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Varghese B, Del Gaudio N, Cobellis G, Altucci L, Nebbioso A. KDM4 Involvement in Breast Cancer and Possible Therapeutic Approaches. Front Oncol 2021; 11:750315. [PMID: 34778065 PMCID: PMC8581295 DOI: 10.3389/fonc.2021.750315] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the second leading cause of cancer death in women, although recent scientific and technological achievements have led to significant improvements in progression-free disease and overall survival of patients. Genetic mutations and epigenetic modifications play a critical role in deregulating gene expression, leading to uncontrolled cell proliferation and cancer progression. Aberrant histone modifications are one of the most frequent epigenetic mechanisms occurring in cancer. In particular, methylation and demethylation of specific lysine residues alter gene accessibility via histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). The KDM family includes more than 30 members, grouped into six subfamilies and two classes based on their sequency homology and catalytic mechanisms, respectively. Specifically, the KDM4 gene family comprises six members, KDM4A-F, which are associated with oncogene activation, tumor suppressor silencing, alteration of hormone receptor downstream signaling, and chromosomal instability. Blocking the activity of KDM4 enzymes renders them "druggable" targets with therapeutic effects. Several KDM4 inhibitors have already been identified as anticancer drugs in vitro in BC cells. However, no KDM4 inhibitors have as yet entered clinical trials due to a number of issues, including structural similarities between KDM4 members and conservation of the active domain, which makes the discovery of selective inhibitors challenging. Here, we summarize our current knowledge of the molecular functions of KDM4 members in BC, describe currently available KDM4 inhibitors, and discuss their potential use in BC therapy.
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Affiliation(s)
- Benluvankar Varghese
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Gilda Cobellis
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy.,Biogem Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
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Pardo JP, Martínez F, Guerra G, Velázquez I, Rendón JL, Mendoza G. An alternative model for the transmembrane segments of the yeast H+-ATPase. Yeast 1999; 15:1585-93. [PMID: 10572256 DOI: 10.1002/(sici)1097-0061(199911)15:15<1585::aid-yea483>3.0.co;2-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An alternative topological model for the yeast plasma membrane H(+)-ATPase from K. lactis was deduced by joint prediction, using 11 algorithms for the prediction of transmembrane segments complemented with hydrophobic moment analysis. Similarly to the model currently used in the literature, this alternative model contains 10 transmembrane segments, four in the N-half and six in the C-half of the protein. However, the distribution of the membrane-associated segments on the C-half of the enzyme differs in both models. Nine of the 10 transmembrane segments are highly hydrophobic with low hydrophobic moments, and are probably involved in structural roles. The fifth transmembrane segment is, on the other hand, less hydrophobic, with the highest hydrophobic moment, suggesting that this segment might have a dynamic role in the coupling of the hydrolysis of ATP with the translocation of protons across the membrane. The alignment of the Ca(2+)-ATPase, the Na(+)/K(+)-ATPase and the H(+)-ATPase sequences showed that these proteins have the same topology in the N-half, but important differences were found at the C-half of the enzymes. In contrast with the mammalian ATPases, the fifth transmembrane segment in the H(+)-ATPase appears early in the sequence, giving rise to a shorter cytoplasmic central loop. This alternative model will be useful in the designing of site-directed mutagenesis experiments and contains information for the fitting of the amino acid sequence into the transmembrane region of the three-dimensional model of the ATPase.
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Affiliation(s)
- J P Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, 04510 México D.F., México.
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3
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Abstract
The P-type ATPases are integral membrane proteins that generate essential transmembrane ion gradients in virtually all living cells. The structures of two of these have recently been elucidated at a resolution of 8 A. When considered together with the large body of biochemical information that has accrued for these transporters and for enzymes in general, this new structural information is providing tantalizing insights regarding the molecular mechanism of active ion transport catalyzed by these proteins.
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Affiliation(s)
- G A Scarborough
- Department of Pharmacology, CB 7365 Mary Ellen Jones Building, University of North Carolina, Chapel Hill, NC 27599, USA.
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4
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Abstract
Electron cryocrystallography of precipitant-induced two-dimensional surface crystals of the neurospora plasma membrane H+ - ATPase and tubular crystals of the sarcoplasmic reticulum Ca(2+)-ATPase has recently yielded structure maps for these ion transporters at a resolution of about 8 A. The membrane-embedded regions of these closely related enzymes are similar, but the cytoplasmic regions appear to be significantly different.
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Affiliation(s)
- W Kühlbrandt
- Max-Planck-Institut für Biophysik, Abteilung Strukturbiologie, Frankfurt am Main, Germany.
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5
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Auer M, Scarborough GA, Kühlbrandt W. Three-dimensional map of the plasma membrane H+-ATPase in the open conformation. Nature 1998; 392:840-3. [PMID: 9572146 DOI: 10.1038/33967] [Citation(s) in RCA: 162] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The H+-ATPase from the plasma membrane of Neurospora crassa is an integral membrane protein of relative molecular mass 100K, which belongs to the P-type ATPase family that includes the plasma membrane Na+/K+-ATPase and the sarcoplasmic reticulum Ca2+-ATPase. The H+-ATPase pumps protons across the cell's plasma membrane using ATP as an energy source, generating a membrane potential in excess of 200mV. Despite the importance of P-type ATPases in controlling membrane potential and intracellular ion concentrations, little is known about the molecular mechanism they use for ion transport. This is largely due to the difficulty in growing well ordered crystals and the resulting lack of detail in the three-dimensional structure of these large membrane proteins. We have now obtained a three-dimensional map of the H+-ATPase by electron crystallography of two-dimensional crystals grown directly on electron microscope grids. At an in-plane resolution of 8 A, this map reveals ten membrane-spanning alpha-helices in the membrane domain, and four major cytoplasmic domains in the open conformation of the enzyme without bound ligands.
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Affiliation(s)
- M Auer
- Max-Planck-Institut für Biophysik, Abteilung Strukturbiologie, Frankfurt am Main, Germany
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Affiliation(s)
- G A Scarborough
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill 27599, USA.
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7
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Vigneron L, Ruysschaert JM, Goormaghtigh E. Fourier transform infrared spectroscopy study of the secondary structure of the reconstituted Neurospora crassa plasma membrane H(+)-ATPase and of its membrane-associated proteolytic peptides. J Biol Chem 1995; 270:17685-96. [PMID: 7629067 DOI: 10.1074/jbc.270.30.17685] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We reconstituted purified plasma membrane H(+)-ATPase from Neurospora crassa into soybean phospholipid vesicles (lipid/ATPase ratio of 5:1 w/w). The proteoliposomes contained an active ATPase, oriented inside-out. They were subjected to proteolysis by using Pronase, proteinase K, trypsin, and carboxypeptidase Y. Fourier transform infrared attenuated total reflection spectroscopy indicates that the amount of protein remaining after hydrolysis and elimination of the extramembrane domain of ATPase represents about 43% of the intact protein. The secondary structure of intact ATPase and of the membrane-associated domain of ATPase was determined by infrared spectroscopy. The membrane domain shows a typical alpha-helix and beta-sheet absorption. Polarized infrared spectroscopy reveals that the orientation of the helices is about perpendicular to the membrane. Amide hydrogen/deuterium exchange kinetics performed for the intact H(+)-ATPase and for the membrane-associated domain demonstrate that this part of ATPase shows less accessibility to the solvent than the entire protein but remains much more accessible to the solvent than bacteriorhodopsin membrane segments.
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Affiliation(s)
- L Vigneron
- Laboratoire de Chimie Physique des Macromolecules aux Interfaces, Université Libre de Bruxelles, Belgium
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8
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Vigneron L, Scarborough GA, Ruysschaert JM, Goormaghtigh E. Reconstitution of the Neurospora crassa plasma membrane H(+)-adenosine triphosphatase. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1236:95-104. [PMID: 7794959 DOI: 10.1016/0005-2736(95)00028-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The purified H(+)-ATPase of the Neurospora crassa plasma membrane has been reconstituted by a gel filtration method into lipidic vesicles using sodium deoxycholate as the detergent. Reconstitution was performed for lipid/ATPase ratios ranging from 1000:1 to 5:1 (w/w). Whatever the lipid/ATPase ratio, the ATPase molecules completely associate with the lipid vesicles. The ATPase specific activity is identical for all proteoliposomes regardless of the lipid/ATPase ratio, but the H+ transport decreases at high protein/lipid ratios, suggesting that the proteoliposomes are more leaky to H+ as the amount of protein inserted into the lipidic membrane increases. Analysis of the fragments generated by trypsin proteolysis in the presence and in the absence of MgATP+ vanadate indicate that most of the reconstituted ATPase molecules are able to assume the transition state of the enzyme dephosphorylation reaction, and are therefore functional. The orientation (inside-out or rightside-out) of the ATPase molecules in the vesicles is independent of the lipid/ATPase ratio chosen for the reconstitution. For all the lipid/ATPase ratios tested, most of the ATPase molecules (> 99%) expose their cytoplasmic side to the outside of the reconstituted proteoliposomes. The size of the vesicles increases parallel to the ATPase amount. Although the H+ leakiness of our preparation at low lipid/protein ratios prevents proton pumping measurements, the reconstitution procedure described here has the main advantage on other procedures to allow the obtention of vesicles at high protein-to-lipid ratios, facilitating further structural characterization of the ATPase by biochemical and biophysical techniques. Therefore, the procedure described here could be of general interest in the field of membrane protein study.
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Affiliation(s)
- L Vigneron
- Laboratoire des Macromolécules aux Interfaces, Université Libre de Bruxelles, Belgium
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Buurman ET, Kim KT, Epstein W. Genetic evidence for two sequentially occupied K+ binding sites in the Kdp transport ATPase. J Biol Chem 1995; 270:6678-85. [PMID: 7896809 DOI: 10.1074/jbc.270.12.6678] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Substrate binding sites in Kdp, a P-type ATPase of Escherichia coli, were identified by the isolation and characterization of mutants with reduced affinity for K+, its cation substrate. Most of the mutants have an altered KdpA subunit, a hydrophobic subunit not found in other P-type ATPases. Topological analysis of KdpA and the locations of the residues changed in the mutants suggest that KdpA has 10 membrane-spanning segments and forms two separate and distinct sites where K+ is bound. One site is formed by three periplasmic loops of the protein and is inferred to be the site of initial binding. The other site is cytoplasmic. We believe K+ moves from the periplasmic site through the membrane to the cytoplasmic site where it becomes "occluded," i.e. inexchangeable with K+ outside the membrane. Membrane-spanning parts of KdpA probably form the path for transmembrane movement of K+. The kinetics of cation transport in the mutants indicate that each of the two binding sites contributes to the observed Km for cations as well as to the marked discrimination between K+ and Rb+ characteristic of wild-type Kdp. Energy coupling in Kdp, mediated by the KdpB subunit, is performed by a different subunit from the one that mediates transport.
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Affiliation(s)
- E T Buurman
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637
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10
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Membrane topology of a P-type ATPase. The MgtB magnesium transport protein of Salmonella typhimurium. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)41553-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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11
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Serrano R, Monk BC, Villalba JM, Montesinos C, Weiler EW. Epitope mapping and accessibility of immunodominant regions of yeast plasma membrane H(+)-ATPase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 212:737-44. [PMID: 7681777 DOI: 10.1111/j.1432-1033.1993.tb17712.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Immunodominant regions of yeast plasma membrane H(+)-ATPase have been mapped by two different approaches. A rabbit polyclonal antibody was used to screen a library of random fragments of the ATPase gene in a bacterial expression plasmid. In addition, the epitopes recognized by a panel of mouse monoclonal antibodies against the ATPase were mapped by reactions with defined fragments of the enzyme expressed in Escherichia coli. Both methodologies indicated that two regions within the amino-terminal part of the ATPase (at amino acid positions 5-105 and 168-255) contain most of the antigenic determinants. The accessibility of the monoclonal antibodies to their epitopes in native and solvent-perturbed ATPase preparations was investigated by immunofluorescence studies on yeast protoplasts. Cells fixed and permeabilized with formaldehyde were either treated with or without detergents and organic solvents. ELISA competition tests with plasma membrane vesicles and with detergent-purified ATPase incubated in solution with the monoclonal antibodies gave similar results. All the epitopes were accessible in detergent-treated ATPase preparations. In contrast, only the epitopes at amino acids 24-56 were accessible in ATPase preparations not treated with detergents or organic solvents. These epitopes were cytoplasmic because protoplast permeabilization was required for decoration by the reactive monoclonal antibodies.
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Affiliation(s)
- R Serrano
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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12
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Rao R, Nakamoto RK, Verjovski-Almeida S, Slayman CW. Structure and function of the yeast plasma-membrane H(+)-ATPase. Ann N Y Acad Sci 1992; 671:195-203. [PMID: 1288321 DOI: 10.1111/j.1749-6632.1992.tb43796.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- R Rao
- Department of Genetics and Cellular & Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06510
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13
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Seto-Young D, Monk BC, Perlin DS. Assessing hydrophobic regions of the plasma membrane H(+)-ATPase from Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1102:213-9. [PMID: 1390824 DOI: 10.1016/0005-2728(92)90102-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The hydrophobic, photoactivatable probe TID [3-trifluoromethyl-3-(m-[125I]iodophenyl)diazirine] was used to label the plasma membrane H(+)-ATPase from Saccharomyces cerevisiae. The H(+)-ATPase accounted for 43% of the total label associated with plasma membrane protein and incorporated 0.3 mol of [125I]TID per mol of 100 kDa polypeptide. The H(+)-ATPase was purified by octyl glucoside extraction and glycerol gradient centrifugation, and was cleaved by either cyanogen bromide digestion or limited tryptic proteolysis to isolate labeled fragments. Cyanogen bromide digestion resulted in numerous labeled fragments of mass less than 21 kDa. Seven fragments suitable for microsequence analysis were obtained by electrotransfer to poly(vinylidene difluoride) membranes. Five different regions of amino-acid sequence were identified, including fragments predicted to encompass both membrane-spanning and cytoplasmic protein structure domains. Most of the labeling of the cytoplasmic domain was concentrated in a region comprising amino acids 347 to 529. This catalytic region contains the site of phosphorylation and was previously suggested to be hydrophobic in character (Goffeau, A. and De Meis, L. (1990) J. Biol. 265, 15503-15505). Complementary labeling information was obtained from an analysis of limited tryptic fragments enriched for hydrophobic character. Six principal labeled fragments, of 29.6, 20.6, 16, 13.1, 11.4 and 9.7 kDa, were obtained. These fragments were found to comprise most of the putative transmembrane region and a portion of the cytoplasmic region that overlapped with the highly labeled active site-containing cyanogen bromide fragment. Overall, the extensive labeling of protein structure domains known to lie outside the bilayer suggests that [125I]TID labeling patterns cannot be unambiguously interpreted for the purpose of discerning membrane-embedded protein structure domains. It is proposed that caution should be applied in the interpretation of [125I]TID labeling patterns of the yeast plasma membrane H(+)-ATPase and that new and diverse approaches should be developed to provide a more definitive topology model.
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Affiliation(s)
- D Seto-Young
- Public Health Research Institute, New York, NY 10016
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14
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Assessing hydrophobic regions of the plasma membrane H+-ATPase from Saccharomyces cerevisiae. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0167-4838(92)90512-c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Rao US, Bauzon DD, Scarborough GA. Cytoplasmic location of amino acids 359-440 of the Neurospora crassa plasma membrane H(+)-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1108:153-8. [PMID: 1386255 DOI: 10.1016/0005-2736(92)90020-m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The topographic location of the region comprising amino acids 359-440 of the Neurospora crassa plasma membrane H(+)-ATPase has been elucidated using reconstituted proteoliposomes and protein chemical techniques. Proteoliposomes containing H(+)-ATPase molecules oriented predominantly with their cytoplasmic surface facing outward were cleaved with trypsin and the resulting digest was subjected to centrifugation on a glycerol step gradient to separate the released and liposome-bound peptides. The released peptides were recovered in the upper regions of the step gradient, whereas the liposome-bound peptides were recovered near the 40% glycerol interface. The released peptides present in the upper fractions were reduced, 14C-carboxy-methylated, and then separated by high performance liquid chromatography. Two radioactive cysteine-containing peptides with retention times of about 162 and 182 min were identified as H(+)-ATPase peptides comprising residues Leu363-Lys379 and Leu388-Arg414, respectively, by comparison to standards prepared from the purified ATPase. This information thus establishes a cytoplasmic location for residues 359-418 in the H(+)-ATPase polypeptide chain. It also infers a cytoplasmic location for residues 419-440, since this stretch of amino acids is too short to cross the membrane and return between regions known to be cytoplasmically located. These results and the results of other recent experiments establish the topographical location of nearly all of the 919 residues in the H(+)-ATPase molecule.
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Affiliation(s)
- U S Rao
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill 27599-7365
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Chapter 4 The Neurospora crassa plasma membrane H+ -ATPase. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/s0167-7306(08)60066-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Rao U, Hennessey J, Scarborough G. Identification of the membrane-embedded regions of the Neurospora crassa plasma membrane H(+)-ATPase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)98749-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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