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Poly(styrene-co-4-hydroxystyrene) nanofiber membrane for highly selective and efficient Rb+ capture from high salinity solution. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2023.123334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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2
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Santos-Pereira C, Rodrigues LR, Côrte-Real M. Emerging insights on the role of V-ATPase in human diseases: Therapeutic challenges and opportunities. Med Res Rev 2021; 41:1927-1964. [PMID: 33483985 DOI: 10.1002/med.21782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/05/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
The control of the intracellular pH is vital for the survival of all organisms. Membrane transporters, both at the plasma and intracellular membranes, are key players in maintaining a finely tuned pH balance between intra- and extracellular spaces, and therefore in cellular homeostasis. V-ATPase is a housekeeping ATP-driven proton pump highly conserved among prokaryotes and eukaryotes. This proton pump, which exhibits a complex multisubunit structure based on cell type-specific isoforms, is essential for pH regulation and for a multitude of ubiquitous and specialized functions. Thus, it is not surprising that V-ATPase aberrant overexpression, mislocalization, and mutations in V-ATPase subunit-encoding genes have been associated with several human diseases. However, the ubiquitous expression of this transporter and the high toxicity driven by its off-target inhibition, renders V-ATPase-directed therapies very challenging and increases the need for selective strategies. Here we review emerging evidence linking V-ATPase and both inherited and acquired human diseases, explore the therapeutic challenges and opportunities envisaged from recent data, and advance future research avenues. We highlight the importance of V-ATPases with unique subunit isoform molecular signatures and disease-associated isoforms to design selective V-ATPase-directed therapies. We also discuss the rational design of drug development pipelines and cutting-edge methodological approaches toward V-ATPase-centered drug discovery. Diseases like cancer, osteoporosis, and even fungal infections can benefit from V-ATPase-directed therapies.
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Affiliation(s)
- Cátia Santos-Pereira
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal.,Department of Biological Engineering, Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Lígia R Rodrigues
- Department of Biological Engineering, Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Manuela Côrte-Real
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
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3
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Wang Z, Detomasi TC, Chang CJ. A dual-fluorophore sensor approach for ratiometric fluorescence imaging of potassium in living cells. Chem Sci 2020; 12:1720-1729. [PMID: 34163931 PMCID: PMC8179100 DOI: 10.1039/d0sc03844j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Potassium is the most abundant intracellular metal in the body, playing vital roles in regulating intracellular fluid volume, nutrient transport, and cell-to-cell communication through nerve and muscle contraction. On the other hand, aberrant alterations in K+ homeostasis contribute to a diverse array of diseases spanning cardiovascular and neurological disorders to diabetes to kidney disease to cancer. There is an unmet need for studies of K+ physiology and pathology owing to the large differences in intracellular versus extracellular K+ concentrations ([K+]intra = 150 mM, [K+]extra = 3–5 mM). With a relative dearth of methods to reliably measure dynamic changes in intracellular K+ in biological specimens that meet the dual challenges of low affinity and high selectivity for K+, particularly over Na+, currently available fluorescent K+ sensors are largely optimized with high-affinity receptors that are more amenable for extracellular K+ detection. We report the design, synthesis, and biological evaluation of Ratiometric Potassium Sensor 1 (RPS-1), a dual-fluorophore sensor that enables ratiometric fluorescence imaging of intracellular potassium in living systems. RPS-1 links a potassium-responsive fluorescent sensor fragment (PS525) with a low-affinity, high-selectivity crown ether receptor for K+ to a potassium-insensitive reference fluorophore (Coumarin 343) as an internal calibration standard through ester bonds. Upon intracellular delivery, esterase-directed cleavage splits these two dyes into separate fragments to enable ratiometric detection of K+. RPS-1 responds to K+ in aqueous buffer with high selectivity over competing metal ions and is sensitive to potassium ions at steady-state intracellular levels and can respond to decreases or increases from that basal set point. Moreover, RPS-1 was applied for comparative screening of K+ pools across a panel of different cancer cell lines, revealing elevations in basal intracellular K+ in metastatic breast cancer cell lines vs. normal breast cells. This work provides a unique chemical tool for the study of intracellular potassium dynamics and a starting point for the design of other ratiometric fluorescent sensors based on two-fluorophore approaches that do not rely on FRET or related energy transfer designs. We report a dual-fluorophore approach for ratiometric fluorescent imaging of K+ levels in live cells. Intracellular esterases cleave RPS-1 to detach the K+-responsive fluorophore (PS525) from its internal standard (Coumarin 343).![]()
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Affiliation(s)
- Zeming Wang
- Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Tyler C Detomasi
- Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Christopher J Chang
- Department of Chemistry, University of California Berkeley CA 94720 USA .,Department of Molecular and Cell Biology, University of California Berkeley CA 94720 USA.,Helen Wills Neuroscience Institute, University of California Berkeley CA 94720 USA
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4
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Efremov YR, Proskurina AS, Potter EA, Dolgova EV, Efremova OV, Taranov OS, Ostanin AA, Chernykh ER, Kolchanov NA, Bogachev SS. Cancer Stem Cells: Emergent Nature of Tumor Emergency. Front Genet 2018; 9:544. [PMID: 30505319 PMCID: PMC6250818 DOI: 10.3389/fgene.2018.00544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022] Open
Abstract
A functional analysis of 167 genes overexpressed in Krebs-2 tumor initiating cells was performed. In the first part of the study, the genes were analyzed for their belonging to one or more of the three groups, which represent the three major phenotypic manifestation of malignancy of cancer cells, namely (1) proliferative self-sufficiency, (2) invasive growth and metastasis, and (3) multiple drug resistance. 96 genes out of 167 were identified as possible contributors to at least one of these fundamental properties. It was also found that substantial part of these genes are also known as genes responsible for formation and/or maintenance of the stemness of normal pluri-/multipotent stem cells. These results suggest that the malignancy is simply the ability to maintain the stem cell specific genes expression profile, and, as a consequence, the stemness itself regardless of the controlling effect of stem niches. In the second part of the study, three stress factors combined into the single concept of "generalized cellular stress," which are assumed to activate the expression of these genes, were defined. In addition, possible mechanisms for such activation were identified. The data obtained suggest the existence of a mechanism for the de novo formation of a pluripotent/stem phenotype in the subpopulation of "committed" tumor cells.
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Affiliation(s)
- Yaroslav R Efremov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Anastasia S Proskurina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ekaterina A Potter
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgenia V Dolgova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Oksana V Efremova
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Oleg S Taranov
- The State Research Center of Virology and Biotechnology Vector, Koltsovo, Russia
| | - Aleksandr A Ostanin
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Elena R Chernykh
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey S Bogachev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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5
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Oleandrin and Its Derivative Odoroside A, Both Cardiac Glycosides, Exhibit Anticancer Effects by Inhibiting Invasion via Suppressing the STAT-3 Signaling Pathway. Int J Mol Sci 2018; 19:ijms19113350. [PMID: 30373171 PMCID: PMC6274837 DOI: 10.3390/ijms19113350] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/25/2018] [Accepted: 10/25/2018] [Indexed: 02/07/2023] Open
Abstract
The cardiac glycosides oleandrin and odoroside A, polyphenolic monomer compounds extracted from Nerium oleander, have been found to have antitumor effects on various tumors at low doses. However, the mechanisms of anticancer effects of oleandrin and odoroside A are not well known. Therefore, in this study, we aimed to investigate the anticancer effects of oleandrin and odoroside A and their associated mechanisms in highly metastatic MDA-MB-231 breast cancer cells and radiotherapy-resistant (RT-R) MDA-MB-231 cells. Our results showed that oleandrin and odoroside A dose-dependently decreased the colony formation and the invasion of both cell lines at nanomolar ranges. Furthermore, oleandrin (50 nM) and odoroside A (100 nM) reduced octamer-binding transcription factor 3/4 (OCT3/4) and β-catenin levels and matrix metalloproteinase-9 (MMP-9) activity. Finally, we found that phospho-STAT-3 levels were increased in MDA-MB-231 and RT-R-MDA-MB-231, but not in endothelial cells (ECs), and that the levels were significantly decreased by oleandrin (50 nM) and odoroside A (100 nM). Inhibition of phospho-signal transducer and activator of transcription (STAT)-3 significantly reduced OCT3/4 and β-catenin levels and MMP-9 activity, ultimately resulting in reduced invasion. These results suggest that the anticancer effects of oleandrin and odoroside A might be due to the inhibition of invasion through of phospho-STAT-3-mediated pathways that are involved in the regulation of invasion-related molecules.
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6
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Banerjee M, Cui X, Li Z, Yu H, Cai L, Jia X, He D, Wang C, Gao T, Xie Z. Na/K-ATPase Y260 Phosphorylation-mediated Src Regulation in Control of Aerobic Glycolysis and Tumor Growth. Sci Rep 2018; 8:12322. [PMID: 30120256 PMCID: PMC6098021 DOI: 10.1038/s41598-018-29995-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/23/2018] [Indexed: 12/22/2022] Open
Abstract
We report here the identification of α1 Na/K-ATPase as a major regulator of the proto-oncogene Src kinase and the role of this regulation in control of Warburg effect and tumor growth. Specifically, we discovered Y260 in α1 Na/K-ATPase as a Src-specific phosphorylation and binding site and that Y260 phosphorylation is required for Src-mediated signal transduction in response to a number of stimuli including EGF. As such, it enables a dynamic control of aerobic glycolysis. However, such regulation appears to be lost or attenuated in human cancers as the expression of Na/K-ATPase α1 was significantly decreased in prostate, breast and kidney cancers, and further reduced in corresponding metastatic lesions in patient samples. Consistently, knockdown of α1 Na/K-ATPase led to a further increase in lactate production and the growth of tumor xenograft. These findings suggest that α1 Na/K-ATPase works as a tumor suppressor and that a loss of Na/K-ATPase-mediated Src regulation may lead to Warburg phenotype in cancer.
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Affiliation(s)
- Moumita Banerjee
- Marshall Institute for Interdisciplinary Research (MIIR), Marshall University, Huntington, West Virginia, 25703, USA
| | - Xiaoyu Cui
- Marshall Institute for Interdisciplinary Research (MIIR), Marshall University, Huntington, West Virginia, 25703, USA
| | - Zhichuan Li
- Department of Physiology and Pharmacology and Medicine, University of Toledo College of Medicine, Toledo, Ohio, 43614, USA
| | - Hui Yu
- Marshall Institute for Interdisciplinary Research (MIIR), Marshall University, Huntington, West Virginia, 25703, USA
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Liquan Cai
- Marshall Institute for Interdisciplinary Research (MIIR), Marshall University, Huntington, West Virginia, 25703, USA
| | - Xuelian Jia
- Marshall Institute for Interdisciplinary Research (MIIR), Marshall University, Huntington, West Virginia, 25703, USA
| | - Daheng He
- Department of Cancer Biostatistics, Markey Cancer Research Center, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Chi Wang
- Department of Cancer Biostatistics, Markey Cancer Research Center, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Tianyan Gao
- Department of Molecular and Cellular Biochemistry, Markey Cancer Research Center, University of Kentucky, Lexington, Kentucky, 40536, USA
| | - Zijian Xie
- Marshall Institute for Interdisciplinary Research (MIIR), Marshall University, Huntington, West Virginia, 25703, USA.
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7
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Christiansen D, Bishop DJ, Broatch JR, Bangsbo J, McKenna MJ, Murphy RM. Cold-water immersion after training sessions: effects on fiber type-specific adaptations in muscle K + transport proteins to sprint-interval training in men. J Appl Physiol (1985) 2018; 125:429-444. [PMID: 29745801 DOI: 10.1152/japplphysiol.00259.2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Effects of regular use of cold-water immersion (CWI) on fiber type-specific adaptations in muscle K+ transport proteins to intense training, along with their relationship to changes in mRNA levels after the first training session, were investigated in humans. Nineteen recreationally active men (24 ± 6 yr, 79.5 ± 10.8 kg, 44.6 ± 5.8 ml·kg-1·min-1) completed six weeks of sprint-interval cycling, either without (passive rest; CON) or with training sessions followed by CWI (15 min at 10°C; COLD). Muscle biopsies were obtained before and after training to determine abundance of Na+, K+-ATPase isoforms (α1-3, β1-3) and phospholemman (FXYD1) and after recovery treatments (+0 h and +3 h) on the first day of training to measure mRNA content. Training increased ( P < 0.05) the abundance of α1 and β3 in both fiber types and β1 in type-II fibers and decreased FXYD1 in type-I fibers, whereas α2 and α3 abundance was not altered by training ( P > 0.05). CWI after each session did not influence responses to training ( P > 0.05). However, α2 mRNA increased after the first session in COLD (+0 h, P < 0.05) but not in CON ( P > 0.05). In both conditions, α1 and β3 mRNA increased (+3 h; P < 0.05) and β2 mRNA decreased (+3 h; P < 0.05), whereas α3, β1, and FXYD1 mRNA remained unchanged ( P > 0.05) after the first session. In summary, Na+,K+-ATPase isoforms are differently regulated in type I and II muscle fibers by sprint-interval training in humans, which, for most isoforms, do not associate with changes in mRNA levels after the first training session. CWI neither impairs nor improves protein adaptations to intense training of importance for muscle K+ regulation. NEW & NOTEWORTHY Although cold-water immersion (CWI) after training and competition has become a routine for many athletes, limited published evidence exists regarding its impact on training adaptation. Here, we show that CWI can be performed regularly without impairing training-induced adaptations at the fiber-type level important for muscle K+ handling. Furthermore, sprint-interval training invoked fiber type-specific adaptations in K+ transport proteins, which may explain the dissociated responses of whole-muscle protein levels and K+ transport function to training previously reported.
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Affiliation(s)
- Danny Christiansen
- Institute for Health and Sport, Victoria University , Melbourne, Victoria , Australia.,Department of Nutrition, Exercise, and Sports, University of Copenhagen , Copenhagen , Denmark
| | - David J Bishop
- Institute for Health and Sport, Victoria University , Melbourne, Victoria , Australia.,School of Medical and Health Sciences, Edith Cowan University , Perth, Western Australia , Australia
| | - James R Broatch
- Institute for Health and Sport, Victoria University , Melbourne, Victoria , Australia
| | - Jens Bangsbo
- Department of Nutrition, Exercise, and Sports, University of Copenhagen , Copenhagen , Denmark
| | - Michael J McKenna
- Institute for Health and Sport, Victoria University , Melbourne, Victoria , Australia
| | - Robyn M Murphy
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University , Melbourne, Victoria , Australia
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8
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Kandil EI, El-Sonbaty SM, Moawed FS, Khedr OM. Anticancer redox activity of gallium nanoparticles accompanied with low dose of gamma radiation in female mice. Tumour Biol 2018; 40:1010428317749676. [PMID: 29587600 DOI: 10.1177/1010428317749676] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Guided treatments with nanoparticles and radiotherapy are a new approach in cancer therapy. This study evaluated the beneficial antitumor effects of γ-radiation together with gallium nanoparticles against solid Ehrlich carcinoma in female mice. Gallium nanoparticles were biologically synthesized using Lactobacillus helveticus cells. Transmission electron microscopy showed gallium nanoparticles with size range of 8-20 nm. In vitro study of gallium nanoparticles on MCF-7 revealed IC50 of 8.0 μg. Gallium nanoparticles (0.1 mg/kg body weight) were injected intraperitoneally daily on the seventh day of Ehrlich carcinoma cells inoculation. Whole-body γ-radiation was carried out at a single dose of 0.25 Gy on eighth day after tumor inoculation. Biochemical analysis showed that solid Ehrlich carcinoma induced a significant increase in alanine aminotransferase activity and creatinine level in serum, calcium, and iron concentrations in liver tissue compared to normal control. Treatment of Ehrlich carcinoma-bearing mice with gallium nanoparticles and/or low dose of γ-radiation exposure significantly reduced tumor volume, decreased alanine aminotransferase and creatinine levels in serum, increased lipid peroxidation, and decreased glutathione content as well as calcium and iron concentrations in liver and tumor tissues with intense DNA fragmentation accompanied compared to untreated tumor cells. Moreover, mitochondria in the treated groups displayed a significant increase in Na+/K+-ATPase, complexes II and III with significant reduction in CYP450 gene expression, which may indicate a synergistic effect of gallium nanoparticles and/or low dose of γ-radiation combination against Ehrlich carcinoma injury, and this results were well appreciated with the histopathological findings in the tumor tissue. We conclude that combined treatment of gallium nanoparticles and low dose of gamma-radiation resulted in suppressive induction of cytotoxic effects on cancer cells.
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Affiliation(s)
- Eman I Kandil
- 1 Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sawsan M El-Sonbaty
- 2 Radiation Microbiology Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Fatma Sm Moawed
- 3 Health Radiation Research Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Ola Ms Khedr
- 1 Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
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9
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Pereira CS, Guedes JP, Gonçalves M, Loureiro L, Castro L, Gerós H, Rodrigues LR, Côrte-Real M. Lactoferrin selectively triggers apoptosis in highly metastatic breast cancer cells through inhibition of plasmalemmal V-H+-ATPase. Oncotarget 2018; 7:62144-62158. [PMID: 27556694 PMCID: PMC5308717 DOI: 10.18632/oncotarget.11394] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 08/08/2016] [Indexed: 01/12/2023] Open
Abstract
Breast cancer is the most common type of cancer affecting women. Despite the good prognosis when detected early, significant challenges remain in the treatment of metastatic breast cancer. The recruitment of the vacuolar H+-ATPase (V-H+-ATPase) to the plasma membrane, where it mediates the acidification of the tumor microenvironment (TME), is a recognized feature involved in the acquisition of a metastatic phenotype in breast cancer. Therefore, inhibitors of this pump have emerged as promising anticancer drugs. Lactoferrin (Lf) is a natural pro-apoptotic iron-binding glycoprotein with strong anticancer activity whose mechanism of action is not fully understood. Here, we show that bovine Lf (bLf) preferentially induces apoptosis in the highly metastatic breast cancer cell lines Hs 578T and MDA-MB-231, which display a prominent localisation of V-H+-ATPase at the plasma membrane, but not in the lowly metastatic T-47D or in the non-tumorigenic MCF-10-2A cell lines. We also demonstrate that bLf decreases the extracellular acidification rate and causes intracellular acidification in metastatic breast cancer cells and, much like the well-known proton pump inhibitors concanamycin A and bafilomycin A1, inhibits V-H+-ATPase in sub-cellular fractions. These data further support that bLf targets V-H+-ATPase and explain the selectivity of bLf for cancer cells, especially for highly metastatic breast cancer cells. Altogether, our results pave the way for more rational in vivo studies aiming to explore this natural non-toxic compound for metastatic breast cancer therapy.
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Affiliation(s)
- Cátia S Pereira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal.,Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana P Guedes
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal.,Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Braga, Portugal
| | - Marília Gonçalves
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Luís Loureiro
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Lisandra Castro
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal.,Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Department of Biology, University of Minho, Braga, Portugal
| | - Lígia R Rodrigues
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Braga, Portugal
| | - Manuela Côrte-Real
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
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10
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Zhou B, Sun Q, Kong DX. Predicting cancer-relevant proteins using an improved molecular similarity ensemble approach. Oncotarget 2017; 7:32394-407. [PMID: 27083051 PMCID: PMC5078021 DOI: 10.18632/oncotarget.8716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/28/2016] [Indexed: 12/15/2022] Open
Abstract
In this study, we proposed an improved algorithm for identifying proteins relevant to cancer. The algorithm was named two-layer molecular similarity ensemble approach (TL-SEA). We applied TL-SEA to analyzing the correlation between anticancer compounds (against cell lines K562, MCF7 and A549) and active compounds against separate target proteins listed in BindingDB. Several associations between cancer types and related proteins were revealed using this chemoinformatics approach. An analysis of the literature showed that 26 of 35 predicted proteins were correlated with cancer cell proliferation, apoptosis or differentiation. Additionally, interactions between proteins in BindingDB and anticancer chemicals were also predicted. We discuss the roles of the most important predicted proteins in cancer biology and conclude that TL-SEA could be a useful tool for inferring novel proteins involved in cancer and revealing underlying molecular mechanisms.
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Affiliation(s)
- Bin Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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11
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Ruan P, Shen J, Santella RM, Zhou S, Wang S. NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals. Nucleic Acids Res 2016; 44:e134. [PMID: 27302130 PMCID: PMC5027497 DOI: 10.1093/nar/gkw546] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/04/2016] [Indexed: 12/13/2022] Open
Abstract
DNA methylation plays an important role in many biological processes. Existing epigenome-wide association studies (EWAS) have successfully identified aberrantly methylated genes in many diseases and disorders with most studies focusing on analysing methylation sites one at a time. Incorporating prior biological information such as biological networks has been proven to be powerful in identifying disease-associated genes in both gene expression studies and genome-wide association studies (GWAS) but has been under studied in EWAS. Although recent studies have noticed that there are differences in methylation variation in different groups, only a few existing methods consider variance signals in DNA methylation studies. Here, we present a network-assisted algorithm, NEpiC, that combines both mean and variance signals in searching for differentially methylated sub-networks using the protein–protein interaction (PPI) network. In simulation studies, we demonstrate the power gain from using both the prior biological information and variance signals compared to using either of the two or neither information. Applications to several DNA methylation datasets from the Cancer Genome Atlas (TCGA) project and DNA methylation data on hepatocellular carcinoma (HCC) from the Columbia University Medical Center (CUMC) suggest that the proposed NEpiC algorithm identifies more cancer-related genes and generates better replication results.
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Affiliation(s)
- Peifeng Ruan
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China
| | - Jing Shen
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Regina M Santella
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Shuigeng Zhou
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
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12
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Barghouth PG, Thiruvalluvan M, Oviedo NJ. Bioelectrical regulation of cell cycle and the planarian model system. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2629-37. [PMID: 25749155 DOI: 10.1016/j.bbamem.2015.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/13/2015] [Accepted: 02/23/2015] [Indexed: 12/27/2022]
Abstract
Cell cycle regulation through the manipulation of endogenous membrane potentials offers tremendous opportunities to control cellular processes during tissue repair and cancer formation. However, the molecular mechanisms by which biophysical signals modulate the cell cycle remain underappreciated and poorly understood. Cells in complex organisms generate and maintain a constant voltage gradient across the plasma membrane known as the transmembrane potential. This potential, generated through the combined efforts of various ion transporters, pumps and channels, is known to drive a wide range of cellular processes such as cellular proliferation, migration and tissue regeneration while its deregulation can lead to tumorigenesis. These cellular regulatory events, coordinated by ionic flow, correspond to a new and exciting field termed molecular bioelectricity. We aim to present a brief discussion on the biophysical machinery involving membrane potential and the mechanisms mediating cell cycle progression and cancer transformation. Furthermore, we present the planarian Schmidtea mediterranea as a tractable model system for understanding principles behind molecular bioelectricity at both the cellular and organismal level. This article is part of a Special Issue entitled: Membrane channels and transporters in cancers.
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Affiliation(s)
- Paul G Barghouth
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California at Merced, 5200 North Lake Road, Merced, CA 95343, USA; Quantitative and Systems Biology Graduate Program, University of California at Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Manish Thiruvalluvan
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California at Merced, 5200 North Lake Road, Merced, CA 95343, USA; Quantitative and Systems Biology Graduate Program, University of California at Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Néstor J Oviedo
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California at Merced, 5200 North Lake Road, Merced, CA 95343, USA; Quantitative and Systems Biology Graduate Program, University of California at Merced, 5200 North Lake Road, Merced, CA 95343, USA; Health Sciences Research Institute, University of California at Merced, 5200 North Lake Road, Merced, CA 95343, USA.
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