151
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Bou Antoun N, Chioni AM. Dysregulated Signalling Pathways Driving Anticancer Drug Resistance. Int J Mol Sci 2023; 24:12222. [PMID: 37569598 PMCID: PMC10418675 DOI: 10.3390/ijms241512222] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
One of the leading causes of death worldwide, in both men and women, is cancer. Despite the significant development in therapeutic strategies, the inevitable emergence of drug resistance limits the success and impedes the curative outcome. Intrinsic and acquired resistance are common mechanisms responsible for cancer relapse. Several factors crucially regulate tumourigenesis and resistance, including physical barriers, tumour microenvironment (TME), heterogeneity, genetic and epigenetic alterations, the immune system, tumour burden, growth kinetics and undruggable targets. Moreover, transforming growth factor-beta (TGF-β), Notch, epidermal growth factor receptor (EGFR), integrin-extracellular matrix (ECM), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), phosphoinositol-3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR), wingless-related integration site (Wnt/β-catenin), Janus kinase/signal transducers and activators of transcription (JAK/STAT) and RAS/RAF/mitogen-activated protein kinase (MAPK) signalling pathways are some of the key players that have a pivotal role in drug resistance mechanisms. To guide future cancer treatments and improve results, a deeper comprehension of drug resistance pathways is necessary. This review covers both intrinsic and acquired resistance and gives a comprehensive overview of recent research on mechanisms that enable cancer cells to bypass barriers put up by treatments, and, like "satellite navigation", find alternative routes by which to carry on their "journey" to cancer progression.
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Affiliation(s)
| | - Athina-Myrto Chioni
- School of Life Sciences Pharmacy and Chemistry, Biomolecular Sciences Department, Kingston University London, Kingston-upon-Thames KT1 2EE, UK;
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152
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Yang SZ, Peng LT. Significance of the plasma membrane H +-ATPase and V-ATPase for growth and pathogenicity in pathogenic fungi. ADVANCES IN APPLIED MICROBIOLOGY 2023; 124:31-53. [PMID: 37597947 DOI: 10.1016/bs.aambs.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Pathogenic fungi are widespread and cause a variety of diseases in human beings and other organisms. At present, limited classes of antifungal agents are available to treat invasive fungal diseases. With the wide use of the commercial antifungal agents, drug resistance of pathogenic fungi are continuously increasing. Therefore, exploring effective antifungal agents with novel drug targets is urgently needed to cope with the challenges that the antifungal area faces. pH homeostasis is vital for multiple cellular processes, revealing the potential for defining novel drug targets. Fungi have evolved a number of strategies to maintain a stable pH internal environment in response to rapid metabolism and a dramatically changing extracellular environment. Among them, plasma membrane H+-ATPase (PMA) and vacuolar H+-ATPase (V-ATPase) play a central role in the regulation of pH homeostasis system. In this chapter, we will summarize the current knowledge about pH homeostasis and its regulation mechanisms in pathogenic fungi, especially for the recent advances in PMA and V-ATPase, which would help in revealing the regulating mechanism of pH on cell growth and pathogenicity, and further designing effective drugs and identify new targets for combating fungal diseases.
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Affiliation(s)
- S Z Yang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China.
| | - L T Peng
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
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153
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Hirose H, Nakata E, Zhang Z, Shibano Y, Maekawa M, Morii T, Futaki S. Macropinoscope: Real-Time Simultaneous Tracking of pH and Cathepsin B Activity in Individual Macropinosomes. Anal Chem 2023. [PMID: 37468434 DOI: 10.1021/acs.analchem.3c01645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
A fluorescent sensor that allows simultaneous analysis of environmental factors in a limited cellular space is useful for understanding precise molecular interactions in live cells and their biological responses. Macropinocytosis is a ubiquitous endocytic pathway for massive uptake of extracellular fluids, resulting in the formation of macropinosomes. Although macropinocytosis may impact intracellular delivery and cancer proliferation, information on the intracellular behaviors of macropinosomes is limited. Here, we aimed to develop a macropinoscope, a sensor that simultaneously detects pH and cathepsin B activity in individual macropinosomes. A macropinosome-specific marker, dextran (70 kDa), was employed as a platform, onto which fluorescein, Oregon Green, and tetramethylrhodamine were loaded for ratiometric pH sensing and imaging. A cathepsin-B-cleavable peptide sequence bearing sulfo-Cy5 and the quencher BHQ-3 was also mounted; cleavage of the sequence was detected as an increase in sulfo-Cy5 fluorescence. A steep decrease in pH was observed 5-10 min after macropinosome formation, which was accompanied by an immediate increase in cathepsin B activity. Our design concept will lead to the development of other macropinoscopes for the simultaneous detection of other parameters in individual macropinosomes.
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Affiliation(s)
- Hisaaki Hirose
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yuya Shibano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masashi Maekawa
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Minato, Tokyo 105-8512, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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154
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Tkachenko Y, Khmyz V, Buta A, Isaev D, Maximyuk O, Krishtal O. Acid-sensing ion channel blocker diminazene facilitates proton-induced excitation of afferent nerves in a similar manner that Na +/H + exchanger blockers do. Front Cell Neurosci 2023; 17:1131661. [PMID: 37502464 PMCID: PMC10368877 DOI: 10.3389/fncel.2023.1131661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Tissue acidification causes sustained activation of primary nociceptors, which causes pain. In mammals, acid-sensing ion channels (ASICs) are the primary acid sensors; however, Na+/H+ exchangers (NHEs) and TRPV1 receptors also contribute to tissue acidification sensing. ASICs, NHEs, and TRPV1 receptors are found to be expressed in nociceptive nerve fibers. ASIC inhibitors reduce peripheral acid-induced hyperalgesia and suppress inflammatory pain. Also, it was shown that pharmacological inhibition of NHE1 promotes nociceptive behavior in acute pain models, whereas inhibition of TRPV1 receptors gives relief. The murine skin-nerve preparation was used in this study to assess the activation of native polymodal nociceptors by mild acidification (pH 6.1). We have found that diminazene, a well-known antagonist of ASICs did not suppress pH-induced activation of CMH-fibers at concentrations as high as 25 μM. Moreover, at 100 μM, it induces the potentiation of the fibers' response to acidic pH. At the same time, this concentration virtually completely inhibited ASIC currents in mouse dorsal root ganglia (DRG) neurons (IC50 = 17.0 ± 4.5 μM). Non-selective ASICs and NHEs inhibitor EIPA (5-(N-ethyl-N-isopropyl)amiloride) at 10 μM, as well as selective NHE1 inhibitor zoniporide at 0.5 μM induced qualitatively the same effects as 100 μM of diminazene. Our results indicate that excitation of afferent nerve terminals induced by mild acidification occurs mainly due to the NHE1, rather than acid-sensing ion channels. At high concentrations, diminazene acts as a weak blocker of the NHE. It lacks chemical similarity with amiloride, EIPA, and zoniporide, so it may represent a novel structural motif for the development of NHE antagonists. However, the effect of diminazene on the acid-induced excitation of primary nociceptors remains enigmatic and requires additional investigations.
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155
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Richardson BJ, Zhang C, Rauthe P, Unterreiner AN, Golberg DV, Poad BLJ, Frisch H. Peptide Self-Assembly Controlled Photoligation of Polymers. J Am Chem Soc 2023. [PMID: 37433011 DOI: 10.1021/jacs.3c03961] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Highly efficient chemical ligations that operate in water under mild conditions are the foundation of bioorthogonal chemistry. However, the toolbox of suitable reactions is limited. Conventional approaches to expand this toolbox aim at altering the inherent reactivity of functional groups to design new reactions that meet the required benchmarks. Inspired by controlled reaction environments that enzymes provide, we report a fundamentally different approach that makes inefficient reactions highly efficient within defined local environments. Contrasting enzymatically catalyzed reactions, the reactivity controlling self-assembled environment is brought about by the ligation targets themselves─avoiding the use of a catalyst. Targeting [2 + 2] photocycloadditions, which are inefficient at low concentrations and readily quenched by oxygen, short β-sheet encoded peptide sequences are inserted between a hydrophobic photoreactive styrylpyrene unit and a hydrophilic polymer. In water, electrostatic repulsion of deprotonated amino acid residues governs the formation of small self-assembled structures, which enable a highly efficient photoligation of the polymer, reaching ∼90% ligation within 2 min (0.034 mM). Upon protonation at low pH, the self-assembly changes into 1D fibers, altering photophysical properties and shutting down the photocycloaddition reaction. Using the reversible morphology change, it is possible to switch the photoligation "ON" or "OFF" under constant irradiation simply by varying the pH. Importantly, in dimethylformamide, the photoligation reaction did not occur even at 10-fold higher concentrations (0.34 mM). The self-assembly into a specific architecture, encoded into the polymer ligation target, enables a highly efficient ligation that overcomes the concentration limitations and high oxygen sensitivity of [2 + 2] photocycloadditions.
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Affiliation(s)
- Bailey J Richardson
- School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
- Centre for Materials Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
| | - Chao Zhang
- School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
- Centre for Materials Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
- Central Analytical Research Facility, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
| | - Pascal Rauthe
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, Karlsruhe 76131, Germany
| | - Andreas-Neil Unterreiner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, Karlsruhe 76131, Germany
| | - Dmitri V Golberg
- School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
- Centre for Materials Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
| | - Berwyck L J Poad
- School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
- Centre for Materials Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
- Central Analytical Research Facility, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
| | - Hendrik Frisch
- School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
- Centre for Materials Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
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156
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Mozaffari M, Nyström NN, Li A, Bellyou M, Scholl TJ, Bartha R. Intracellular Acidification in a Rat C6 Glioma Model following Cariporide Injection Investigated by CEST-MRI. Metabolites 2023; 13:823. [PMID: 37512530 PMCID: PMC10386045 DOI: 10.3390/metabo13070823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Acidification of cancerous tissue induced pharmacologically may slow tumor growth and can be detected using magnetic resonance imaging. Numerous studies have shown that pharmacologically inhibiting specific transporters, such as the Na+/H+ exchanger 1 (NHE1), can alter glycolitic metabolism and affect tumor acidosis. The sodium proton exchanger inhibitor Cariporide can acidify U87MG gliomas in mice. This study aimed to determine whether Cariporide could acidify C6 glioma tumors in rats with an intact immune system. C6 glioma cells were implanted in the right brain hemisphere of ten rats. Chemical exchange saturation transfer (CEST) MRI (9.4T) was acquired on days 7-8 and 14-15 after implantation to measure in vivo tissue intracellular pH (pHi) within the tumors and on the contralateral side. pHi was basic relative to contralateral tissue at both time points assessed using the amine and amide concentration-independent detection (AACID) value. On day 14-15, measurements were made before and up to 160 min after Cariporide injection (N = 6). Twenty minutes after drug injection, the average AACID value in the tumor significantly increased by ∼6.4% compared to pre-injection, corresponding to 0.31 ± 0.20 lower pHi, while in contralateral tissue, AACID value increased significantly by ∼4.3% compared to pre-injection, corresponding to 0.22 ± 0.19 lower pHi. Control rats without tumors showed no changes following injection of Cariporide dissolved in 10% or 1% DMSO and diluted in PBS. This study demonstrates the sensitivity of CEST-based pH-weighted imaging for monitoring the response of tumors to pharmacologically induced acidification.
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Affiliation(s)
- Maryam Mozaffari
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Nivin N Nyström
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alex Li
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Miranda Bellyou
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
| | - Timothy J Scholl
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Robert Bartha
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Centre for Functional and Metabolic Mapping, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada
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157
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Suresh S, Mirasole A, Ravasi T, Vizzini S, Schunter C. Brain transcriptome of gobies inhabiting natural CO 2 seeps reveal acclimation strategies to long-term acidification. Evol Appl 2023; 16:1345-1358. [PMID: 37492147 PMCID: PMC10363848 DOI: 10.1111/eva.13574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/27/2023] Open
Abstract
Ocean acidification (OA) is known to affect the physiology, survival, behaviour and fitness of various fish species with repercussions at the population, community and ecosystem levels. Some fish species, however, seem to acclimate rapidly to OA conditions and even thrive in acidified environments. The molecular mechanisms that enable species to successfully inhabit high CO2 environments have not been fully elucidated especially in wild fish populations. Here, we used the natural CO2 seep in Vulcano Island, Italy to study the effects of elevated CO2 exposure on the brain transcriptome of the anemone goby, a species with high population density in the CO2 seep and investigate their potential for acclimation. Compared to fish from environments with ambient CO2, gobies living in the CO2 seep showed differences in the expression of transcripts involved in ion transport and pH homeostasis, cellular stress, immune response, circadian rhythm and metabolism. We also found evidence of potential adaptive mechanisms to restore the functioning of GABAergic pathways, whose activity can be affected by exposure to elevated CO2 levels. Our findings indicate that gobies living in the CO2 seep may be capable of mitigating CO2-induced oxidative stress and maintaining physiological pH while meeting the consequent increased energetic costs. The conspicuous difference in the expression of core circadian rhythm transcripts could provide an adaptive advantage by increasing the flexibility of physiological processes in elevated CO2 conditions thereby facilitating acclimation. Our results show potential molecular processes of acclimation to elevated CO2 in gobies enabling them to thrive in the acidified waters of Vulcano Island.
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Affiliation(s)
- Sneha Suresh
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Alice Mirasole
- Department of Integrative Marine EcologyIschia Marine Centre, Stazione Zoologica Anton DohrnNaplesItaly
| | - Timothy Ravasi
- Marine Climate Change UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Salvatrice Vizzini
- Department of Earth and Marine SciencesUniversity of PalermoPalermoItaly
- CoNISMa, National Inter‐University Consortium for Marine ScienceRomaItaly
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongHong Kong SARChina
- State Key Laboratory of Marine PollutionCity University of Hong KongHong Kong SARChina
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158
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Holendova B, Plecita-Hlavata L. Cysteine residues in signal transduction and its relevance in pancreatic beta cells. Front Endocrinol (Lausanne) 2023; 14:1221520. [PMID: 37455926 PMCID: PMC10339824 DOI: 10.3389/fendo.2023.1221520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Cysteine is one of the least abundant but most conserved amino acid residues in proteins, playing a role in their structure, metal binding, catalysis, and redox chemistry. Thiols present in cysteines can be modified by post-translational modifications like sulfenylation, acylation, or glutathionylation, regulating protein activity and function and serving as signals. Their modification depends on their position in the structure, surrounding amino acids, solvent accessibility, pH, etc. The most studied modifications are the redox modifications by reactive oxygen, nitrogen, and sulfur species, leading to reversible changes that serve as cell signals or irreversible changes indicating oxidative stress and cell damage. Selected antioxidants undergoing reversible oxidative modifications like peroxiredoxin-thioredoxin system are involved in a redox-relay signaling that can propagate to target proteins. Cysteine thiols can also be modified by acyl moieties' addition (derived from lipid metabolism), resulting in protein functional modification or changes in protein anchoring in the membrane. In this review, we update the current knowledge on cysteine modifications and their consequences in pancreatic β-cells. Because β-cells exhibit well-balanced redox homeostasis, the redox modifications of cysteines here serve primarily for signaling purposes. Similarly, lipid metabolism provides regulatory intermediates that have been shown to be necessary in addition to redox modifications for proper β-cell function and, in particular, for efficient insulin secretion. On the contrary, the excess of reactive oxygen, nitrogen, and sulfur species and the imbalance of lipids under pathological conditions cause irreversible changes and contribute to oxidative stress leading to cell failure and the development of type 2 diabetes.
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Affiliation(s)
| | - Lydie Plecita-Hlavata
- Laboratory of Pancreatic Islet Research, Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
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159
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He X, Wei Y, Wu J, Wang Q, Bergholz JS, Gu H, Zou J, Lin S, Wang W, Xie S, Jiang T, Lee J, Asara JM, Zhang K, Cantley LC, Zhao JJ. Lysine vitcylation is a novel vitamin C-derived protein modification that enhances STAT1-mediated immune response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546774. [PMID: 37425798 PMCID: PMC10327172 DOI: 10.1101/2023.06.27.546774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Vitamin C (vitC) is a vital nutrient for health and also used as a therapeutic agent in diseases such as cancer. However, the mechanisms underlying vitC's effects remain elusive. Here we report that vitC directly modifies lysine without enzymes to form vitcyl-lysine, termed "vitcylation", in a dose-, pH-, and sequence-dependent manner across diverse proteins in cells. We further discover that vitC vitcylates K298 site of STAT1, which impairs its interaction with the phosphatase PTPN2, preventing STAT1 Y701 dephosphorylation and leading to increased STAT1-mediated IFN pathway activation in tumor cells. As a result, these cells have increased MHC/HLA class-I expression and activate immune cells in co-cultures. Tumors collected from vitC-treated tumor-bearing mice have enhanced vitcylation, STAT1 phosphorylation and antigen presentation. The identification of vitcylation as a novel PTM and the characterization of its effect in tumor cells opens a new avenue for understanding vitC in cellular processes, disease mechanisms, and therapeutics.
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160
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Michl J, Monterisi S, White B, Blaszczak W, Hulikova A, Abdullayeva G, Bridges E, Yin Z, Bodmer WF, Swietach P. Acid-adapted cancer cells alkalinize their cytoplasm by degrading the acid-loading membrane transporter anion exchanger 2, SLC4A2. Cell Rep 2023; 42:112601. [PMID: 37270778 DOI: 10.1016/j.celrep.2023.112601] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/16/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023] Open
Abstract
Acidic environments reduce the intracellular pH (pHi) of most cells to levels that are sub-optimal for growth and cellular functions. Yet, cancers maintain an alkaline cytoplasm despite low extracellular pH (pHe). Raised pHi is thought to be beneficial for tumor progression and invasiveness. However, the transport mechanisms underpinning this adaptation have not been studied systematically. Here, we characterize the pHe-pHi relationship in 66 colorectal cancer cell lines and identify the acid-loading anion exchanger 2 (AE2, SLC4A2) as a regulator of resting pHi. Cells adapt to chronic extracellular acidosis by degrading AE2 protein, which raises pHi and reduces acid sensitivity of growth. Acidity inhibits mTOR signaling, which stimulates lysosomal function and AE2 degradation, a process reversed by bafilomycin A1. We identify AE2 degradation as a mechanism for maintaining a conducive pHi in tumors. As an adaptive mechanism, inhibiting lysosomal degradation of AE2 is a potential therapeutic target.
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Affiliation(s)
- Johanna Michl
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Stefania Monterisi
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Bobby White
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Wiktoria Blaszczak
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Alzbeta Hulikova
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Gulnar Abdullayeva
- MRC Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Esther Bridges
- Department of NDM Experimental Medicine, MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, JR Hospital, Headington, Oxford OX3 9DS, UK
| | - Zinan Yin
- Department of NDM Experimental Medicine, MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, JR Hospital, Headington, Oxford OX3 9DS, UK
| | - Walter F Bodmer
- MRC Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK.
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161
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Pereira LM, Portapilla GB, Brancini GTP, Possato B, Bronzon da Costa CM, Abreu-Filho PG, Wainwright M, Yatsuda AP, Braga GÚL. The potential of phenothiazinium dyes as cytotoxicity markers in cisplatin-treated cells. Sci Rep 2023; 13:10203. [PMID: 37353536 PMCID: PMC10290130 DOI: 10.1038/s41598-023-36721-0] [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: 03/08/2023] [Accepted: 06/08/2023] [Indexed: 06/25/2023] Open
Abstract
Assessing the in vitro toxicity of compounds on cell cultures is an important step during the screening of candidate molecules for diverse applications. Among the strategies employed to determine cytotoxicity, MTT, neutral red, and resazurin are commonly used. Methylene blue (MB), a phenothiazinium salt, has several uses, such as dye, redox indicator, and even as treatment for human disease and health conditions, such as malaria and methemoglobinemia. However, MB has only been sparsely used as a cellular toxicity indicator. As a viability indicator, MB is mostly applied to fixed cultures at high concentrations, especially when compared to MTT or neutral red. Here we show that MB and its related compounds new methylene blue (NMB), toluidine blue O (TBO), and dimethylmethylene blue (DMMB) can be used as cytotoxicity indicators in live (non-fixed) cells treated for 72 h with DMSO and cisplatin. We compared dye uptake between phenothiazinium dyes and neutral red by analyzing supernatant and cell content via visible spectra scanning and microscopy. All dyes showed a similar ability to assess cell toxicity compared to either MTT or neutral red. Our method represents a cost-effective alternative to in vitro cytotoxicity assays using cisplatin or DMSO, indicating the potential of phenothiazinium dyes for the screening of candidate drugs and other applications.
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Affiliation(s)
- Luiz Miguel Pereira
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café, sn/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Gisele Bulhões Portapilla
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café, sn/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Guilherme Thomaz Pereira Brancini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café, sn/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Bruna Possato
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café, sn/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Cássia Mariana Bronzon da Costa
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café, sn/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Péricles Gama Abreu-Filho
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café, sn/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Mark Wainwright
- Department of Biology, Edge Hill University, Ormskirk, L39 4QP, UK
| | - Ana Patrícia Yatsuda
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café, sn/n, Ribeirão Preto, SP, 14040-903, Brazil.
- Departamento de Análises Clínicas, Bromatológicas e Toxicológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil.
| | - Gilberto Úbida Leite Braga
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café, sn/n, Ribeirão Preto, SP, 14040-903, Brazil.
- Departamento de Análises Clínicas, Bromatológicas e Toxicológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil.
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162
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Gumerova NI, Rompel A. Speciation atlas of polyoxometalates in aqueous solutions. SCIENCE ADVANCES 2023; 9:eadi0814. [PMID: 37343109 DOI: 10.1126/sciadv.adi0814] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
Speciation is the key parameter in solution chemistry that describes the composition, concentration, and oxidation state of each chemical form of an element present in a sample. The speciation study of complex polyatomic ions has remained challenging because of the large number of factors affecting stability and the limited number of direct methods. To address these challenges, we developed the speciation atlas of 10 polyoxometalates commonly used in catalytic and biological applications in aqueous solutions, where the speciation atlas provides both a species distribution database and a predictive model for other polyoxometalates to be used. Compiled for six different polyoxometalate archetypes with three types of addenda ions based on 1309 nuclear magnetic resonance spectra under 54 different conditions, the atlas has revealed a previously unknown behavior of polyoxometalates that may account for their potency as biological agents and catalysts. The atlas is intended to promote the interdisciplinary use of metal oxides in various scientific fields.
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Affiliation(s)
- Nadiia I Gumerova
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Josef-Holaubek-Platz 2, 1090 Wien, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Josef-Holaubek-Platz 2, 1090 Wien, Austria
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163
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Zhang L, Guo J, You Q, Xu Y. A water-soluble fluorescent pH probe and its application for monitoring lysosomal pH changes in living cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023. [PMID: 37317586 DOI: 10.1039/d3ay00343d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Intracellular pH plays a crucial role in many cellular processes, and abnormal intracellular pH has been linked to common diseases such as cancer and Alzheimer's. To address this issue, a water-soluble fluorescent pH probe was designed based on the protonation/deprotonation of the 4-methylpiperazin-1-yl group, using dicyanoisophorone as the fluorophore. In the neutral form of the probe, fluorescence is quenched due to charge transfer from the 4-methylpiperazin-1-yl group to the fluorophore upon excitation. Under acidic conditions, protonation of the 4-methylpiperazin-1-yl group inhibits the photoinduced electron transfer process, leading to an increase in fluorescence intensity. Density-functional theory calculations also verified the fluorescence OFF-ON mechanism. The probe exhibits high selectivity, photostability, fast response to pH changes, and low cytotoxicity to cells. Additionally, the probe selectively accumulates in lysosomes, with a high Pearson coefficient (0.95) using LysoTracker Green DND-26 as a reference. Notably, the probe can monitor lysosomal pH changes in living cells and track pH changes stimulated by chloroquine. We anticipate that the probe has potential for diagnosing pH-related diseases.
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Affiliation(s)
- Lei Zhang
- Department of Biology, Xinzhou Teachers University, Xinzhou, Shanxi Province 034000, P. R. of China
| | - Jun Guo
- ShanXi Weipu Testing Technology Co. Ltd, Taiyuan, Shanxi Province 030012, P. R. of China
| | - Qihua You
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian Province 361024, P. R. of China.
| | - Yuqing Xu
- School of Physics and Optoelectronics Engineering, Ludong University, Yantai, Shandong Province 264025, P. R. of China
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164
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Lee S, Jiao M, Zhang Z, Yu Y. Nanoparticles for Interrogation of Cell Signaling. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:333-351. [PMID: 37314874 PMCID: PMC10627408 DOI: 10.1146/annurev-anchem-092822-085852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cell functions rely on signal transduction-the cascades of molecular interactions and biochemical reactions that relay extracellular signals to the cell interior. Dissecting principles governing the signal transduction process is critical for the fundamental understanding of cell physiology and the development of biomedical interventions. The complexity of cell signaling is, however, beyond what is accessible by conventional biochemistry assays. Thanks to their unique physical and chemical properties, nanoparticles (NPs) have been increasingly used for the quantitative measurement and manipulation of cell signaling. Even though research in this area is still in its infancy, it has the potential to yield new, paradigm-shifting knowledge of cell biology and lead to biomedical innovations. To highlight this importance, we summarize in this review studies that pioneered the development and application of NPs for cell signaling, from quantitative measurements of signaling molecules to spatiotemporal manipulation of cell signal transduction.
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Affiliation(s)
- Seonik Lee
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Mengchi Jiao
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Zihan Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Yan Yu
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
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165
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Chmiel P, Gęca K, Michalski A, Kłosińska M, Kaczyńska A, Polkowski WP, Pelc Z, Skórzewska M. Vista of the Future: Novel Immunotherapy Based on the Human V-Set Immunoregulatory Receptor for Digestive System Tumors. Int J Mol Sci 2023; 24:9945. [PMID: 37373091 PMCID: PMC10297928 DOI: 10.3390/ijms24129945] [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: 04/26/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
While gastrointestinal tumors remain a multifactorial and prevalent group of malignancies commonly treated surgically in combination with chemotherapy and radiotherapy, advancements regarding immunotherapeutic approaches continue to occur. Entering a new era of immunotherapy focused on overcoming resistance to preceding therapies caused the emergence of new therapeutic strategies. A promising solution surfaces with a V-domain Ig suppressor of T-cell activation (VISTA), a negative regulator of a T-cell function expressed in hematopoietic cells. Due to VISTA's ability to act as both a ligand and a receptor, several therapeutic approaches can be potentially developed. A broad expression of VISTA was discovered on various tumor-growth-controlling cells, which proved to increase in specific tumor microenvironment (TME) conditions, thus serving as a rationale behind the development of new VISTA-targeting. Nevertheless, VISTA's ligands and signaling pathways are still not fully understood. The uncertain results of clinical trials suggest the need for future examining inhibitor agents for VISTA and implicating a double immunotherapeutic blockade. However, more research is needed before the breakthrough can be achieved. This review discusses perspectives and novel approaches presented in the current literature. Based on the results of the ongoing studies, VISTA might be considered a potential target in combined therapy, especially for treating gastrointestinal malignancies.
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166
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Goshisht MK, Tripathi N, Patra GK, Chaskar M. Organelle-targeting ratiometric fluorescent probes: design principles, detection mechanisms, bio-applications, and challenges. Chem Sci 2023; 14:5842-5871. [PMID: 37293660 PMCID: PMC10246671 DOI: 10.1039/d3sc01036h] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/27/2023] [Indexed: 06/10/2023] Open
Abstract
Biological species, including reactive oxygen species (ROS), reactive sulfur species (RSS), reactive nitrogen species (RNS), F-, Pd2+, Cu2+, Hg2+, and others, are crucial for the healthy functioning of cells in living organisms. However, their aberrant concentration can result in various serious diseases. Therefore, it is essential to monitor biological species in cellular organelles such as the cell membrane, mitochondria, lysosome, endoplasmic reticulum, Golgi apparatus, and nucleus. Among various fluorescent probes for species detection within the organelles, ratiometric fluorescent probes have drawn special attention as a potential way to get beyond the drawbacks of intensity-based probes. This method depends on measuring the intensity change of two emission bands (caused by an analyte), which produces an efficient internal referencing that increases the detection's sensitivity. This review article discusses the literature publications (from 2015 to 2022) on organelle-targeting ratiometric fluorescent probes, the general strategies, the detecting mechanisms, the broad scope, and the challenges currently faced by fluorescent probes.
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Affiliation(s)
- Manoj Kumar Goshisht
- Department of Chemistry, Natural and Applied Sciences, University of Wisconsin-Green Bay 2420 Nicolet Drive Green Bay WI 54311-7001 USA
- Department of Chemistry, Government Naveen College Tokapal Bastar Chhattisgarh 494442 India
| | - Neetu Tripathi
- Department of Chemistry, Guru Nanak Dev University Amritsar Punjab 143005 India
| | - Goutam Kumar Patra
- Department of Chemistry, Faculty of Physical Sciences Guru Ghasidas Vishwavidyalaya Bilaspur Chhattisgarh 495009 India
| | - Manohar Chaskar
- Department of Technology, Savitribai Phule Pune University Ganeshkhind Pune 411007 India
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167
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Wang H, Rubinstein JL. CryoEM of V-ATPases: Assembly, disassembly, and inhibition. Curr Opin Struct Biol 2023; 80:102592. [PMID: 37272327 DOI: 10.1016/j.sbi.2023.102592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 06/06/2023]
Abstract
Vacuolar-type ATPases (V-ATPases) are responsible for the acidification of intracellular compartments in almost all eukaryotic cells, while in some specialized cells they acidify the extracellular environment. As ubiquitous proton pumps, these large membrane-embedded enzymes are involved in many fundamental cellular processes that require tight control of pH. Consequently, V-ATPase malfunction or aberrant activity has been linked to numerous diseases. In the past ten years, electron cryomicroscopy (cryoEM) of yeast V-ATPases has revealed the architecture and rotary catalytic mechanism of these macromolecular machines. More recently, studies have revealed the structures of V-ATPases in animals and plants, uncovered aspects of how V-ATPases are assembled and regulated by reversible dissociation, and shown how V-ATPase activity can be modulated by proteins and small molecule inhibitors. In this review, we highlight these recent developments.
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Affiliation(s)
- Hanlin Wang
- Molecular Medicine Program, The Hospital for Sick Children, M5G 0A4, Toronto, Canada; Department of Biochemistry, The University of Toronto, M5G 1L7, Toronto, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, M5G 0A4, Toronto, Canada; Department of Biochemistry, The University of Toronto, M5G 1L7, Toronto, Canada; Department of Medical Biophysics, The University of Toronto, M5S 1A8, Toronto, Canada.
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168
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Cuesta-Rubio O, Monzote L, Fernández-Acosta R, Pardo-Andreu GL, Rastrelli L. A review of nemorosone: Chemistry and biological properties. PHYTOCHEMISTRY 2023; 210:113674. [PMID: 37044362 DOI: 10.1016/j.phytochem.2023.113674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Nemorosone is a bicyclic polyprenylated acylphloroglucinol derivative originally isolated from Clusia spp. and it can be obtained through chemical synthesis employing different synthetic strategies. Since its discovery, it has attracted great attention both from a biological and chemical viewpoint. In the present article, we attempted to review various chemical and biological topics around nemorosone, with an emphasis on its antiproliferative activities. For this purpose, relevant data was collected from different scientific databases including Google Scholar, PubMed, Scopus and ISI Web of Knowledge. This natural compound has shown activity against several types of malignancies such as leukemia, human colorectal, pancreatic, and breast cancer because it modulates multiple molecular pathways. Nemorosone has both cytostatic and cytotoxic activity and it also seems to induce apoptosis and ferroptosis. Additionally, it has antimicrobial capabilities against Gram-positive bacteria and parasites belonging to genus Leishmania. Its promising antiproliferative pre-clinical effects deserve further attention for anticancer and anti-parasitic drug development and translation to the clinic.
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Affiliation(s)
- Osmany Cuesta-Rubio
- Universidad Técnica de Machala, Facultad de Ciencias Químicas y de la Salud, Ave. Panamericana km 5½, 070101, Machala, Ecuador.
| | - Lianet Monzote
- Departamento de Parasitología, Instituto de Medicina Tropical Pedro Kourí, Autopista Novia del Mediodía Km 6 1/2, 11400, La Habana, Cuba.
| | - Roberto Fernández-Acosta
- Department of Pharmacy, Institute of Pharmaceutical and Food Sciences, University of Havana, 222 St. # 2317, La Coronela, 13600, Havana, Cuba.
| | - Gilberto Lázaro Pardo-Andreu
- Center for Research and Biological Evaluation, Institute of Pharmaceutical and Food Sciences, University of Havana, 222 St. # 2317, 13600, Havana, Cuba.
| | - Luca Rastrelli
- Universitá degli Studi di Salerno, Dipartimento di Farmacia, Via Giovanni Paolo II, 84084, Fisciano, SA, Italy; NBFC, National Biodiversity Future Center, Palermo, 90133, Italy.
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169
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Chae BJ, Lee KS, Hwang I, Yu JW. Extracellular Acidification Augments NLRP3-Mediated Inflammasome Signaling in Macrophages. Immune Netw 2023; 23:e23. [PMID: 37416933 PMCID: PMC10320421 DOI: 10.4110/in.2023.23.e23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 07/08/2023] Open
Abstract
Inflammation is a series of host defense processes in response to microbial infection and tissue injury. Inflammatory processes frequently cause extracellular acidification in the inflamed region through increased glycolysis and lactate secretion. Therefore, the immune cells infiltrating the inflamed region encounter an acidic microenvironment. Extracellular acidosis can modulate the innate immune response of macrophages; however, its role for inflammasome signaling still remains elusive. In the present study, we demonstrated that macrophages exposed to an acidic microenvironment exhibited enhanced caspase-1 processing and IL-1β secretion compared with those under physiological pH. Moreover, exposure to an acidic pH increased the ability of macrophages to assemble the NLR family pyrin domain containing 3 (NLRP3) inflammasome in response to an NLRP3 agonist. This acidosis-mediated augmentation of NLRP3 inflammasome activation occurred in bone marrow-derived macrophages but not in bone marrow-derived neutrophils. Notably, exposure to an acidic environment caused a reduction in the intracellular pH of macrophages but not neutrophils. Concordantly, macrophages, but not neutrophils, exhibited NLRP3 agonist-mediated translocation of chloride intracellular channel protein 1 (CLIC1) into their plasma membranes under an acidic microenvironment. Collectively, our results demonstrate that extracellular acidosis during inflammation can increase the sensitivity of NLRP3 inflammasome formation and activation in a CLIC1-dependent manner. Thus, CLIC1 may be a potential therapeutic target for NLRP3 inflammasome-mediated pathological conditions.
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Affiliation(s)
- Byeong Jun Chae
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Kyung-Seo Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Inhwa Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Je-Wook Yu
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
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170
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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171
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Pippalapalli J, Lumb A. The respiratory system and acid-base disorders. BJA Educ 2023; 23:221-228. [PMID: 37223696 PMCID: PMC10201398 DOI: 10.1016/j.bjae.2023.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/01/2023] [Indexed: 05/25/2023] Open
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172
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Chan CWT, Chan K, Yam VWW. Induced Self-Assembly and Disassembly of Alkynylplatinum(II) 2,6-Bis(benzimidazol-2'-yl)pyridine Complexes with Charge Reversal Properties: "Proof-of-Principle" Demonstration of Ratiometric Förster Resonance Energy Transfer Sensing of pH. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25122-25133. [PMID: 35766435 DOI: 10.1021/acsami.2c05677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A series of pH-responsive alkynylplatinum(II) 2,6-bis(benzimidazol-2'-yl)pyridine (bzimpy) complexes with charge-reversal properties was synthesized, and the supramolecular assemblies between conjugated polyelectrolyte, PFP-OSO3-, and [Pt{bzimpy(TEG)2}{C≡C-C6H3-(COOH)2-3,5}]Cl (1) have been studied using UV-vis absorption, emission, and resonance light scattering (RLS) spectroscopy. An efficient Förster resonance energy transfer (FRET) from PFP-OSO3- donor to the aggregated 1 as acceptor with the aid of Pt(II)···Pt(II) interactions has been presented, which leads to a growth of triplet metal-metal-to-ligand charge transfer (3MMLCT) emission in the low-energy red region. The two-component PFP-OSO3--1 ensemble was then exploited as a "proof-of-principle" concept strategy for pH sensing by tracking the ratiometric emission changes. With the aid of judicious molecular design on the pH-driven charge-reversal property, the polyelectrolyte-induced self-assembly and the FRET from PFP-OSO3- to the platinum(II) aggregates have been modulated. Together with its excellent reversibility and photostability, the extra stability provided by the Pt(II)···Pt(II) and π-π stacking interactions on top of the electrostatic and hydrophobic interactions existing in polyelectrolye-complex assemblies has led to a selective and sensitive pH sensing assay.
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Affiliation(s)
- Calford Wai-Ting Chan
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Kevin Chan
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
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173
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Wu X, Yang K, He S, Zhu F, Kang S, Liu B, Sun C, Pang W, Wang Y. Dual-functional gold nanorods micro pattern guiding cell alignment and cellular microenvironment monitoring. J Colloid Interface Sci 2023; 647:429-437. [PMID: 37269739 DOI: 10.1016/j.jcis.2023.05.167] [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: 01/06/2023] [Revised: 05/10/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
Surface topography has become a powerful tool to control cell behaviors, however, it's still difficult to monitor cellular microenvironment changes during topography-induced cell responses. Here, a dual-functional platform integrating cell alignment with extracellular pH (pHe) measurement is proposed. The platform is fabricated by assembling gold nanorods (AuNRs) into micro pattern via wettability difference interface method, which provides topographical cues and surface-enhanced Raman scattering (SERS) effect for cell alignment and biochemical detection respectively. Results demonstrate that contact guidance and cell morphology changes are achieved by the AuNRs micro pattern, and pHe are also obtained by the changes of SERS spectra during cell alignment, where the pHe near cytoplasm is lower than nucleus, revealing the heterogeneity of extracellular microenvironment. Moreover, a correlation between lower extracellular pH and higher cell migration ability is revealed, and AuNRs micro pattern can differentiate cells with different migration ability, which may be an inheritable character during cell division. Furthermore, mesenchymal stem cells response dramatically to AuNRs micro pattern, showing different morphology and increased pHe level, offering the potential of impacting stem cell differentiation. This approach provides a new idea for the research of cell regulation and response mechanism.
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Affiliation(s)
- Xiaoyu Wu
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Kai Yang
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Shan He
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Feng Zhu
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Shenghui Kang
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Bohua Liu
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Chongling Sun
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Wei Pang
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Yanyan Wang
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China.
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174
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Yang J, Zhao Z, Jiang S, Zhang L, Zhao K, Li ZT, Ma D. pH-sensing supramolecular fluorescent probes discovered by library screening. Talanta 2023; 263:124716. [PMID: 37257239 DOI: 10.1016/j.talanta.2023.124716] [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: 04/13/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
A new design concept for pH-sensing supramolecular fluorescent probes is reported. Supramolecular fluorescent pH probes based on pro-guest are designed and prepared. Pro-guests are designed to degrade under acidic condition and convert to competitive guests to displace encapsulated dyes, which leads to a significant enhancement in fluorescence intensity. A library of potential fluorescent pH probes is generated and screened to discover workable probes. These probes are capable of detecting the acidic pH in solution phase. We confirm that these supramolecular probes could detect the acidic environment in endosomal compartments in live cells.
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Affiliation(s)
- Jingyu Yang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Zizhen Zhao
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Siyang Jiang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Lingyu Zhang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Kai Zhao
- School of Life Science & Institute of Advanced Studies, Taizhou University, Jiaojiang, 318000, Zhejiang, China
| | - Zhan-Ting Li
- Department of Chemistry, Fudan University, Shanghai, 200438, China.
| | - Da Ma
- School of Pharmaceutical Engineering & Institute of Advanced Studies, Taizhou University, Jiaojiang, 318000, Zhejiang, China.
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175
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Vlasova A, Polyakova A, Gromova A, Dolotova S, Bukhalovich S, Bagaeva D, Bondarev N, Tsybrov F, Kovalev K, Mikhailov A, Sidorov D, Bogorodskiy A, Ilyinsky N, Kuklin A, Vlasov A, Borshchevskiy V, Ivanovich V. Optogenetic cytosol acidification of mammalian cells using an inward proton-pumping rhodopsin. Int J Biol Macromol 2023:124949. [PMID: 37224908 DOI: 10.1016/j.ijbiomac.2023.124949] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023]
Abstract
Ion gradients are a universal form of energy, information storage and conversion in living cells. Advances in optogenetics inspire the development of novel tools towards control of different cellular processes with light. Rhodopsins are perspective tools for optogenetic manipulation of ion gradients in cells and subcellular compartments, controlling pH of the cytosol and intracellular organelles. The key step of the development of new optogenetic tools is evaluation of their efficiency. Here, we used a high-throughput quantitative method for comparing efficiency of proton-pumping rhodopsins in Escherichia coli cells. This approach allowed us to show that an inward proton pump xenorhodopsin from Nanosalina sp. (NsXeR) is a powerful tool for optogenetic control of pH of mammalian subcellular compartments. Further, we demonstrate that NsXeR can be used for fast optogenetic acidification of the cytosol of mammalian cells. This is the first evidence of optogenetic cytosol acidification by an inward proton pump at physiological pH values. Our approach offers unique opportunities to study cellular metabolism at normal and pathological conditions and might help to understand the role of pH dysregulation in cellular dysfunctions.
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Affiliation(s)
- A Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - A Polyakova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - A Gromova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - S Dolotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - S Bukhalovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - D Bagaeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - N Bondarev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - F Tsybrov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - K Kovalev
- European Molecular Biology Laboratory, Hamburg, Germany
| | - A Mikhailov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - D Sidorov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - A Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - N Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - A Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - A Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - V Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia.
| | - V Ivanovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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176
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Zhao W, Xu W, Tang J, Kaushik S, Chang CEA, Zhao L. Key Amino Acid Residues of Mitochondrial Transcription Factor A Synergize with Abasic (AP) Site Dynamics To Facilitate AP-Lyase Reactions. ACS Chem Biol 2023; 18:1168-1179. [PMID: 36930463 PMCID: PMC10198963 DOI: 10.1021/acschembio.3c00047] [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: 03/18/2023]
Abstract
Human mitochondrial DNA (mtDNA) encodes 37 essential genes and plays a critical role in mitochondrial and cellular functions. mtDNA is susceptible to damage by endogenous and exogenous chemicals. Damaged mtDNA molecules are counteracted by the redundancy, repair, and degradation of mtDNA. In response to difficult-to-repair or excessive amounts of DNA lesions, mtDNA degradation is a crucial mitochondrial genome maintenance mechanism. Nevertheless, the molecular basis of mtDNA degradation remains incompletely understood. Recently, mitochondrial transcription factor A (TFAM) has emerged as a factor in degrading damaged mtDNA containing abasic (AP) sites. TFAM has AP-lyase activity, which cleaves DNA at AP sites. Human TFAM and its homologs contain a higher abundance of Glu than that of the proteome. To decipher the role of Glu in TFAM-catalyzed AP-DNA cleavage, we constructed TFAM variants and used biochemical assays, kinetic simulations, and molecular dynamics (MD) simulations to probe the functional importance of E187 near a key residue K186. Our previous studies showed that K186 is a primary residue to cleave AP-DNA via Schiff base chemistry. Here, we demonstrate that E187 facilitates β-elimination, key to AP-DNA strand scission. MD simulations showed that extrahelical confirmation of the AP lesion and the flexibility of E187 in TFAM-DNA complexes facilitate AP-lyase reactions. Together, highly abundant Lys and Glu residues in TFAM promote AP-DNA strand scission, supporting the role of TFAM in AP-DNA turnover and implying the breadth of this process across different species.
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Affiliation(s)
- Wenxin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Jin Tang
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Shivansh Kaushik
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
| | - Chia-En A. Chang
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California, 92521, United States
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California, 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California, 92521, United States
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177
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Cai Z, Liu T, Lin Q, He J, Lei X, Luo F, Huang Y. Basis for Accurate Protein p Ka Prediction with Machine Learning. J Chem Inf Model 2023; 63:2936-2947. [PMID: 37146199 DOI: 10.1021/acs.jcim.3c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
pH regulates protein structures and the associated functions in many biological processes via protonation and deprotonation of ionizable side chains where the titration equilibria are determined by pKa's. To accelerate pH-dependent molecular mechanism research in the life sciences or industrial protein and drug designs, fast and accurate pKa prediction is crucial. Here we present a theoretical pKa data set PHMD549, which was successfully applied to four distinct machine learning methods, including DeepKa, which was proposed in our previous work. To reach a valid comparison, EXP67S was selected as the test set. Encouragingly, DeepKa was improved significantly and outperforms other state-of-the-art methods, except for the constant-pH molecular dynamics, which was utilized to create PHMD549. More importantly, DeepKa reproduced experimental pKa orders of acidic dyads in five enzyme catalytic sites. Apart from structural proteins, DeepKa was found applicable to intrinsically disordered peptides. Further, in combination with solvent exposures, it is revealed that DeepKa offers the most accurate prediction under the challenging circumstance that hydrogen bonding or salt bridge interaction is partly compensated by desolvation for a buried side chain. Finally, our benchmark data qualify PHMD549 and EXP67S as the basis for future developments of protein pKa prediction tools driven by artificial intelligence. In addition, DeepKa built on PHMD549 has been proven an efficient protein pKa predictor and thus can be applied immediately to, for example, pKa database construction, protein design, drug discovery, and so on.
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Affiliation(s)
- Zhitao Cai
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Tengzi Liu
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Qiaoling Lin
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Jiahao He
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Xiaowei Lei
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Fangfang Luo
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen 361021, China
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178
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Chen R, Wang L, Ding G, Han G, Qiu K, Sun Y, Diao J. Constant Conversion Rate of Endolysosomes Revealed by a pH-Sensitive Fluorescent Probe. ACS Sens 2023; 8:2068-2078. [PMID: 37141429 DOI: 10.1021/acssensors.3c00340] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Endolysosome dynamics plays an important role in autophagosome biogenesis. Hence, imaging the subcellular dynamics of endolysosomes using high-resolution fluorescent imaging techniques would deepen our understanding of autophagy and benefit the development of pharmaceuticals against endosome-related diseases. Taking advantage of the intramolecular charge-transfer mechanism, herein we report a cationic quinolinium-based fluorescent probe (PyQPMe) that exhibits excellent pH-sensitive fluorescence in endolysosomes at different stages of interest. A systematic photophysical and computational study on PyQPMe was carried out to rationalize its highly pH-dependent absorption and emission spectra. The large Stokes shift and strong fluorescence intensity of PyQPMe can effectively reduce the background noise caused by excitation light and microenvironments and provide a high signal-to-noise ratio for high-resolution imaging of endolysosomes. By applying PyQPMe as a small molecular probe in live cells, we were able to reveal a constant conversion rate from early endosomes to late endosomes/lysosomes during autophagy at the submicron level.
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Affiliation(s)
- Rui Chen
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Lei Wang
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - Guodong Ding
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Guanqun Han
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Kangqiang Qiu
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - Yujie Sun
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Jiajie Diao
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
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179
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Guo B, Shen T, Liu Y, Jing J, Shao C, Zhang X. An endoplasmic reticulum-specific ratiometric fluorescent probe for imaging esterase in living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 291:122389. [PMID: 36689909 DOI: 10.1016/j.saa.2023.122389] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Esterase is primarily distributed in the endoplasmic reticulum (ER) and often overexpressed in cancer cells. Therefore, the detection of esterase in ER is significant for monitoring the metabolic process of various esters and evaluating the efficacy of chemotherapeutic prodrugs. However, only few fluorescent probes can detect esterase in the ER due to the lack of ER-specificity. More seriously, these probes are often limited by low pearson's colocalization coefficient and one single wavelength emission. To solve those problems, an ER-specific ratiometric fluorescent probe (ER-EST) is designed for detecting esterase in living cells. The ER-EST shows a ratiometric and red-shifted emission (125 nm) from 435 to 560 nm after hydrolysis by esterase. The fluorescence intensity ratio of ER-EST displays quantitative response to the esterase activity (0-0.5 U/mL) with low detection limit of 1.8 × 10-4 U/mL. Importantly, the ER-EST with good biocompatibility and excellent ER-targeted ability was successfully employed to ratiometric image the endogenous endoplasmic reticulum esterase in living cells.
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Affiliation(s)
- Bingpeng Guo
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, PR China
| | - Tianjiao Shen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yifan Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
| | - Jing Jing
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China.
| | - Changxiang Shao
- School of Chemistry and Pharmaceutical Engineering, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271099, PR China.
| | - Xiaoling Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China.
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180
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Huang Y, Liang J, Fan Z. A review: Small organic molecule dual/multi-organelle-targeted fluorescent probes. Talanta 2023; 259:124529. [PMID: 37084606 DOI: 10.1016/j.talanta.2023.124529] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
In recent years, the dual/multi-organelle-targeted fluorescent probe based on small organic molecules has good biocompatibility and can visualize the interaction between different organelles, which has attracted much attention. In addition, these probes can also be used to detect small molecules in the organelle environment, such as active sulfur species (RSS), reactive oxygen species (ROS), pH, viscosity and so on. However, the review of dual/multi-organelle-targeted fluorescent probe for small organic molecules lacks a systematic summary, which may hinder the development of this field. In this review, we will focus on the design strategies and bioimaging applications of dual/multi-organelle-targeted fluorescent probe, and classify them into six classes according to different organelles targeted. The first class probe targeted mitochondria and lysosome. The second class probe targeted endoplasmic reticulum and lysosome. The third class probe targeted mitochondria and lipid droplets. The fourth class probe targeted endoplasmic reticulum and lipid droplets. The fifth class probe targeted lysosome and lipid droplets. The sixth class multi-targeted probe. The mechanism of these probes targeting organelles and the visualization of the interaction between different organelles are emphasized, and the prospect and future development direction of this research field are prospected. This will provide a systematic idea for the development and functional research of dual/multi-organelle-targeted fluorescent probe, and promote its research in related physiological and pathological medicine field in the future.
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Affiliation(s)
- Yongfei Huang
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials of Ministry of Education & School of Chemistry and Materials Science of Shanxi Normal University, TaiYuan, 030032, China
| | - Junping Liang
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials of Ministry of Education & School of Chemistry and Materials Science of Shanxi Normal University, TaiYuan, 030032, China
| | - Zhefeng Fan
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials of Ministry of Education & School of Chemistry and Materials Science of Shanxi Normal University, TaiYuan, 030032, China.
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181
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Barua A, Hatzikirou H. Cell Decision Making through the Lens of Bayesian Learning. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25040609. [PMID: 37190396 PMCID: PMC10137733 DOI: 10.3390/e25040609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 05/17/2023]
Abstract
Cell decision making refers to the process by which cells gather information from their local microenvironment and regulate their internal states to create appropriate responses. Microenvironmental cell sensing plays a key role in this process. Our hypothesis is that cell decision-making regulation is dictated by Bayesian learning. In this article, we explore the implications of this hypothesis for internal state temporal evolution. By using a timescale separation between internal and external variables on the mesoscopic scale, we derive a hierarchical Fokker-Planck equation for cell-microenvironment dynamics. By combining this with the Bayesian learning hypothesis, we find that changes in microenvironmental entropy dominate the cell state probability distribution. Finally, we use these ideas to understand how cell sensing impacts cell decision making. Notably, our formalism allows us to understand cell state dynamics even without exact biochemical information about cell sensing processes by considering a few key parameters.
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Affiliation(s)
- Arnab Barua
- Departement de Biochimie, Université de Montréal, Montréal, QC H3T 1C5, Canada
- Centre Robert-Cedergren en Bio-Informatique et Génomique, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Haralampos Hatzikirou
- Center for Information Services and High Performance Computing, Technische Univesität Dresden, 01062 Dresden, Germany
- Mathematics Department, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
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182
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Nag M, Clark AC. Conserved folding landscape of monomeric initiator caspases. J Biol Chem 2023; 299:103075. [PMID: 36858199 PMCID: PMC10074801 DOI: 10.1016/j.jbc.2023.103075] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
The apoptotic caspase subfamily evolved into two subfamilies-monomeric initiators and dimeric effectors; both subfamilies share a conserved caspase-hemoglobinase fold with a protease domain containing a large subunit and a small subunit. Sequence variations in the conserved caspase-hemoglobinase fold resulted in changes in oligomerization, enzyme specificity, and regulation, making caspases an excellent model for examining the mechanisms of molecular evolution in fine-tuning structure, function, and allosteric regulation. We examined the urea-induced equilibrium folding/unfolding of two initiator caspases, monomeric caspase-8 and cFLIPL, over a broad pH range. Both proteins unfold by a three-state equilibrium mechanism that includes a partially folded intermediate. In addition, both proteins undergo a conserved pH-dependent conformational change that is controlled by an evolutionarily conserved mechanism. We show that the conformational free energy landscape of the caspase monomer is conserved in the monomeric and dimeric subfamilies. Molecular dynamics simulations in the presence or the absence of urea, coupled with limited trypsin proteolysis and mass spectrometry, show that the small subunit is unstable in the protomer and unfolds prior to the large subunit. In addition, the unfolding of helix 2 in the large subunit results in disruption of a conserved allosteric site. Because the small subunit forms the interface for dimerization, our results highlight an important driving force for the evolution of the dimeric caspase subfamily through stabilizing the small subunit.
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Affiliation(s)
- Mithun Nag
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - A Clay Clark
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.
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183
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Kumar S, Vassallo JD, Nattamai KJ, Hassan A, Karns R, Vollmer A, Soller K, Sakk V, Sacma M, Nemkov T, D'Alessandro A, Geiger H. pH regulates hematopoietic stem cell potential via polyamines. EMBO Rep 2023; 24:e55373. [PMID: 36943011 PMCID: PMC10157373 DOI: 10.15252/embr.202255373] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Upon ex vivo culture, hematopoietic stem cells (HSCs) quickly lose potential and differentiate into progenitors. The identification of culture conditions that maintain the potential of HSCs ex vivo is therefore of high clinical interest. Here, we demonstrate that the potential of murine and human HSCs is maintained when cultivated for 2 days ex vivo at a pH of 6.9, in contrast to cultivation at the commonly used pH of 7.4. When cultivated at a pH of 6.9, HSCs remain smaller, less metabolically active, less proliferative and show enhanced reconstitution ability upon transplantation compared to HSC cultivated at pH 7.4. HSCs kept at pH 6.9 show an attenuated polyamine pathway. Pharmacological inhibition of the polyamine pathway in HSCs cultivated at pH 7.4 with DFMO mimics phenotypes and potential of HSCs cultivated at pH 6.9. Ex vivo exposure to a pH of 6.9 is therefore a positive regulator of HSC function by reducing polyamines. These findings might improve HSC short-term cultivation protocols for transplantation and gene therapy interventions.
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Affiliation(s)
- Sachin Kumar
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Jeffrey D Vassallo
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Kalpana J Nattamai
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Aishlin Hassan
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA
| | | | - Karin Soller
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Vadim Sakk
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Mehmet Sacma
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Travis Nemkov
- University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | | | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
- Aging Research Center, Ulm University, Ulm, Germany
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184
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Brewer K, Bai F, Blencowe A. pH-Responsive Poly(ethylene glycol)- b-poly(2-vinylpyridine) Micelles for the Triggered Release of Therapeutics. Pharmaceutics 2023; 15:pharmaceutics15030977. [PMID: 36986838 PMCID: PMC10056943 DOI: 10.3390/pharmaceutics15030977] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The use of pH-responsive polymeric micelles is a promising approach to afford the targeted, pH-mediated delivery of hydrophobic drugs within the low-pH tumour milieu and intracellular organelles of cancer cells. However, even for a common pH-responsive polymeric micelle system-e.g., those utilising poly(ethylene glycol)-b-poly(2-vinylpyridine) (PEG-b-PVP) diblock copolymers-there is a lack of available data describing the compatibility of hydrophobic drugs, as well as the relationships between copolymer microstructure and drug compatibility. Furthermore, synthesis of the constituent pH-responsive copolymers generally requires complex temperature control or degassing procedures that limit their accessibility. Herein we report the facile synthesis of a series of diblock copolymers via visible-light-mediated photocontrolled reversible addition-fragmentation chain-transfer polymerisation, with a constant PEG block length (90 repeat units (RUs)) and varying PVP block lengths (46-235 RUs). All copolymers exhibited narrow dispersity values (Đ ≤ 1.23) and formed polymeric micelles with low polydispersity index (PDI) values (typically <0.20) at physiological pH (7.4), within a suitable size range for passive tumour targeting (<130 nm). The encapsulation and release of three hydrophobic drugs (cyclin-dependent kinase inhibitor (CDKI)-73, gossypol, and doxorubicin) were investigated in vitro at pH 7.4-4.5 to simulate drug release within the tumour milieu and cancer cell endosome. Marked differences in drug encapsulation and release were observed when the PVP block length was increased from 86 to 235 RUs. With a PVP block length of 235 RUs, the micelles exhibited differing encapsulation and release properties for each drug. Minimal release was observed for doxorubicin (10%, pH 4.5) and CDKI-73 exhibited moderate release (77%, pH 4.5), whereas gossypol exhibited the best combination of encapsulation efficiency (83%) and release (91% pH 4.5) overall. These data demonstrate the drug selectivity of the PVP core, where both the block molecular weight and hydrophobicity of the core (and accordingly the hydrophobicity of the drug) have a significant effect on drug encapsulation and release. These systems remain a promising means of achieving targeted, pH-responsive drug delivery-albeit for select, compatible hydrophobic drugs-which warrants their further investigation to develop and evaluate clinically relevant micelle systems.
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Affiliation(s)
- Kyle Brewer
- Applied Chemistry and Translational Biomaterials (ACTB) Group, Centre for Pharmaceutical Innovation (CPI), UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Fengxiang Bai
- Applied Chemistry and Translational Biomaterials (ACTB) Group, Centre for Pharmaceutical Innovation (CPI), UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Anton Blencowe
- Applied Chemistry and Translational Biomaterials (ACTB) Group, Centre for Pharmaceutical Innovation (CPI), UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
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185
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Zhang R, Bons J, Scheidemantle G, Liu X, Bielska O, Carrico C, Rose J, Heckenbach I, Scheibye-Knudsen M, Schilling B, Verdin E. Histone malonylation is regulated by SIRT5 and KAT2A. iScience 2023; 26:106193. [PMID: 36879797 PMCID: PMC9985052 DOI: 10.1016/j.isci.2023.106193] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/18/2022] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
The posttranslational modification lysine malonylation is found in many proteins, including histones. However, it remains unclear whether histone malonylation is regulated or functionally relevant. Here, we report that availability of malonyl-co-enzyme A (malonyl-CoA), an endogenous malonyl donor, affects lysine malonylation, and that the deacylase SIRT5 selectively reduces malonylation of histones. To determine if histone malonylation is enzymatically catalyzed, we knocked down each of the 22 lysine acetyltransferases (KATs) to test their malonyltransferase potential. KAT2A knockdown in particular reduced histone malonylation levels. By mass spectrometry, H2B_K5 was highly malonylated and regulated by SIRT5 in mouse brain and liver. Acetyl-CoA carboxylase (ACC), the malonyl-CoA producing enzyme, was partly localized in the nucleolus, and histone malonylation increased nucleolar area and ribosomal RNA expression. Levels of global lysine malonylation and ACC expression were higher in older mouse brains than younger mice. These experiments highlight the role of histone malonylation in ribosomal gene expression.
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Affiliation(s)
- Ran Zhang
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Grace Scheidemantle
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Olga Bielska
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Chris Carrico
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Indra Heckenbach
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Nørregade 10, Copenhagen, Denmark
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Nørregade 10, Copenhagen, Denmark
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
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186
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Adachi J, Oda H, Fukushima T, Lestari B, Kimura H, Sugai H, Shiraki K, Hamaguchi R, Sato K, Kinbara K. Dense and Acidic Organelle-Targeted Visualization in Living Cells: Application of Viscosity-Responsive Fluorescence Utilizing Restricted Access to Minimum Energy Conical Intersection. Anal Chem 2023; 95:5196-5204. [PMID: 36930819 PMCID: PMC10061370 DOI: 10.1021/acs.analchem.2c04133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Cell-imaging methods with functional fluorescent probes are an indispensable technique to evaluate physical parameters in cellular microenvironments. In particular, molecular rotors, which take advantage of the twisted intramolecular charge transfer (TICT) process, have helped evaluate microviscosity. However, the involvement of charge-separated species in the fluorescence process potentially limits the quantitative evaluation of viscosity. Herein, we developed viscosity-responsive fluorescent probes for cell imaging that are not dependent on the TICT process. We synthesized AnP2-H and AnP2-OEG, both of which contain 9,10-di(piperazinyl)anthracene, based on 9,10-bis(N,N-dialkylamino)anthracene that adopts a nonflat geometry at minimum energy conical intersection. AnP2-H and AnP2-OEG exhibited enhanced fluorescence as the viscosity increased, with sensitivities comparable to those of conventional molecular rotors. In living cell systems, AnP2-OEG showed low cytotoxicity and, reflecting its viscosity-responsive property, allowed specific visualization of dense and acidic organelles such as lysosomes, secretory granules, and melanosomes under washout-free conditions. These results provide a new direction for developing functional fluorescent probes targeting dense organelles.
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Affiliation(s)
- Junya Adachi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Toshiaki Fukushima
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Beni Lestari
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroka Sugai
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Rei Hamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kohei Sato
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kazushi Kinbara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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187
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Xue YW, Miura K, Itoh H, Inoue M. C-Terminal modification of polytheonamide B uncouples its dual functions in MCF-7 cancer cells. Chem Commun (Camb) 2023; 59:3914-3917. [PMID: 36919651 DOI: 10.1039/d2cc05915k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Polytheonamide B (1) is an exceptionally large peptide that forms a transmembrane ion channel. The potent cytotoxicity of 1 against MCF-7 cancer cells originates from its two ion transport functions. Compound 1 depolarizes the plasma membrane and neutralizes acidic lysosomes. Here, we describe how we uncoupled these functions by designing and synthesizing new analogues of 1.
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Affiliation(s)
- Yun-Wei Xue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Kensuke Miura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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188
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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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189
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Xiao C, Izquierdo-Roca V, Rivera-Gil P. Real Time and Spatiotemporal Quantification of pH and H 2O 2 Imbalances with a Multiplex Surface-Enhanced Raman Spectroscopy Nanosensor. ACS MATERIALS AU 2023; 3:164-175. [PMID: 38089722 PMCID: PMC9999477 DOI: 10.1021/acsmaterialsau.2c00069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/29/2022] [Accepted: 12/29/2022] [Indexed: 06/03/2024]
Abstract
Oxidative stress is involved in many aging-related pathological disorders and is the result of defective cellular management of redox reactions. Particularly, hydrogen peroxide (H2O2), is a major byproduct and a common oxidative stress biomarker. Monitoring its dynamics and a direct correlation to diseases remains a challenge due to the complexity of redox reactions. Sensitivity and specificity are major drawbacks for H2O2 sensors regardless of their readout. Luminiscent boronate-based probes such as 3-mercaptophenylboronic acid (3-MPBA) are emerging as the most effective quantitation tool due to their specificity and sensitivity. Problems associated with these probes are limited intracellular sensing, water solubility, selectivity, and quenching. We have synthesized a boronate-based nanosensor with a surface-enhanced Raman spectroscopy (SERS) readout to solve these challenges. Furthermore, we found out that environmental pH gradients, as found in biological samples, affect the sensitivity of boronate-based sensors. When the sensor is in an alkaline environment, the oxidation of 3-MPBA by H2O2 is more favored than in an acidic environment. This leads to different H2O2 measurements depending on pH. To solve this issue, we synthesized a multiplex nanosensor capable of concomitantly quantifying pH and H2O2. Our nanosensor first measures the local pH and based on this value, provides the amount of H2O2. It seems that this pH-dependent sensitivity effect applies to all boronic acid based probes. We tested the multiplexing ability by quantitatively measuring intra- and extracellular pH and H2O2 dynamics under physiological and pathological conditions on healthy cells and cells in which H+ and/or H2O2 homeostasis has been altered.
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Affiliation(s)
- Can Xiao
- Department
of Medicine and Life Sciences, Universitat
Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Victor Izquierdo-Roca
- Catalonia
Institute for Energy Research (IREC), Jardins de les Dones de Negre 1, 08930 Sant Adrià del Besòs-Barcelona, Spain
| | - Pilar Rivera-Gil
- Department
of Medicine and Life Sciences, Universitat
Pompeu Fabra, Carrer Doctor Aiguader 88, 08003 Barcelona, Spain
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190
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Zheng Y, Ye Z, Zhang X, Xiao Y. Recruiting Rate Determines the Blinking Propensity of Rhodamine Fluorophores for Super-Resolution Imaging. J Am Chem Soc 2023; 145:5125-5133. [PMID: 36815733 DOI: 10.1021/jacs.2c11395] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Live-cell single-molecule localization microscopy has advanced with the development of self-blinking rhodamines. A pKcycling of <6 is recognized as the criterion for self-blinking, yet a few rhodamines matching the standard fail for super-resolution reconstruction. To resolve this controversy, we constructed two classic rhodamines (pKcycling < 6) and four sulfonamide rhodamines with three exhibited exceptional larger pKcycling characteristics (6.91-7.34). A kinetic study uncovered slow equilibrium rates, and limited switch numbers resulted in the reconstruction failure of some rhodamines. From the kinetic disparity, a recruiting rate was first abstracted to reveal the natural switching frequency of spirocycling equilibrium. The new parameter independent from applying a laser satisfactorily explained the imaging failure, efficacious for determining the propensity of self-blinking from a kinetic perspective. Following the prediction from this parameter, the sulfonamide rhodamines enabled live-cell super-resolution imaging of various organelles through Halo-tag technology. It is determined that the recruiting rate would be a practical indicator of self-blinking and imaging performance.
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Affiliation(s)
- Ying Zheng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Zhiwei Ye
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Xue Zhang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian 116024, China
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191
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Appel LM, Benedum J, Engl M, Platzer S, Schleiffer A, Strobl X, Slade D. SPOC domain proteins in health and disease. Genes Dev 2023; 37:140-170. [PMID: 36927757 PMCID: PMC10111866 DOI: 10.1101/gad.350314.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Since it was first described >20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
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192
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Tuli F, Kane PM. Chimeric a-subunit isoforms generate functional yeast V-ATPases with altered regulatory properties in vitro and in vivo. Mol Biol Cell 2023; 34:ar14. [PMID: 36598799 PMCID: PMC10011726 DOI: 10.1091/mbc.e22-07-0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
V-ATPases are highly regulated proton pumps that acidify organelles. The V-ATPase a-subunit is a two-domain protein containing a C-terminal transmembrane domain responsible for proton transport and an N-terminal cytosolic domain (aNT) that is a regulatory hub, integrating environmental inputs to regulate assembly, localization, and V-ATPase activity. The yeast Saccharomyces cerevisiae encodes only two organelle-specific a-isoforms, Stv1 in the Golgi and Vph1 in the vacuole. On the basis of recent structures, we designed chimeric yeast aNTs in which the globular proximal and distal ends are exchanged. The Vph1 proximal-Stv1 distal (VPSD) aNT chimera binds to the glucose-responsive RAVE assembly factor in vitro but exhibits little binding to PI(3,5)P2. The Stv1 proximal-Vph1 distal (SPVD) aNT lacks RAVE binding but binds more tightly to phosphoinositides than Vph1 or Stv1. When attached to the Vph1 C-terminal domain in vivo, both chimeras complement growth defects of a vph1∆ mutant, but only the SPVD chimera exhibits wild-type V-ATPase activity. Cells containing the SPVD chimera adapt more slowly to a poor carbon source than wild-type cells but grow more rapidly than wild-type cells after a shift to alkaline pH. This is the first example of a "redesigned" V-ATPase with altered regulatory properties and adaptation to specific stresses.
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Affiliation(s)
- Farzana Tuli
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210
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193
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Cassari L, Pavan A, Zoia G, Chinellato M, Zeni E, Grinzato A, Rothenberger S, Cendron L, Dettin M, Pasquato A. SARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works. Int J Mol Sci 2023; 24:4791. [PMID: 36902222 PMCID: PMC10003014 DOI: 10.3390/ijms24054791] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the etiological agent responsible for the worldwide pandemic and has now claimed millions of lives. The virus combines several unusual characteristics and an extraordinary ability to spread among humans. In particular, the dependence of the maturation of the envelope glycoprotein S from Furin enables the invasion and replication of the virus virtually within the entire body, since this cellular protease is ubiquitously expressed. Here, we analyzed the naturally occurring variation of the amino acids sequence around the cleavage site of S. We found that the virus grossly mutates preferentially at P positions, resulting in single residue replacements that associate with gain-of-function phenotypes in specific conditions. Interestingly, some combinations of amino acids are absent, despite the evidence supporting some cleavability of the respective synthetic surrogates. In any case, the polybasic signature is maintained and, as a consequence, Furin dependence is preserved. Thus, no escape variants to Furin are observed in the population. Overall, the SARS-CoV-2 system per se represents an outstanding example of the evolution of substrate-enzyme interaction, demonstrating a fast-tracked optimization of a protein stretch towards the Furin catalytic pocket. Ultimately, these data disclose important information for the development of drugs targeting Furin and Furin-dependent pathogens.
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Affiliation(s)
- Leonardo Cassari
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Angela Pavan
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Giulia Zoia
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Chinellato
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Elena Zeni
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Alessandro Grinzato
- European Synchrotron Radiation Facility, 71, Avenue des Martyrs, 38000 Grenoble, France
| | - Sylvia Rothenberger
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy
| | - Monica Dettin
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Antonella Pasquato
- Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
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194
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Onesto V, Forciniti S, Alemanno F, Narayanankutty K, Chandra A, Prasad S, Azzariti A, Gigli G, Barra A, De Martino A, De Martino D, del Mercato LL. Probing Single-Cell Fermentation Fluxes and Exchange Networks via pH-Sensing Hybrid Nanofibers. ACS NANO 2023; 17:3313-3323. [PMID: 36573897 PMCID: PMC9979640 DOI: 10.1021/acsnano.2c06114] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/19/2022] [Indexed: 05/31/2023]
Abstract
The homeostatic control of their environment is an essential task of living cells. It has been hypothesized that, when microenvironmental pH inhomogeneities are induced by high cellular metabolic activity, diffusing protons act as signaling molecules, driving the establishment of exchange networks sustained by the cell-to-cell shuttling of overflow products such as lactate. Despite their fundamental role, the extent and dynamics of such networks is largely unknown due to the lack of methods in single-cell flux analysis. In this study, we provide direct experimental characterization of such exchange networks. We devise a method to quantify single-cell fermentation fluxes over time by integrating high-resolution pH microenvironment sensing via ratiometric nanofibers with constraint-based inverse modeling. We apply our method to cell cultures with mixed populations of cancer cells and fibroblasts. We find that the proton trafficking underlying bulk acidification is strongly heterogeneous, with maximal single-cell fluxes exceeding typical values by up to 3 orders of magnitude. In addition, a crossover in time from a networked phase sustained by densely connected "hubs" (corresponding to cells with high activity) to a sparse phase dominated by isolated dipolar motifs (i.e., by pairwise cell-to-cell exchanges) is uncovered, which parallels the time course of bulk acidification. Our method addresses issues ranging from the homeostatic function of proton exchange to the metabolic coupling of cells with different energetic demands, allowing for real-time noninvasive single-cell metabolic flux analysis.
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Affiliation(s)
- Valentina Onesto
- Institute
of Nanotechnology, National Research Council
(CNR-NANOTEC), c/o Campus Ecotekne, via Monteroni, 73100Lecce, Italy
| | - Stefania Forciniti
- Institute
of Nanotechnology, National Research Council
(CNR-NANOTEC), c/o Campus Ecotekne, via Monteroni, 73100Lecce, Italy
| | - Francesco Alemanno
- Institute
of Nanotechnology, National Research Council
(CNR-NANOTEC), c/o Campus Ecotekne, via Monteroni, 73100Lecce, Italy
- Dipartimento
di Matematica e Fisica E. De Giorgi, University
of Salento, 73100Lecce, Italy
- Istituto
Nazionale di Fisica Nucleare (INFN), Sezione di Lecce, 73100Lecce, Italy
| | | | - Anil Chandra
- Institute
of Nanotechnology, National Research Council
(CNR-NANOTEC), c/o Campus Ecotekne, via Monteroni, 73100Lecce, Italy
| | - Saumya Prasad
- Institute
of Nanotechnology, National Research Council
(CNR-NANOTEC), c/o Campus Ecotekne, via Monteroni, 73100Lecce, Italy
| | - Amalia Azzariti
- IRCCS
Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124Bari, Italy
| | - Giuseppe Gigli
- Institute
of Nanotechnology, National Research Council
(CNR-NANOTEC), c/o Campus Ecotekne, via Monteroni, 73100Lecce, Italy
- Dipartimento
di Matematica e Fisica E. De Giorgi, University
of Salento, 73100Lecce, Italy
| | - Adriano Barra
- Dipartimento
di Matematica e Fisica E. De Giorgi, University
of Salento, 73100Lecce, Italy
- Istituto
Nazionale di Fisica Nucleare (INFN), Sezione di Lecce, 73100Lecce, Italy
| | - Andrea De Martino
- Politecnico
di Torino, Corso Duca degli Abruzzi, 24, I-10129Torino, Italy
- Italian Institute
for Genomic Medicine, IRCCS Candiolo, SP-142, I-10060Candiolo, Italy
| | - Daniele De Martino
- Biofisika
Institutua (UPV/EHU, CSIC) and Fundación Biofísica Bizkaia, LeioaE-48940, Spain
- Ikerbasque
Foundation, Bilbao48013, Spain
| | - Loretta L. del Mercato
- Institute
of Nanotechnology, National Research Council
(CNR-NANOTEC), c/o Campus Ecotekne, via Monteroni, 73100Lecce, Italy
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195
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Organelle-Targeted Fluorescent Probes for Sulfane Sulfur Species. Antioxidants (Basel) 2023; 12:antiox12030590. [PMID: 36978838 PMCID: PMC10045342 DOI: 10.3390/antiox12030590] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Sulfane sulfurs, which include hydropersulfides (RSSH), hydrogen polysulfides (H2Sn, n > 1), and polysulfides (RSnR, n > 2), play important roles in cellular redox biology and are closely linked to hydrogen sulfide (H2S) signaling. While most studies on sulfane sulfur detection have focused on sulfane sulfurs in the whole cell, increasing the recognition of the effects of reactive sulfur species on the functions of various subcellular organelles has emerged. This has driven a need for organelle-targeted detection methods. However, the detection of sulfane sulfurs, particularly of RSSH and H2Sn, in biological systems is still a challenge due to their low endogenous concentrations and instabilities. In this review, we summarize the development and design of organelle-targeted fluorescent sulfane sulfur probes, examine their organelle-targeting strategies and choices of fluorophores (e.g., ratiometric, near-infrared, etc.), and discuss their mechanisms and ability to detect endogenous and exogenous sulfane sulfur species. We also present the advantages and limitations of the probes and propose directions for future work on this topic.
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196
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Nadendla K, Simpson GG, Becher J, Journeaux T, Cabeza-Cabrerizo M, Bernardes GJL. Strategies for Conditional Regulation of Proteins. JACS AU 2023; 3:344-357. [PMID: 36873677 PMCID: PMC9975842 DOI: 10.1021/jacsau.2c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Design of the next-generation of therapeutics, biosensors, and molecular tools for basic research requires that we bring protein activity under control. Each protein has unique properties, and therefore, it is critical to tailor the current techniques to develop new regulatory methods and regulate new proteins of interest (POIs). This perspective gives an overview of the widely used stimuli and synthetic and natural methods for conditional regulation of proteins.
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Affiliation(s)
- Karthik Nadendla
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Grant G. Simpson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Julie Becher
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Toby Journeaux
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Mar Cabeza-Cabrerizo
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CB2 1EW, Cambridge, U.K.
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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197
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Mariottini D, Idili A, Ercolani G, Ricci F. Thermo-Programmed Synthetic DNA-Based Receptors. ACS NANO 2023; 17:1998-2006. [PMID: 36689298 PMCID: PMC9933611 DOI: 10.1021/acsnano.2c07039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Herein, we present a generalizable and versatile strategy to engineer synthetic DNA ligand-binding devices that can be programmed to load and release a specific ligand at a defined temperature. We do so by re-engineering two model DNA-based receptors: a triplex-forming bivalent DNA-based receptor that recognizes a specific DNA sequence and an ATP-binding aptamer. The temperature at which these receptors load/release their ligands can be finely modulated by controlling the entropy associated with the linker connecting the two ligand-binding domains. The availability of a set of receptors with tunable and reversible temperature dependence allows achieving complex load/release behavior such as sustained ligand release over a wide temperature range. Similar programmable thermo-responsive synthetic ligand-binding devices can be of utility in applications such as drug delivery and production of smart materials.
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Affiliation(s)
- Davide Mariottini
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Andrea Idili
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Gianfranco Ercolani
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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198
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Contu VR, Sakai R, Fujiwara Y, Kabuta C, Wada K, Kabuta T. Nucleic acid uptake occurs independent of lysosomal acidification but dependent on ATP consumption during RNautophagy/DNautophagy. Biochem Biophys Res Commun 2023; 644:105-111. [PMID: 36640664 DOI: 10.1016/j.bbrc.2022.12.090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023]
Abstract
RNautophagy/DNautophagy (RDA) is an autophagic process that refers to the direct uptake of nucleic acids by lysosomes for degradation. Autophagy relies on lysosomes and lysosomal acidification is crucial for the degradation of intracellular components. However, whether lysosomal acidification interferes with nucleic acid uptake during RDA is unclear. In this study, we focused on vacuolar H+-ATPase (V-ATPase), the major proton pump responsible for maintaining an acidic pH in lysosomes. Our results show that lysosomes take up nucleic acids independently of the intralysosomal acidic pH during RDA. Isolated lysosomes treated with bafilomycin A1, a potent V-ATPase inhibitor, did not degrade, but took up RNA at similar levels as the control lysosomes. Similarly, the knockdown of Atp6v1a, the gene that encodes V-ATPase catalytic subunit A, did not affect the RNA uptake ability of isolated lysosomes. In addition, we demonstrated that nucleic acid uptake by isolated lysosomes necessitates ATP consumption, although V-ATPase is not required for the uptake process. These results broaden our understanding of the mechanisms underlying nucleic acid degradation via autophagy.
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Affiliation(s)
- Viorica Raluca Contu
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan; Department of Neurology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Ryohei Sakai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan
| | - Yuuki Fujiwara
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan; Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Chihana Kabuta
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan
| | - Keiji Wada
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan
| | - Tomohiro Kabuta
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan.
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199
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Fan J, Yu H, Lu X, Xue R, Guan J, Xu Y, Qi Y, He L, Yu W, Abay S, Li Z, Huo S, Li L, Lv M, Li W, Chen W, Han B. Overlooked Spherical Nanoparticles Exist in Plant Extracts: From Mechanism to Therapeutic Applications. ACS APPLIED MATERIALS & INTERFACES 2023; 15:8854-8871. [PMID: 36757908 DOI: 10.1021/acsami.2c19065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
To date, plant medicine research has focused mainly on the chemical compositions of plant extracts and their medicinal effects. However, the therapeutic or toxic effects of nanoparticles in plant extracts remain unclear. In this study, large numbers of spherical nanoparticles were discovered in some plant extracts. Nanoparticles in Turkish galls extracts were used as an example to examine their pH responsiveness, free radical scavenging, and antibacterial capabilities. By utilizing the underlying formation mechanism of these nanoparticles, a general platform to produce spherical nanoparticles via direct self-assembly of Turkish gall extracts and various functional proteins was developed. The results showed that the nanoparticles retained both the antibacterial ability and intracellular carrier ability of the original protein or catechol. This work introduces a new member of the plant-derived edible nanoparticle (PDEN) family, establishes a simple and versatile platform for mass production nanoparticles, and provides new insight into the formation mechanism of nanoparticles during plant extraction.
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Affiliation(s)
- Jingmin Fan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Hang Yu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Xin Lu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Rui Xue
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Jiawei Guan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Yu Xu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Yunyun Qi
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Linyun He
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Wei Yu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Sirapil Abay
- Xinjiang Institute of Traditional Uygur Medicine, Urumqi 830049, China
| | - Zhijian Li
- Xinjiang Institute of Traditional Uygur Medicine, Urumqi 830049, China
| | - Shixia Huo
- Xinjiang Institute of Traditional Uygur Medicine, Urumqi 830049, China
| | - Le Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Mengying Lv
- Department of Pharmacy/The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
| | - Wenxin Li
- Laboratory of Nano-biology and Medicine, Shanghai Institute of Applied Physics, Shanghai 201800, China
| | - Wen Chen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
| | - Bo Han
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Shihezi University, Shihezi 832002, China
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200
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Fang H, Chen Y, Jiang Z, He W, Guo Z. Fluorescent Probes for Biological Species and Microenvironments: from Rational Design to Bioimaging Applications. Acc Chem Res 2023; 56:258-269. [PMID: 36652599 DOI: 10.1021/acs.accounts.2c00643] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Some important biological species and microenvironments maintain a complex and delicate dynamic balance in life systems, participating in the regulation of various physiological processes and playing indispensable roles in maintaining the healthy development of living bodies. Disruption of their homeostasis in living organisms can cause various diseases and even death. Therefore, real time monitoring of these biological species and microenvironments during different physiological and pathological processes is of great significance. Fluorescent-probe-based techniques have been recognized as one of the most powerful tools for real time imaging in biological samples. In this Account, we introduce the representative works from our group in the field of fluorescent probes for biological imaging capable of detecting metal ions, small bioactive molecules, and the microenvironment. The design strategies of small molecule fluorescent probes and their applications in biological imaging will be discussed. By regulating the design strategy and mechanism (e.g., ICT, PeT, and FRET) of the electronic and spectral characteristics of the fluorescent platforms, these chemical probes show high selectivity and diverse functions, which can be used for imaging of various physiological and pathological processes. Through the exploration of the rational response mechanism and design strategy, combined with a variety of imaging techniques, such as super-resolution imaging, photoacoustic (PA) imaging, etc., we have realized multimode imaging of the important biological analytes from the subcellular level to the in vivo level, which provides powerful means to study the physiological and pathological functions of these species and microenvironments. This Account aims to offer insights and inspiration for the development of novel fluorescent probes for biological imaging, which could provide powerful tools for the study of chemical biology. Overall, we represent a series of turn-on/turn-off/ratiometric fluorescent/PA probes to visually and dynamically trace biological species and microenvironments in cells and even in vivo that seek higher resolution and depth molecular imaging to improve diagnostic methods and clarify new discoveries related to chemical biology. Our future efforts will be devoted to developing multiorganelle targeted fluorescent probes to study the mechanism of subcellular organelle interaction and employing various dual-mode probes of NIR II and PA imaging to investigate the development of related diseases and treat the related diseases at subcellular and in vivo levels.
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Affiliation(s)
- Hongbao Fang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), 163 Xianlin Avenue, Nanjing University, Nanjing 210023, China
| | - Yuncong Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), 163 Xianlin Avenue, Nanjing University, Nanjing 210023, China.,Nanchuang (Jiangsu) Institute of Chemistry and Health, 3-1 Xinjinhu Road, Nanjing 211899, China
| | - Zhiyong Jiang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), 163 Xianlin Avenue, Nanjing University, Nanjing 210023, China
| | - Weijiang He
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), 163 Xianlin Avenue, Nanjing University, Nanjing 210023, China.,Nanchuang (Jiangsu) Institute of Chemistry and Health, 3-1 Xinjinhu Road, Nanjing 211899, China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), 163 Xianlin Avenue, Nanjing University, Nanjing 210023, China.,Nanchuang (Jiangsu) Institute of Chemistry and Health, 3-1 Xinjinhu Road, Nanjing 211899, China
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