-MPs-pH for the first time. First of all, the compositions and types of DFR-MPs-pH are introduced by summarizing different organic fluorophores-based molecule systems. Then, construction strategies are analyzed based on specific components, structures, properties and functions of DFR-MPs-pH. Afterward, biosensing and bioimaging applications are discussed in detail, primarily referring to pH sensing and imaging detection at the levels of living cells and small animals. Finally, biomedicine applications are fully summarized, majorly involving bio-toxicity evaluation, bio-distribution, biomedical diagnosis and therapeutics. Meanwhile, the current status, challenges and perspectives are rationally commented after detailed discussions of representative and state-of-the-art studies. Overall, this present review is comprehensive, in-time and in-depth, and can facilitate the following further exploration of new and versatile DFR-MPs-pH systems toward rational design, facile preparation, superior properties, adjustable functions and highly efficient applications in promising fields.
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Affiliation(s)
- Rijun Gui
- College of Chemistry and Chemical Engineering, Intellectual Property Research Institute, Qingdao University, Shandong, 266071, PR China.
| | - Hui Jin
- College of Chemistry and Chemical Engineering, Intellectual Property Research Institute, Qingdao University, Shandong, 266071, PR China
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2
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Lund LM, Marchi AN, Alderfer L, Hall E, Hammer J, Trull KJ, Hanjaya-Putra D, White KA. Intracellular pH dynamics respond to microenvironment stiffening and mediate vasculogenic mimicry through β-catenin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597454. [PMID: 38895391 PMCID: PMC11185592 DOI: 10.1101/2024.06.04.597454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dysregulated intracellular pH (pHi) dynamics and an altered tumor microenvironment have emerged as drivers of cancer cell phenotypes. However, the molecular integration between the physical properties of the microenvironment and dynamic intracellular signaling responses remains unclear. Here, we use two metastatic cell models, one breast and one lung, to assess pHi response to varying extracellular matrix (ECM) stiffness. To experimentally model ECM stiffening, we use two tunable-stiffness hydrogel systems: Matrigel and hyaluronic acid (HA) gels, which mimic the increased protein secretion and crosslinking associated with ECM stiffening. We find that single-cell pHi decreases with increased ECM stiffness in both hydrogel systems and both metastatic cell types. We also observed that stiff ECM promotes vasculogenic mimicry (VM), a phenotype associated with metastasis and resistance. Importantly, we show that decreased pHi is both a necessary and sufficient mediator of VM, as raising pHi on stiff ECM reduces VM phenotypes and lowering pHi on soft ECM drives VM. We characterize β-catenin as a pH-dependent molecular mediator of pH-dependent VM, where stiffness-driven changes in β-catenin abundance can be overridden by increased pHi. We uncover a dynamic relationship between matrix stiffness and pHi, thus suggesting pHi dynamics can override mechanosensitive cell responses to the extracellular microenvironment.
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3
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Kisor KP, Ruiz DG, Jacobson MP, Barber DL. A role for pH dynamics regulating transcription factor DNA binding selectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595212. [PMID: 38826444 PMCID: PMC11142074 DOI: 10.1101/2024.05.21.595212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression and whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX and MITF/Myc. Focusing on FOX family transcription factors, we used unbiased SELEX-seq to identify pH-dependent DNA binding motif preferences, then confirm pH-regulated binding affinities for FOXC2, FOXM1, and FOXN1 to a canonical FkhP DNA motif that are 2.5 to 7.5 greater at pH 7.0 compared with pH 7.5. For FOXC2, we also find greater activity for an FkhP motif at lower pHi in cells and that pH-regulated binding and activity are dependent on a conserved histidine (His122) in the DBD. RNA-seq with FOXC2 also reveals pH-dependent differences in enriched promoter motifs. Our findings identify pH-regulated transcription factor-DNA binding selectivity with relevance to how pHi dynamics can regulate gene expression for myriad cell behaviours.
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4
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Czowski BJ, White KA. Intracellular pH regulates β-catenin with low pHi increasing adhesion and signaling functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586349. [PMID: 38585883 PMCID: PMC10996556 DOI: 10.1101/2024.03.22.586349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Intracellular pH (pHi) dynamics are linked to cell processes including proliferation, migration, and differentiation. The adherens junction (AJ) and signaling protein β-catenin has decreased abundance at high pHi due to increased proteasomal-mediated degradation. However, the effects of low pHi on β-catenin abundance and functions have not been characterized. Here, we show that low pHi stabilizes β-catenin in epithelial cells using population-level and single-cell assays. β-catenin abundance is increased at low pHi and decreased at high pHi. We also assay single-cell protein degradation rates to show that β-catenin half-life is longer at low compared to high pHi. Importantly, we show that AJs are not disrupted by β-catenin loss at high pHi due to rescue by plakoglobin. Finally, we show that low pHi increases β-catenin transcriptional activity in single cells and is indistinguishable from a Wnt-on state. This work characterizes pHi as a rheostat regulating β-catenin abundance, stability, and function and implicates β-catenin as a molecular mediator of pHi-dependent cell processes.
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Affiliation(s)
- Brandon J Czowski
- Department of Chemistry and Biochemistry, University of Notre Dame
- Harper Cancer Research Institute, University of Notre Dame
| | - Katharine A White
- Department of Chemistry and Biochemistry, University of Notre Dame
- Harper Cancer Research Institute, University of Notre Dame
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5
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Liu Y, Reyes E, Castillo-Azofeifa D, Klein OD, Nystul T, Barber DL. Intracellular pH dynamics regulates intestinal stem cell lineage specification. Nat Commun 2023; 14:3745. [PMID: 37353491 PMCID: PMC10290085 DOI: 10.1038/s41467-023-39312-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/06/2023] [Indexed: 06/25/2023] Open
Abstract
Intracellular pH dynamics is increasingly recognized to regulate myriad cell behaviors. We report a finding that intracellular pH dynamics also regulates adult stem cell lineage specification. We identify an intracellular pH gradient in mouse small intestinal crypts, lowest in crypt stem cells and increasing along the crypt column. Disrupting this gradient by inhibiting H+ efflux by Na+/H+ exchanger 1 abolishes crypt budding and blocks differentiation of Paneth cells, which are rescued with exogenous WNT. Using single-cell RNA sequencing and lineage tracing we demonstrate that intracellular pH dynamics acts downstream of ATOH1, with increased pH promoting differentiation toward the secretory lineage. Our findings indicate that an increase in pH is required for the lineage specification that contributes to crypt maintenance, establishing a role for intracellular pH dynamics in cell fate decisions within an adult stem cell lineage.
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Affiliation(s)
- Yi Liu
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Efren Reyes
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David Castillo-Azofeifa
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
- Immunology Discovery, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Todd Nystul
- Departments of Anatomy, University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, 94143, USA.
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6
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Dwivedi SK, Arachchige DL, Vohs T, Tang J, Usimaki K, Olowolagba AM, Fritz DR, Luck RL, Werner T, Liu H. Near-infrared rhodol dyes bearing salicylaldehyde moieties for ratiometric pH sensing in live cells during mitophagy and under hypoxia conditions. J Mater Chem B 2023; 11:2852-2861. [PMID: 36808460 PMCID: PMC10171916 DOI: 10.1039/d2tb02791g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
We describe a simple but efficient approach to make fluorescent probes A and B based on rhodol dyes incorporated with salicyaldehyde moiety for monitoring pH changes in mitochondria under oxidative stresses and hypoxia conditions, and for tracking mitophagy processes. Probes A and B possess pKa values (pKa ≈ 6.41 and 6.83 respectively) near physiological pH and exhibit decent mitochondria-targeted capabilities, low cytotoxicity, and useful ratiometric and reversible pH responses, which make the probes appropriate for monitoring pH fluctuations of mitochondria in living cells with built-in calibration feature for quantitative analysis. The probes have been effectively useful for the ratiometric determination of pH variations of mitochondria under the stimuli of carbonyl cyanide-4(trifluoromethoxy)phenylhydrazone (FCCP), hydrogen peroxide (H2O2), and N-acetyl cysteine (NAC), and during mitophagy triggered by cell nutrient deprivation, and under hypoxia conditions with cobalt chloride (CoCl2) treatment in living cells. In addition, probe A was efficient in visualizing pH changes in the larvae of fruit flies.
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Affiliation(s)
- Sushil K Dwivedi
- Department of Chemistry, and Research Health Institute, Michigan Technological University, Houghton, MI 49931, USA.
| | - Dilka Liyana Arachchige
- Department of Chemistry, and Research Health Institute, Michigan Technological University, Houghton, MI 49931, USA.
| | - Tara Vohs
- Department of Chemistry, and Research Health Institute, Michigan Technological University, Houghton, MI 49931, USA.
| | - Jiani Tang
- High School, Houghton Portage Township Schools, Houghton, MI 49931, USA
| | - Kyle Usimaki
- Department of Chemistry, and Research Health Institute, Michigan Technological University, Houghton, MI 49931, USA.
| | - Adenike Mary Olowolagba
- Department of Chemistry, and Research Health Institute, Michigan Technological University, Houghton, MI 49931, USA.
| | - Delaney Raine Fritz
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA.
| | - Rudy L Luck
- Department of Chemistry, and Research Health Institute, Michigan Technological University, Houghton, MI 49931, USA.
| | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA.
| | - Haiying Liu
- Department of Chemistry, and Research Health Institute, Michigan Technological University, Houghton, MI 49931, USA.
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7
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Inhibition of NHE1 transport activity and gene transcription in DRG neurons in oxaliplatin-induced painful peripheral neurotoxicity. Sci Rep 2023; 13:3991. [PMID: 36894669 PMCID: PMC9998445 DOI: 10.1038/s41598-023-31095-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Oxaliplatin (OHP)-induced peripheral neurotoxicity (OIPN), one of the major dose-limiting side effects of colorectal cancer treatment, is characterized by both acute and chronic syndromes. Acute exposure to low dose OHP on dorsal root ganglion (DRG) neurons is able to induce an increase in intracellular calcium and proton concentration, thus influencing ion channels activity and neuronal excitability. The Na+/H+ exchanger isoform-1 (NHE1) is a plasma membrane protein that plays a pivotal role in intracellular pH (pHi) homeostasis in many cell types, including nociceptors. Here we show that OHP has early effects on NHE1 activity in cultured mouse DRG neurons: the mean rate of pHi recovery was strongly reduced compared to vehicle-treated controls, reaching levels similar to those obtained in the presence of cariporide (Car), a specific NHE1 antagonist. The effect of OHP on NHE1 activity was sensitive to FK506, a specific calcineurin (CaN) inhibitor. Lastly, molecular analyses revealed transcriptional downregulation of NHE1 both in vitro, in mouse primary DRG neurons, and in vivo, in an OIPN rat model. Altogether, these data suggest that OHP-induced intracellular acidification of DRG neurons largely depends on CaN-mediated NHE1 inhibition, revealing new mechanisms that OHP could exert to alter neuronal excitability, and providing novel druggable targets.
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8
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Munan S, Ali M, Yadav R, Mapa K, Samanta A. PET- and ICT-Based Ratiometric Probe: An Unusual Phenomenon of Morpholine-Conjugated Fluorophore for Mitochondrial pH Mapping during Mitophagy. Anal Chem 2022; 94:11633-11642. [PMID: 35968673 DOI: 10.1021/acs.analchem.2c02177] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitochondrial functions are heavily influenced by acid-base homeostasis. Hence, elucidation of the mitochondrial pH is essential in living cells, and its alterations during pathologies is an interesting question to be addressed. Small molecular fluorescent probes are progressively applied to quantify the mitochondrial pH by fluorescence imaging. Herein, we designed a unique small molecular fluorescent probe, PM-Mor-OH, based on the lipophilic morpholine ligand-conjugated pyridinium derivative of "IndiFluors". The morpholine-conjugated fluorescent probe usually localized the lysosome. However, herein, we observed unusual phenomena of morpholine-tagged PM-Mor-OH that localized mitochondria explicitly. The morpholine ligand also plays a pivotal role in tuning optical properties via photoinduced electron transfer (PET) during internal pH alteration (ΔpHi). In the mitophagy process, lysosomes engulf damaged mitochondria, leading to ΔpHi, which can be monitored using our probe. It exhibited "ratiometric" emission at single wavelength excitation (ex. 488) and is suitable for monitoring and quantifying the ΔpHi using confocal microscope high-resolution image analysis during mitophagy. The bathochromic emission shifts due to intramolecular charge transfer (ICT) in basic pH were well explained by the time-dependent density functional theory (TD-DFT/PCM). Similarly, the change in the emission ratio (green/red) with pH variations was also validated by the PET process. In addition, PM-Mor-OH can quantify the pH change during oxidative stress induced by rapamycin, mutant A53T α-synuclein-mediated protein misfolding stress in mitochondria, and during starvation. Rapamycin-induced mitophagy was further elucidated by the translocation of mCherry Parkin to damaged mitochondria, which well correlates with our probe. Thus, PM-Mito-OH is a valuable probe for visualizing mitophagy and can act as a suitable tool for the diagnosis of mitochondrial diseases.
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Affiliation(s)
- Subrata Munan
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Delhi NCR, NH 91, Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Mudassar Ali
- Protein Homeostasis Laboratory, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Delhi NCR, NH 91, Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Rashmi Yadav
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Delhi NCR, NH 91, Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Koyeli Mapa
- Protein Homeostasis Laboratory, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Delhi NCR, NH 91, Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Animesh Samanta
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Delhi NCR, NH 91, Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
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9
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Michelis S, Danglot L, Vauchelles R, Klymchenko AS, Collot M. Imaging and Measuring Vesicular Acidification with a Plasma Membrane-Targeted Ratiometric pH Probe. Anal Chem 2022; 94:5996-6003. [PMID: 35377610 DOI: 10.1021/acs.analchem.2c00574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tracking the pH variation of intracellular vesicles throughout the endocytosis pathway is of prior importance to better assess the cell trafficking and metabolism of cells. Small molecular fluorescent pH probes are valuable tools in bioimaging but are generally not targeted to intracellular vesicles or are directly targeted to acidic lysosomes, thus not allowing the dynamic observation of the vesicular acidification. Herein, we designed Mem-pH, a fluorogenic ratiometric pH probe based on chromenoquinoline with appealing photophysical properties, which targets the plasma membrane (PM) of cells and further accumulates in the intracellular vesicles by endocytosis. The exposition of Mem-pH toward the vesicle's lumen allowed to monitor the acidification of the vesicles throughout the endocytic pathway and enabled the measurement of their pH via ratiometric imaging.
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Affiliation(s)
- Sophie Michelis
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Lydia Danglot
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014 Paris, France
| | - Romain Vauchelles
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
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10
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Yamazaki Y, Eura Y, Kokame K. V-ATPase V0a1 promotes Weibel-Palade body biogenesis through the regulation of membrane fission. eLife 2021; 10:71526. [PMID: 34904569 PMCID: PMC8718113 DOI: 10.7554/elife.71526] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/13/2021] [Indexed: 01/09/2023] Open
Abstract
Membrane fission, the division of a membrane-bound structure into two discrete compartments, is essential for diverse cellular events, such as endocytosis and vesicle/granule biogenesis; however, the process remains unclear. The hemostatic protein von Willebrand factor is produced in vascular endothelial cells and packaged into specialized secretory granules, Weibel–Palade bodies (WPBs) at the trans-Golgi network (TGN). Here, we reported that V0a1, a V-ATPase component, is required for the membrane fission of WPBs. We identified two V0a isoforms in distinct populations of WPBs in cultured endothelial cells, V0a1 and V0a2, on mature and nascent WPBs, respectively. Although WPB buds were formed, WPBs could not separate from the TGN in the absence of V0a1. Screening using dominant–negative forms of known membrane fission regulators revealed protein kinase D (PKD) as an essential factor in biogenesis of WPBs. Further, we showed that the induction of wild-type PKDs in V0a1-depleted cells does not support the segregation of WPBs from the TGN; suggesting a primary role of V0a1 in the membrane fission of WPBs. The identification of V0a1 as a new membrane fission regulator should facilitate the understanding of molecular events that enable membrane fission.
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Affiliation(s)
- Yasuo Yamazaki
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Yuka Eura
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Koichi Kokame
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center, Osaka, Japan
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11
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FLIM-Based Intracellular and Extracellular pH Measurements Using Genetically Encoded pH Sensor. BIOSENSORS-BASEL 2021; 11:bios11090340. [PMID: 34562930 PMCID: PMC8468847 DOI: 10.3390/bios11090340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 02/04/2023]
Abstract
The determination of pH in live cells and tissues is of high importance in physiology and cell biology. In this report, we outline the process of the creation of SypHerExtra, a genetically encoded fluorescent sensor that is capable of measuring extracellular media pH in a mildly alkaline range. SypHerExtra is a protein created by fusing the previously described pH sensor SypHer3s with the neurexin transmembrane domain that targets its expression to the cytoplasmic membrane. We showed that with excitation at 445 nm, the fluorescence lifetime of both SypHer3s and SypHerExtra strongly depend on pH. Using FLIM microscopy in live eukaryotic cells, we demonstrated that SypHerExtra can be successfully used to determine extracellular pH, while SypHer3s can be applied to measure intracellular pH. Thus, these two sensors are suitable for quantitative measurements using the FLIM method, to determine intracellular and extracellular pH in a range from pH 7.5 to 9.5 in different biological systems.
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12
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Chin M, Patwardhan AR, Ang KH, Wang AL, Alquezar C, Welch M, Nguyen PT, Grabe M, Molofsky AV, Arkin MR, Kao AW. Genetically Encoded, pH-Sensitive mTFP1 Biosensor for Probing Lysosomal pH. ACS Sens 2021; 6:2168-2180. [PMID: 34102054 PMCID: PMC8240087 DOI: 10.1021/acssensors.0c02318] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 04/08/2021] [Indexed: 12/15/2022]
Abstract
Lysosomes are important sites for macromolecular degradation, defined by an acidic lumenal pH of ∼4.5. To better understand lysosomal pH, we designed a novel, genetically encoded, fluorescent protein (FP)-based pH biosensor called Fluorescence Indicator REporting pH in Lysosomes (FIRE-pHLy). This biosensor was targeted to lysosomes with lysosomal-associated membrane protein 1 (LAMP1) and reported lumenal pH between 3.5 and 6.0 with monomeric teal fluorescent protein 1 (mTFP1), a bright cyan pH-sensitive FP variant with a pKa of 4.3. Ratiometric quantification was enabled with cytosolically oriented mCherry using high-content quantitative imaging. We expressed FIRE-pHLy in several cellular models and quantified the alkalinizing response to bafilomycin A1, a specific V-ATPase inhibitor. In summary, we have engineered FIRE-pHLy, a specific, robust, and versatile lysosomal pH biosensor, that has broad applications for investigating pH dynamics in aging- and lysosome-related diseases, as well as in lysosome-based drug discovery.
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Affiliation(s)
- Marcus
Y. Chin
- Memory
and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
- Small
Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Anand R. Patwardhan
- Memory
and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| | - Kean-Hooi Ang
- Small
Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Austin L. Wang
- Memory
and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| | - Carolina Alquezar
- Memory
and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| | - Mackenzie Welch
- Memory
and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
| | - Phi T. Nguyen
- Weill
Institute for Neurosciences, Department of Psychiatry, University of California, San Francisco, California 94158, United States
| | - Michael Grabe
- Cardiovascular
Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Anna V. Molofsky
- Weill
Institute for Neurosciences, Department of Psychiatry, University of California, San Francisco, California 94158, United States
| | - Michelle R. Arkin
- Small
Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Aimee W. Kao
- Memory
and Aging Center, Department of Neurology, University of California, San Francisco, California 94158, United States
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13
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Ponsford AH, Ryan TA, Raimondi A, Cocucci E, Wycislo SA, Fröhlich F, Swan LE, Stagi M. Live imaging of intra-lysosome pH in cell lines and primary neuronal culture using a novel genetically encoded biosensor. Autophagy 2021; 17:1500-1518. [PMID: 32515674 PMCID: PMC8205096 DOI: 10.1080/15548627.2020.1771858] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/11/2022] Open
Abstract
Disorders of lysosomal physiology have increasingly been found to underlie the pathology of a rapidly growing cast of neurodevelopmental disorders and sporadic diseases of aging. One cardinal aspect of lysosomal (dys)function is lysosomal acidification in which defects trigger lysosomal stress signaling and defects in proteolytic capacity. We have developed a genetically encoded ratiometric probe to measure lysosomal pH coupled with a purification tag to efficiently purify lysosomes for both proteomic and in vitro evaluation of their function. Using our probe, we showed that lysosomal pH is remarkably stable over a period of days in a variety of cell types. Additionally, this probe can be used to determine that lysosomal stress signaling via TFEB is uncoupled from gross changes in lysosomal pH. Finally, we demonstrated that while overexpression of ARL8B GTPase causes striking alkalinization of peripheral lysosomes in HEK293 T cells, peripheral lysosomes per se are no less acidic than juxtanuclear lysosomes in our cell lines.Abbreviations: ARL8B: ADP ribosylation factor like GTPase 8B; ATP: adenosine triphosphate; ATP5F1B/ATPB: ATP synthase F1 subunit beta; ATP6V1A: ATPase H+ transporting V1 subunit A; Baf: bafilomycin A1; BLOC-1: biogenesis of lysosome-related organelles complex 1; BSA: bovine serum albumin; Cos7: African green monkey kidney fibroblast-like cell line; CQ: chloroquine; CTSB: cathepsin B; CYCS: cytochrome c, somatic; DAPI: 4',6-diamidino -2- phenylindole; DIC: differential interference contrast; DIV: days in vitro; DMEM: Dulbecco's modified Eagle's medium; E8: embryonic day 8; EEA1: early endosome antigen 1; EGTA: ethylene glycol-bis(β-aminoethyl ether)-N,N,N',N'-tetraacetic acid; ER: endoplasmic reticulum; FBS: fetal bovine serum; FITC: fluorescein isothiocyanate; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GOLGA2/GM130: golgin A2; GTP: guanosine triphosphate; HEK293T: human embryonic kidney 293 cells, that expresses a mutant version of the SV40 large T antigen; HeLa: Henrietta Lacks-derived cell; HEPES: 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid; HRP: horseradish peroxidase; IGF2R/ciM6PR: insulin like growth factor 2 receptor; LAMP1/2: lysosomal associated membrane protein 1/2; LMAN2/VIP36: lectin, mannose binding 2; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; PCR: polymerase chain reaction; PDL: poly-d-lysine; PGK1p: promotor from human phosphoglycerate kinase 1; PIKFYVE: phosphoinositide kinase, FYVE-type zinc finger containing; PPT1/CLN1: palmitoyl-protein thioesterase 1; RPS6KB1/p70: ribosomal protein S6 kinase B1; STAT3: signal transducer and activator of transcription 3; TAX1BP1: Tax1 binding protein 1; TFEB: transcription factor EB; TGN: trans-Golgi network; TGOLN2/TGN46: trans-Golgi network protein 2; TIRF: total internal reflection fluorescence; TMEM106B: transmembrane protein 106B; TOR: target of rapamycin; TRPM2: transient receptor potential cation channel subfamily M member 2; V-ATPase: vacuolar-type proton-translocating ATPase; VPS35: VPS35 retromer complex component.
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Affiliation(s)
- Amy H. Ponsford
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Thomas A. Ryan
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Andrea Raimondi
- Experimental Imaging Center, San Raffaele Scientific Institute, Milan, Italy
| | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Susanne A. Wycislo
- Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany
- Centre of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Osnabrück, Germany
| | - Laura E. Swan
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Massimiliano Stagi
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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14
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Manoli SS, Kisor K, Webb BA, Barber DL. Ethyl isopropyl amiloride decreases oxidative phosphorylation and increases mitochondrial fusion in clonal untransformed and cancer cells. Am J Physiol Cell Physiol 2021; 321:C147-C157. [PMID: 34038242 DOI: 10.1152/ajpcell.00001.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Many cancer cells, regardless of their tissue origin or genetic landscape, have increased expression or activity of the plasma membrane Na-H exchanger NHE1 and a higher intracellular pH (pHi) compared with untransformed cells. A current perspective that remains to be validated is that increased NHE1 activity and pHi enable a Warburg-like metabolic reprogramming of increased glycolysis and decreased mitochondrial oxidative phosphorylation. We tested this perspective and find it is not accurate for clonal pancreatic and breast cancer cells. Using the pharmacological reagent ethyl isopropyl amiloride (EIPA) to inhibit NHE1 activity and decrease pHi, we observe no change in glycolysis, as indicated by secreted lactate and intracellular pyruvate, despite confirming increased activity of the glycolytic enzyme phosphofructokinase-1 at higher pH. Also, in contrast to predictions, we find a significant decrease in oxidative phosphorylation with EIPA, as indicated by oxygen consumption rate (OCR). Decreased OCR with EIPA is not associated with changes in pathways that fuel oxidative phosphorylation or with mitochondrial membrane potential but occurs with a change in mitochondrial dynamics that includes a significant increase in elongated mitochondrial networks, suggesting increased fusion. These findings conflict with current paradigms on increased pHi inhibiting oxidative phosphorylation and increased oxidative phosphorylation being associated with mitochondrial fusion. Moreover, these findings raise questions on the suggested use of EIPA-like compounds to limit metabolic reprogramming in cancer cells.
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Affiliation(s)
- Sagar S Manoli
- Department of Cell and Tissue Biology, University of California, San Francisco, California
| | - Kyle Kisor
- Department of Cell and Tissue Biology, University of California, San Francisco, California
| | - Bradley A Webb
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, California
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15
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An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity. Biochem J 2021; 477:2999-3018. [PMID: 32729927 DOI: 10.1042/bcj20200311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/19/2022]
Abstract
Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate to α-ketoglutarate (αKG) to provide critical cytosolic substrates and drive NADPH-dependent reactions like lipid biosynthesis and glutathione regeneration. In biochemical studies, the forward reaction is studied at neutral pH, while the reverse reaction is typically characterized in more acidic buffers. This led us to question whether IDH1 catalysis is pH-regulated, which would have functional implications under conditions that alter cellular pH, like apoptosis, hypoxia, cancer, and neurodegenerative diseases. Here, we show evidence of catalytic regulation of IDH1 by pH, identifying a trend of increasing kcat values for αKG production upon increasing pH in the buffers we tested. To understand the molecular determinants of IDH1 pH sensitivity, we used the pHinder algorithm to identify buried ionizable residues predicted to have shifted pKa values. Such residues can serve as pH sensors, with changes in protonation states leading to conformational changes that regulate catalysis. We identified an acidic residue buried at the IDH1 dimer interface, D273, with a predicted pKa value upshifted into the physiological range. D273 point mutations had decreased catalytic efficiency and, importantly, loss of pH-regulated catalysis. Based on these findings, we conclude that IDH1 activity is regulated, at least in part, by pH. We show this regulation is mediated by at least one buried acidic residue ∼12 Å from the IDH1 active site. By establishing mechanisms of regulation of this well-conserved enzyme, we highlight catalytic features that may be susceptible to pH changes caused by cell stress and disease.
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16
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Webb BA, Aloisio FM, Charafeddine RA, Cook J, Wittmann T, Barber DL. pHLARE: a new biosensor reveals decreased lysosome pH in cancer cells. Mol Biol Cell 2020; 32:131-142. [PMID: 33237838 PMCID: PMC8120692 DOI: 10.1091/mbc.e20-06-0383] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many lysosome functions are determined by a lumenal pH of ∼5.0, including the activity of resident acid-activated hydrolases. Lysosome pH (pHlys) is often increased in neurodegenerative disorders and predicted to be decreased in cancers, making it a potential target for therapeutics to limit the progression of these diseases. Accurately measuring pHlys, however, is limited by currently used dyes that accumulate in multiple intracellular compartments and cannot be propagated in clonal cells for longitudinal studies or used for in vivo determinations. To resolve this limitation, we developed a genetically encoded ratiometric pHlys biosensor, pHLARE (pHLysosomal Activity REporter), which localizes predominantly in lysosomes, has a dynamic range of pH 4.0 to 6.5, and can be stably expressed in cells. Using pHLARE we show decreased pHlys with inhibiting activity of the mammalian target of rapamycin complex 1 (mTORC1). Also, cancer cells from different tissue origins have a lower pHlys than untransformed cells, and stably expressing oncogenic RasV12 in untransformed cells is sufficient to decrease pHlys. pHLARE is a new tool to accurately measure pHlys for improved understanding of lysosome dynamics, which is increasingly considered a therapeutic target.
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Affiliation(s)
- Bradley A Webb
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94941
| | - Francesca M Aloisio
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94941
| | - Rabab A Charafeddine
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94941
| | - Jessica Cook
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94941
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94941
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94941
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17
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Cancer and pH Dynamics: Transcriptional Regulation, Proteostasis, and the Need for New Molecular Tools. Cancers (Basel) 2020; 12:cancers12102760. [PMID: 32992762 PMCID: PMC7601256 DOI: 10.3390/cancers12102760] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
An emerging hallmark of cancer cells is dysregulated pH dynamics. Recent work has suggested that dysregulated intracellular pH (pHi) dynamics enable diverse cancer cellular behaviors at the population level, including cell proliferation, cell migration and metastasis, evasion of apoptosis, and metabolic adaptation. However, the molecular mechanisms driving pH-dependent cancer-associated cell behaviors are largely unknown. In this review article, we explore recent literature suggesting pHi dynamics may play a causative role in regulating or reinforcing tumorigenic transcriptional and proteostatic changes at the molecular level, and discuss outcomes on tumorigenesis and tumor heterogeneity. Most of the data we discuss are population-level analyses; lack of single-cell data is driven by a lack of tools to experimentally change pHi with spatiotemporal control. Data is also sparse on how pHi dynamics play out in complex in vivo microenvironments. To address this need, at the end of this review, we cover recent advances for live-cell pHi measurement at single-cell resolution. We also discuss the essential role for tool development in revealing mechanisms by which pHi dynamics drive tumor initiation, progression, and metastasis.
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18
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Tsai ES, Joud F, Wiesholler LM, Hirsch T, Hall EAH. Upconversion nanoparticles as intracellular pH messengers. Anal Bioanal Chem 2020; 412:6567-6581. [PMID: 32613570 PMCID: PMC7442772 DOI: 10.1007/s00216-020-02768-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 02/02/2023]
Abstract
Upconversion nanoparticles (UCNPs) should be particularly well suited for measurement inside cells because they can be imaged down to submicrometer dimensions in near real time using fluorescence microscopy, and they overcome problems, such as photobleaching, autofluorescence, and deep tissue penetration, that are commonly encountered in cellular imaging applications. In this study, the performance of an UCNP modified with a pH-sensitive dye (pHAb) is studied. The dye (emission wavelength 580 nm) was attached in a polyethylene imine (PEI) coating on the UCNP and excited via the 540-nm UCNP emission under 980-nm excitation. The UC resonance energy transfer efficiencies at different pHs ranged from 25 to 30% and a Förster distance of 2.56 nm was predicted from these results. Human neuroblastoma SH-SY5Y cells, equilibrated with nigericin H+/K+ ionophore to equalize the intra- and extracellular pH' showed uptake of the UCNP-pHAb conjugate particles and, taking the ratio of the intensity collected from the pHAb emission channel (565-630 nm) to that from the UCNP red emission channel (640-680 nm), produced a sigmoidal pH response curve with an apparent pKa for the UCNP-pHAb of ~ 5.1. The UCNP-pHAb were shown to colocalize with LysoBrite dye, a lysosome marker. Drug inhibitors such as chlorpromazine (CPZ) and nystatin (NYS) that interfere with clathrin-mediated endocytosis and caveolae-mediated endocytosis, respectively, were investigated to elucidate the mechanism of nanoparticle uptake into the cell. This preliminary study suggests that pH indicator-modified UCNPs such as UCNP-pHAb can report pH in SH-SY5Y cells and that the incorporation of the nanoparticles into the cell occurs via clathrin-mediated endocytosis. Graphical abstract.
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Affiliation(s)
- Evaline S Tsai
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Dr., Cambridge, CB3 0AS, UK
| | - Fadwa Joud
- Cancer Research UK Cambridge Institute, University of Cambridge, LiKa Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Lisa M Wiesholler
- Institute of Analytical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Thomas Hirsch
- Institute of Analytical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Elizabeth A H Hall
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Dr., Cambridge, CB3 0AS, UK.
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19
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Liu Y, White KA, Barber DL. Intracellular pH Regulates Cancer and Stem Cell Behaviors: A Protein Dynamics Perspective. Front Oncol 2020; 10:1401. [PMID: 32983969 PMCID: PMC7479815 DOI: 10.3389/fonc.2020.01401] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
The International Society of Cancer Metabolism (ISCaM) meeting on Cancer Metabolic Rewiring, held in Braga Portugal in October 2019, provided an outstanding forum for investigators to present current findings and views, and discuss ideas and future directions on fundamental biology as well as clinical translations. The first session on Cancer pH Dynamics was preceded by the opening keynote presentation from our group entitled Intracellular pH Regulation of Protein Dynamics: From Cancer to Stem Cell Behaviors. In this review we introduce a brief background on intracellular pH (pHi) dynamics, including how it is regulated as well as functional consequences, summarize key findings included in our presentation, and conclude with perspectives on how understanding the role of pHi dynamics in stem cells can be relevant for understanding how pHi dynamics enables cancer progression.
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Affiliation(s)
- Yi Liu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States
| | - Katharine A White
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States
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20
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Oginuma M, Harima Y, Tarazona OA, Diaz-Cuadros M, Michaut A, Ishitani T, Xiong F, Pourquié O. Intracellular pH controls WNT downstream of glycolysis in amniote embryos. Nature 2020; 584:98-101. [PMID: 32581357 PMCID: PMC8278564 DOI: 10.1038/s41586-020-2428-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/02/2020] [Indexed: 02/04/2023]
Abstract
Formation of the body of vertebrate embryos proceeds sequentially by posterior addition of tissues from the tail bud. Cells of the tail bud and the posterior presomitic mesoderm, which control posterior elongation1, exhibit a high level of aerobic glycolysis that is reminiscent of the metabolic status of cancer cells experiencing the Warburg effect2,3. Glycolytic activity downstream of fibroblast growth factor controls WNT signalling in the tail bud3. In the neuromesodermal precursors of the tail bud4, WNT signalling promotes the mesodermal fate that is required for sustained axial elongation, at the expense of the neural fate3,5. How glycolysis regulates WNT signalling in the tail bud is currently unknown. Here we used chicken embryos and human tail bud-like cells differentiated in vitro from induced pluripotent stem cells to show that these cells exhibit an inverted pH gradient, with the extracellular pH lower than the intracellular pH, as observed in cancer cells6. Our data suggest that glycolysis increases extrusion of lactate coupled to protons via the monocarboxylate symporters. This contributes to elevating the intracellular pH in these cells, which creates a favourable chemical environment for non-enzymatic β-catenin acetylation downstream of WNT signalling. As acetylated β-catenin promotes mesodermal rather than neural fate7, this ultimately leads to activation of mesodermal transcriptional WNT targets and specification of the paraxial mesoderm in tail bud precursors. Our work supports the notion that some tumour cells reactivate a developmental metabolic programme.
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Affiliation(s)
- Masayuki Oginuma
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- IMCR, Gunma University, Gunma, Japan
| | - Yukiko Harima
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Oscar A Tarazona
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Arthur Michaut
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Tohru Ishitani
- IMCR, Gunma University, Gunma, Japan
- RIMD, Osaka University, Osaka, Japan
| | - Fengzhu Xiong
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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21
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tpHusion: An efficient tool for clonal pH determination in Drosophila. PLoS One 2020; 15:e0228995. [PMID: 32059043 PMCID: PMC7021318 DOI: 10.1371/journal.pone.0228995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/27/2020] [Indexed: 02/04/2023] Open
Abstract
Genetically encoded pH indicators (GEpHI) have emerged as important tools for investigating intracellular pH (pHi) dynamics in Drosophila. However, most of the indicators are based on the Gal4/UAS binary expression system. Here, we report the generation of a ubiquitously-expressed GEpHI. The fusion protein of super ecliptic pHluorin and FusionRed was cloned under the tubulin promoter (tpHusion) to drive it independently of the Gal4/UAS system. The function of tpHusion was validated in various tissues from different developmental stages of Drosophila. Differences in pHi were also indicated correctly in fixed tissues. Finally, we describe the use of tpHusion for comparative analysis of pHi in manipulated clones and the surrounding cells in epithelial tissues. Our findings establish tpHusion as a robust tool for studying pHi in Drosophila.
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22
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Chávez JC, Darszon A, Treviño CL, Nishigaki T. Quantitative Intracellular pH Determinations in Single Live Mammalian Spermatozoa Using the Ratiometric Dye SNARF-5F. Front Cell Dev Biol 2020; 7:366. [PMID: 32010689 PMCID: PMC6978660 DOI: 10.3389/fcell.2019.00366] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/13/2019] [Indexed: 11/13/2022] Open
Abstract
Intracellular pH (pH i ) plays a crucial role in mammalian sperm physiology. However, it is a challenging task to acquire quantitative single sperm pH i images due to their small size and beating flagella. In this study, we established a robust pH i imaging system using the dual-emission ratiometric pH indicator, SNARF-5F. Simultaneous good signal/noise ratio fluorescence signals were obtained exciting with a green high-power LED (532 nm) and acquiring with an EM-CCD camera through an image splitter with two band-pass filters (550-600 nm, channel 1; 630-650 nm, channel 2). After in vivo calibration, we established an imaging system that allows determination of absolute pH i values in spermatozoa, minimizing cell movement artifacts. Using this system, we determined that bicarbonate increases non-capacitated human pH i with slower kinetics than in mouse spermatozoa. This difference suggests that distinct ionic transporters might be involved in the bicarbonate influx into human and mouse spermatozoa. Alternatively, pH i regulation downstream bicarbonate influx into spermatozoa could be different between the two species.
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Affiliation(s)
| | | | | | - Takuya Nishigaki
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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23
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Pedersen SF, Counillon L. The SLC9A-C Mammalian Na +/H + Exchanger Family: Molecules, Mechanisms, and Physiology. Physiol Rev 2019; 99:2015-2113. [PMID: 31507243 DOI: 10.1152/physrev.00028.2018] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Na+/H+ exchangers play pivotal roles in the control of cell and tissue pH by mediating the electroneutral exchange of Na+ and H+ across cellular membranes. They belong to an ancient family of highly evolutionarily conserved proteins, and they play essential physiological roles in all phyla. In this review, we focus on the mammalian Na+/H+ exchangers (NHEs), the solute carrier (SLC) 9 family. This family of electroneutral transporters constitutes three branches: SLC9A, -B, and -C. Within these, each isoform exhibits distinct tissue expression profiles, regulation, and physiological roles. Some of these transporters are highly studied, with hundreds of original articles, and some are still only rudimentarily understood. In this review, we present and discuss the pioneering original work as well as the current state-of-the-art research on mammalian NHEs. We aim to provide the reader with a comprehensive view of core knowledge and recent insights into each family member, from gene organization over protein structure and regulation to physiological and pathophysiological roles. Particular attention is given to the integrated physiology of NHEs in the main organ systems. We provide several novel analyses and useful overviews, and we pinpoint main remaining enigmas, which we hope will inspire novel research on these highly versatile proteins.
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Affiliation(s)
- S F Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; and Université Côte d'Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, LP2M, France, and Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - L Counillon
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; and Université Côte d'Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, LP2M, France, and Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
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24
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Spatiotemporal pH Heterogeneity as a Promoter of Cancer Progression and Therapeutic Resistance. Cancers (Basel) 2019; 11:cancers11071026. [PMID: 31330859 PMCID: PMC6678451 DOI: 10.3390/cancers11071026] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
Dysregulation of pH in solid tumors is a hallmark of cancer. In recent years, the role of altered pH heterogeneity in space, between benign and aggressive tissues, between individual cancer cells, and between subcellular compartments, has been steadily elucidated. Changes in temporal pH-related processes on both fast and slow time scales, including altered kinetics of bicarbonate-CO2 exchange and its effects on pH buffering and gradual, progressive changes driven by changes in metabolism, are further implicated in phenotypic changes observed in cancers. These discoveries have been driven by advances in imaging technologies. This review provides an overview of intra- and extracellular pH alterations in time and space reflected in cancer cells, as well as the available technology to study pH spatiotemporal heterogeneity.
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25
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Arce‐Rodríguez A, Volke DC, Bense S, Häussler S, Nikel PI. Non-invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator. Microb Biotechnol 2019; 12:799-813. [PMID: 31162835 PMCID: PMC6559197 DOI: 10.1111/1751-7915.13439] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 11/30/2022] Open
Abstract
The ability of Pseudomonas species to thrive in all major natural environments (i.e. terrestrial, freshwater and marine) is based on its exceptional capability to adapt to physicochemical changes. Thus, environmental bacteria have to tightly control the maintenance of numerous physiological traits across different conditions. The intracellular pH (pHi ) homoeostasis is a particularly important feature, since the pHi influences a large portion of the biochemical processes in the cell. Despite its importance, relatively few reliable, easy-to-implement tools have been designed for quantifying in vivo pHi changes in Gram-negative bacteria with minimal manipulations. Here we describe a convenient, non-invasive protocol for the quantification of the pHi in bacteria, which is based on the ratiometric fluorescent indicator protein PHP (pH indicator for Pseudomonas). The DNA sequence encoding PHP was thoroughly adapted to guarantee optimal transcription and translation of the indicator in Pseudomonas species. Our PHP-based quantification method demonstrated that pHi is tightly regulated over a narrow range of pH values not only in Pseudomonas, but also in other Gram-negative bacterial species such as Escherichia coli. The maintenance of the cytoplasmic pH homoeostasis in vivo could also be observed upon internal (e.g. redirection of glucose consumption pathways in P. putida) and external (e.g. antibiotic exposure in P. aeruginosa) perturbations, and the PHP indicator was also used to follow dynamic changes in the pHi upon external pH shifts. In summary, our work describes a reliable method for measuring pHi in Pseudomonas, allowing for the detailed investigation of bacterial pHi homoeostasis and its regulation.
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Affiliation(s)
- Alejandro Arce‐Rodríguez
- Department of Molecular BacteriologyHelmholtz Centre for Infection Research38124BraunschweigGermany
| | - Daniel C. Volke
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Sarina Bense
- Department of Molecular BacteriologyHelmholtz Centre for Infection Research38124BraunschweigGermany
| | - Susanne Häussler
- Department of Molecular BacteriologyHelmholtz Centre for Infection Research38124BraunschweigGermany
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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26
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Uchiyama S, Yano K, Fukatsu E, de Silva AP. Precise Proton Mapping near Ionic Micellar Membranes with Fluorescent Photoinduced‐Electron‐Transfer Sensors. Chemistry 2019; 25:8522-8527. [DOI: 10.1002/chem.201806270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/01/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Seiichi Uchiyama
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Kayo Yano
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Eiko Fukatsu
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - A. Prasanna de Silva
- School of Chemistry and Chemical EngineeringQueen's University Belfast BT9 5AG Northern Ireland
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27
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Jost APT, Waters JC. Designing a rigorous microscopy experiment: Validating methods and avoiding bias. J Cell Biol 2019; 218:1452-1466. [PMID: 30894402 PMCID: PMC6504886 DOI: 10.1083/jcb.201812109] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 01/06/2023] Open
Abstract
Images generated by a microscope are never a perfect representation of the biological specimen. Microscopes and specimen preparation methods are prone to error and can impart images with unintended attributes that might be misconstrued as belonging to the biological specimen. In addition, our brains are wired to quickly interpret what we see, and with an unconscious bias toward that which makes the most sense to us based on our current understanding. Unaddressed errors in microscopy images combined with the bias we bring to visual interpretation of images can lead to false conclusions and irreproducible imaging data. Here we review important aspects of designing a rigorous light microscopy experiment: validation of methods used to prepare samples and of imaging system performance, identification and correction of errors, and strategies for avoiding bias in the acquisition and analysis of images.
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28
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Chandirasekar S, You JG, Xue JH, Tseng WL. Synthesis of gold nanocluster-loaded lysozyme nanoparticles for label-free ratiometric fluorescent pH sensing: applications to enzyme–substrate systems and cellular imaging. J Mater Chem B 2019. [DOI: 10.1039/c9tb00640k] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have demonstrated the synthesis of gold nanocluster-loaded lysozyme nanoparticles as a dual-emission probe for ratiometric sensing of pH changes in enzyme–substrate systems and live cells.
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Affiliation(s)
| | - Jyun-Guo You
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424
- Taiwan
| | - Jhe-Hong Xue
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424
- Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424
- Taiwan
- School of Pharmacy
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29
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Silberman A, Goldman O, Boukobza Assayag O, Jacob A, Rabinovich S, Adler L, Lee JS, Keshet R, Sarver A, Frug J, Stettner N, Galai S, Persi E, Halpern KB, Zaltsman-Amir Y, Pode-Shakked B, Eilam R, Anikster Y, Nagamani SCS, Ulitsky I, Ruppin E, Erez A. Acid-Induced Downregulation of ASS1 Contributes to the Maintenance of Intracellular pH in Cancer. Cancer Res 2018; 79:518-533. [PMID: 30573518 DOI: 10.1158/0008-5472.can-18-1062] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/30/2018] [Accepted: 12/17/2018] [Indexed: 12/23/2022]
Abstract
Downregulation of the urea cycle enzyme argininosuccinate synthase (ASS1) by either promoter methylation or by HIF1α is associated with increased metastasis and poor prognosis in multiple cancers. We have previously shown that in normoxic conditions, ASS1 downregulation facilitates cancer cell proliferation by increasing aspartate availability for pyrimidine synthesis by the enzyme complex CAD. Here we report that in hypoxia, ASS1 expression in cancerous cells is downregulated further by HIF1α-mediated induction of miR-224-5p, making the cells more invasive and dependent on upstream substrates of ASS1 for survival. ASS1 was downregulated under acidic conditions, and ASS1-depleted cancer cells maintained a higher intracellular pH (pHi), depended less on extracellular glutamine, and displayed higher glutathione levels. Depletion of substrates of urea cycle enzymes in ASS1-deficient cancers decreased cancer cell survival. Thus, ASS1 levels in cancer are differentially regulated in various environmental conditions to metabolically benefit cancer progression. Understanding these alterations may help uncover specific context-dependent cancer vulnerabilities that may be targeted for therapeutic purposes. SIGNIFICANCE: Cancer cells in an acidic or hypoxic environment downregulate the expression of the urea cycle enzyme ASS1, which provides them with a redox and pH advantage, resulting in better survival.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/3/518/F1.large.jpg.
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Affiliation(s)
- Alon Silberman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Goldman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adi Jacob
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shiran Rabinovich
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Lital Adler
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Joo Sang Lee
- Center for Bioinformatics and Computational Biology and Dept. of Computer Science, University of Maryland, College Park, Maryland.,Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, Maryland
| | - Rom Keshet
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Sarver
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Julia Frug
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.,Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Sivan Galai
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Erez Persi
- Computational Biology and Bioinformatics Branch (CBB), National Library of Medicine, National Center for Biotechnology Information (NCBI), NIH, Bethesda, Maryland
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ben Pode-Shakked
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,The Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Raya Eilam
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yair Anikster
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,The Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Eytan Ruppin
- Center for Bioinformatics and Computational Biology and Dept. of Computer Science, University of Maryland, College Park, Maryland.,Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, Maryland
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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30
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Waadt R, Krebs M, Kudla J, Schumacher K. Multiparameter imaging of calcium and abscisic acid and high-resolution quantitative calcium measurements using R-GECO1-mTurquoise in Arabidopsis. THE NEW PHYTOLOGIST 2017; 216:303-320. [PMID: 28850185 DOI: 10.1111/nph.14706] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/15/2017] [Indexed: 05/17/2023]
Abstract
Calcium signals occur in specific spatio-temporal patterns in response to various stimuli and are coordinated with, for example, hormonal signals, for physiological and developmental adaptations. Quantification of calcium together with other signalling molecules is required for correlative analyses and to decipher downstream calcium-decoding mechanisms. Simultaneous in vivo imaging of calcium and abscisic acid has been performed here to investigate the interdependence of the respective signalling processes in Arabidopsis thaliana roots. Advanced ratiometric genetically encoded calcium indicators have been generated and in vivo calcium calibration protocols were established to determine absolute calcium concentration changes in response to auxin and ATP. In roots, abscisic acid induced long-term basal calcium concentration increases, while auxin triggered rapid signals in the elongation zone. The advanced ratiometric calcium indicator R-GECO1-mTurquoise exhibited an increased calcium signal resolution compared to commonly used Förster resonance energy transfer-based indicators. Quantitative calcium measurements in Arabidopsis root tips using R-GECO1-mTurquoise revealed detailed maps of absolute calcium concentration changes in response to auxin and ATP. Calcium calibration protocols using R-GECO1-mTurquoise enabled high-resolution quantitative imaging of resting cytosolic calcium concentrations and their dynamic changes that revealed distinct hormonal and ATP responses in roots.
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Affiliation(s)
- Rainer Waadt
- Entwicklungsbilogie der Pflanzen, Centre for Organismal Studies, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Melanie Krebs
- Entwicklungsbilogie der Pflanzen, Centre for Organismal Studies, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster, 48149, Germany
| | - Karin Schumacher
- Entwicklungsbilogie der Pflanzen, Centre for Organismal Studies, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
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31
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Tatapudy S, Benitez M, Nystul T. Methods for Imaging Intracellular pH of the Follicle Stem Cell Lineage in Live Drosophila Ovarian Tissue. J Vis Exp 2017. [PMID: 28994781 DOI: 10.3791/56316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Changes in intracellular pH (pHi) play important roles in the regulation of many cellular functions, including metabolism, proliferation, and differentiation. Typically, pHi dynamics are determined in cultured cells, which are amenable to measuring and experimentally manipulating pHi. However, the recent development of new tools and methodologies has made it possible to study pHi dynamics within intact, live tissue. For Drosophila research, one important development was the generation of a transgenic line carrying a pHi biosensor, mCherry::pHluorin. Here, we describe a protocol that we routinely use for imaging live Drosophila ovarioles to measure pHi in the epithelial follicle stem cell (FSC) lineage in mCherry::pHluorin transgenic wild type lines; however, the methods described here can be easily adapted for other tissues, including the wing discs and eye epithelium. We describe techniques for expressing mCherry::pHluorin in the FSC lineage, maintaining ovarian tissue during live imaging, and acquiring and analyzing images to obtain pHi values.
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Affiliation(s)
- Sumitra Tatapudy
- Departments of Anatomy and OB/GYN-RS, University of California, San Francisco
| | - Marimar Benitez
- Departments of Anatomy and OB/GYN-RS, University of California, San Francisco
| | - Todd Nystul
- Departments of Anatomy and OB/GYN-RS, University of California, San Francisco;
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32
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SRpHi ratiometric pH biosensors for super-resolution microscopy. Nat Commun 2017; 8:577. [PMID: 28924139 PMCID: PMC5603529 DOI: 10.1038/s41467-017-00606-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 07/07/2017] [Indexed: 12/02/2022] Open
Abstract
Fluorescence-based biosensors have become essential tools for modern biology, allowing real-time monitoring of biological processes within living cells. Intracellular fluorescent pH probes comprise one of the most widely used families of biosensors in microscopy. One key application of pH probes has been to monitor the acidification of vesicles during endocytosis, an essential function that aids in cargo sorting and degradation. Prior to the development of super-resolution fluorescence microscopy (nanoscopy), investigation of endosomal dynamics in live cells remained difficult as these structures lie at or below the ~250 nm diffraction limit of light microscopy. Therefore, to aid in investigations of pH dynamics during endocytosis at the nanoscale, we have specifically designed a family of ratiometric endosomal pH probes for use in live-cell STED nanoscopy. Ratiometric fluorescent pH probes are useful tools to monitor acidification of vesicles during endocytosis, but the size of vesicles is below the diffraction limit. Here the authors develop a family of ratiometric pH sensors for use in STED super-resolution microscopy, and optimize their delivery to endosomes.
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33
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Ma L, Ouyang Q, Werthmann GC, Thompson HM, Morrow EM. Live-cell Microscopy and Fluorescence-based Measurement of Luminal pH in Intracellular Organelles. Front Cell Dev Biol 2017; 5:71. [PMID: 28871281 PMCID: PMC5566985 DOI: 10.3389/fcell.2017.00071] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/04/2017] [Indexed: 11/16/2022] Open
Abstract
Luminal pH is an important functional feature of intracellular organelles. Acidification of the lumen of organelles such as endosomes, lysosomes, and the Golgi apparatus plays a critical role in fundamental cellular processes. As such, measurement of the luminal pH of these organelles has relevance to both basic research and translational research. At the same time, accurate measurement of intraorganellar pH in living cells can be challenging and may be a limiting hurdle for research in some areas. Here, we describe three powerful methods to measure rigorously the luminal pH of different intracellular organelles, focusing on endosomes, lysosomes, and the Golgi apparatus. The described methods are based on live imaging of pH-sensitive fluorescent probes and include: (1) A protocol based on quantitative, ratiometric measurement of endocytosis of pH-sensitive and pH-insensitive fluorescent conjugates of transferrin; (2) A protocol for the use of proteins tagged with a ratiometric variant of the pH-sensitive intrinsically fluorescent protein pHluorin; and (3) A protocol using the fluorescent dye LysoSensor™. We describe necessary reagents, key procedures, and methods and equipment for data acquisition and analysis. Examples of implementation of the protocols are provided for cultured cells derived from a cancer cell line and for primary cultures of mouse hippocampal neurons. In addition, we present strengths and weaknesses of the different described intraorganellar pH measurement methods. These protocols are likely to be of benefit to many researchers, from basic scientists to those conducting translational research with a focus on diseases in patient-derived cells.
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Affiliation(s)
- Li Ma
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidence, RI, United States.,Brown Institute for Brain Science, Brown UniversityProvidence, RI, United States
| | - Qing Ouyang
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidence, RI, United States.,Brown Institute for Brain Science, Brown UniversityProvidence, RI, United States
| | - Gordon C Werthmann
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidence, RI, United States
| | - Heather M Thompson
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidence, RI, United States.,Brown Institute for Brain Science, Brown UniversityProvidence, RI, United States.,Hassenfeld Child Health Innovation Institute, Brown UniversityProvidence, RI, United States
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidence, RI, United States.,Brown Institute for Brain Science, Brown UniversityProvidence, RI, United States.,Hassenfeld Child Health Innovation Institute, Brown UniversityProvidence, RI, United States
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34
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Ulmschneider B, Grillo-Hill BK, Benitez M, Azimova DR, Barber DL, Nystul TG. Increased intracellular pH is necessary for adult epithelial and embryonic stem cell differentiation. J Cell Biol 2017; 215:345-355. [PMID: 27821494 PMCID: PMC5100294 DOI: 10.1083/jcb.201606042] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/18/2016] [Accepted: 10/05/2016] [Indexed: 12/19/2022] Open
Abstract
Despite extensive knowledge about the transcriptional regulation of stem cell differentiation, less is known about the role of dynamic cytosolic cues. We report that an increase in intracellular pH (pHi) is necessary for the efficient differentiation of Drosophila adult follicle stem cells (FSCs) and mouse embryonic stem cells (mESCs). We show that pHi increases with differentiation from FSCs to prefollicle cells (pFCs) and follicle cells. Loss of the Drosophila Na+-H+ exchanger DNhe2 lowers pHi in differentiating cells, impairs pFC differentiation, disrupts germarium morphology, and decreases fecundity. In contrast, increasing pHi promotes excess pFC cell differentiation toward a polar/stalk cell fate through suppressing Hedgehog pathway activity. Increased pHi also occurs with mESC differentiation and, when prevented, attenuates spontaneous differentiation of naive cells, as determined by expression of microRNA clusters and stage-specific markers. Our findings reveal a previously unrecognized role of pHi dynamics for the differentiation of two distinct types of stem cell lineages, which opens new directions for understanding conserved regulatory mechanisms.
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Affiliation(s)
- Bryne Ulmschneider
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143
| | - Bree K Grillo-Hill
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143.,Department of Biological Sciences, San Jose State University, San Jose, CA 95192
| | - Marimar Benitez
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143
| | - Dinara R Azimova
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Todd G Nystul
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143 .,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143
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35
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Pedersen SF, Novak I, Alves F, Schwab A, Pardo LA. Alternating pH landscapes shape epithelial cancer initiation and progression: Focus on pancreatic cancer. Bioessays 2017; 39. [DOI: 10.1002/bies.201600253] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Stine F. Pedersen
- Section for Cell Biology and Physiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Ivana Novak
- Section for Cell Biology and Physiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Frauke Alves
- Max Planck Institute of Experimental Medicine; Göttingen Germany
- Institute for Diagnostic and Interventional Radiology; University Medical Center; Göttingen Germany
- Department of Hematology and Medical Oncology; University Medical Center; Göttingen Germany
| | - Albrecht Schwab
- Institute of Physiology II; University of Münster; Münster Germany
| | - Luis A. Pardo
- Max Planck Institute of Experimental Medicine; Göttingen Germany
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36
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Zhang L, Su F, Kong X, Lee F, Day K, Gao W, Vecera ME, Sohr JM, Buizer S, Tian Y, Meldrum DR. Ratiometric fluorescent pH-sensitive polymers for high-throughput monitoring of extracellular pH. RSC Adv 2016; 6:46134-46142. [PMID: 27721974 PMCID: PMC5049506 DOI: 10.1039/c6ra06468j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Extracellular pH has a strong effect on cell metabolism and growth. Precisely detecting extracellular pH with high throughput is critical for cell metabolism research and fermentation applications. In this research, a series of ratiometric fluorescent pH sensitive polymers are developed and the ps-pH-neutral is characterized as the best one for exculsive detection of extracellular pH. Poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA) is used as the host polymer to increase the water solubility of the pH sensitive polymer without introducing cell toxicity. The fluorescent emission spectra from the polymeric sensor under excitation at the isosbestic point 455 nm possess two fluorescence peaks at 475 nm and 505 nm, which have different responding trends to pH. This enables the polymer to detect pH using fluorescent maxima at 475 nm and 505 nm (I475nm /I505nm ) ratiometrically. The cell impermeability ensures the sensor can solely detect the environmental pH. The sensor is tested to detect the extracellular pH of bacteria or eukaryotic cells in high throughput assays using a microplate reader. Results showed that the pH sensor can be used for high throughput detection of extracellular pH with high repeatability and low photobleaching effect.
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Affiliation(s)
- Liqiang Zhang
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Fengyu Su
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Xiangxing Kong
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Fred Lee
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Kevin Day
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Weimin Gao
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Mary E. Vecera
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Jeremy M. Sohr
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Sean Buizer
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
| | - Yanqing Tian
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
- Department of Materials Science and Engineering, South University of Science and Technology of China, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong, 518055 (China)
| | - Deirdre R Meldrum
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University, 1001 S. McAlister Ave., P.O. Box 876501, Tempe, AZ 85287 (USA)
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37
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Yang Q, Ye Z, Zhong M, Chen B, Chen J, Zeng R, Wei L, Li HW, Xiao L. Self-Assembled Fluorescent Bovine Serum Albumin Nanoprobes for Ratiometric pH Measurement inside Living Cells. ACS APPLIED MATERIALS & INTERFACES 2016; 8:9629-9634. [PMID: 27015598 DOI: 10.1021/acsami.6b00857] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this work, we demonstrated a new ratiometric method for the quantitative analysis of pH inside living cells. The structure of the nanosensor comprises a biofriendly fluorescent bovine serum albumin (BSA) matrix, acting as a pH probe, and pH-insensitive reference dye Alexa 594 enabling ratiometric quantitative pH measurement. The fluorescent BSA matrix was synthesized by cross-linking of the denatured BSA proteins in ethanol with glutaraldehyde. The size of the as-synthesized BSA nanoparticles can be readily manipulated from 30 to 90 nm, which exhibit decent fluorescence at the peak wavelength of 535 nm with a pH response range of 6-8. The potential of this pH sensor for intracellular pH monitoring was demonstrated inside living HeLa cells, whereby a significant change in fluorescence ratio was observed when the pH of the cell was switched from normal to acidic with anticancer drug treatment. The fast response of the nanosensor makes it a very powerful tool in monitoring the processes occurring within the cytosol.
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Affiliation(s)
- Qiaoyu Yang
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, People's Republic of China
| | - Zhongju Ye
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, People's Republic of China
| | - Meile Zhong
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, People's Republic of China
| | - Bo Chen
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, People's Republic of China
| | - Jian Chen
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology , Xiangtan, Hunan 411201, People's Republic of China
| | - Rongjin Zeng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule of Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology , Xiangtan, Hunan 411201, People's Republic of China
| | - Lin Wei
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, People's Republic of China
| | - Hung-wing Li
- Department of Chemistry, Hongkong Baptist University , Kowloon Tong, Hong Kong, People's Republic of China
| | - Lehui Xiao
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, People's Republic of China
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Yung KY, Zhan Z, Titus AH, Baker GA, Bright FV. Ratiometric, filter-free optical sensor based on a complementary metal oxide semiconductor buried double junction photodiode. Anal Chim Acta 2015; 884:77-82. [PMID: 26073812 DOI: 10.1016/j.aca.2015.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/21/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022]
Abstract
We report a complementary metal oxide semiconductor integrated circuit (CMOS IC) with a buried double junction (BDJ) photodiode that (i) provides a real-time output signal that is related to the intensity ratio at two emission wavelengths and (ii) simultaneously eliminates the need for an optical filter to block Rayleigh scatter. We demonstrate the BDJ platform performance for gaseous NH3 and aqueous pH detection. We also compare the BDJ performance to parallel results obtained by using a slew scanned fluorimeter (SSF). The BDJ results are functionally equivalent to the SSF results without the need for any wavelength filtering or monochromators and the BDJ platform is not prone to errors associated with source intensity fluctuations or sensor signal drift.
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Affiliation(s)
- Ka Yi Yung
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Zhiyong Zhan
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Albert H Titus
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Gary A Baker
- Department of Chemistry, University of Missouri, Columbia, MO 65211-7600, USA
| | - Frank V Bright
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
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Grillo-Hill BK, Choi C, Jimenez-Vidal M, Barber DL. Increased H⁺ efflux is sufficient to induce dysplasia and necessary for viability with oncogene expression. eLife 2015; 4. [PMID: 25793441 PMCID: PMC4392478 DOI: 10.7554/elife.03270] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 03/17/2015] [Indexed: 01/02/2023] Open
Abstract
Intracellular pH (pHi) dynamics is increasingly recognized as an important regulator of a range of normal and pathological cell behaviors. Notably, increased pHi is now acknowledged as a conserved characteristic of cancers and in cell models is confirmed to increase proliferation and migration as well as limit apoptosis. However, the significance of increased pHi for cancer in vivo remains unresolved. Using Drosophila melanogaster, we show that increased pHi is sufficient to induce dysplasia in the absence of other transforming cues and potentiates growth and invasion with oncogenic Ras. Using a genetically encoded biosensor we also confirm increased pHi in situ. Moreover, in Drosophila models and clonal human mammary cells we show that limiting H(+) efflux with oncogenic Raf or Ras induces acidosis and synthetic lethality. Further, we show lethality in invasive primary tumor cell lines with inhibiting H(+) efflux. Synthetic lethality with reduced H(+) efflux and activated oncogene expression could be exploited therapeutically to restrain cancer progression while limiting off-target effects.
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Affiliation(s)
- Bree K Grillo-Hill
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, United States
| | - Changhoon Choi
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, United States
| | - Maite Jimenez-Vidal
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, United States
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, United States
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