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1.
Talanta ; 279: 126578, 2024 Jul 19.
Article in English | MEDLINE | ID: mdl-39032458

ABSTRACT

Accurate detection of ascorbic acid (AA) plays a significant role in food and human physiological processes. Herein, a three-dimensional flexible leaf-like nitrogen-doped hierarchical carbon nanoarrays with high-density carbon nanotube "tentacle" architecture (NC/CNT-Co), which possesses high specific surface area, plenty of active defect sites, and various pore size distributions, was synthesized by the pyrolysis of zeolitic imidazolate framework (ZIF(Co)), while g-C3N4 acted as carbon source and heteroatom doping agent. Benefiting from its unique structure and surface properties, a selective and highly sensitive AA sensor was developed using this material. Compared to powder materials, NC/CNT-Co modified CF (CF@NC/CNT-Co) which don't be extra decorated, exhibits lower detection limit (1 µM), a wider linear range (20-1400 µM), and better stability, showing higher performance in electrocatalysis and detection of AA. Furthermore, CF@NC/CNT-Co also demonstrates high resistance to interference and fouling in AA detection. Particularly, the prepared CF@NC/CNT-Co electrode could determine AA in beverage samples with a recovery rate of 96.3-103.5 %. Therefore, the three-dimensional NC/CNT-Co hierarchical structure can be provided as an original electrode nanomaterial suitable for the selective and sensitive detection of AA, with a wide range of practical applications from food analysis to the pharmaceutical industry.

2.
Chem Commun (Camb) ; 60(51): 6496-6499, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38836703

ABSTRACT

Cobalt substitution for manganese sites in Na0.44MnO2 initiates a dynamic structural evolution process, yielding a composite cathode material comprising intergrown P2 and P3 phases. The novel P2/P3 composite cathode exhibits a reversible phase transition process during Na+ extraction/insertion, showcasing its attractive battery performance in sodium-ion batteries.

3.
J Colloid Interface Sci ; 666: 594-602, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38613981

ABSTRACT

Tailoring the omnidirectional conductivity networks in nickel oxide-based electrodes is important for ensuring their long lifespan, stability, high capacity, and high-rate capability. In this study, nickel metal nanoparticles and a three-dimensional nitrogen-doped carbon matrix were used to embellish the nickel oxide composite NiO-Ni/N-C via simplified hard templating. When a porous nitrogen-doped carbon matrix is present, a rapid pathway would be established for charging and discharging the electrons and lithium ions in a lithium-ion battery, thereby alleviating the volumetric expansion of the NiO nanoparticles during the operation of the battery. Moreover, the Ni0 ions added to serve as active sites to improve the capacity of the NiO-based electrodes and strengthen their conductivities. The multielement-effects of the optimal NiO-Ni/N-C electrode leads it to exhibit a capacity of 1310.8 mAh g-1 at 0.1 A g-1 for 120 loops and a rate capability of 441.5 mAh g-1 at 20.0 A g-1. Kinetic analysis of the prepared electrodes proved their ultrafast ionic and electronic conductivities. This strategy of hard templating reduces the number of routes required for preparing different types of electrodes, including NiO-based electrodes, and improves their electrochemical performance to enable their use in energy storage applications.

4.
Molecules ; 29(5)2024 Feb 21.
Article in English | MEDLINE | ID: mdl-38474463

ABSTRACT

Developing a green, low-carbon, and circular economic system is the key to achieving carbon neutrality. This study investigated the organics removal efficiency in a three-dimensional electrode reactor (3DER) constructed from repurposed industrial solid waste, i.e., Mn-loaded steel slag, as the catalytic particle electrodes (CPE). The CPE, a micron-grade material consisting primarily of transition metals, including Fe and Mn, exhibited excellent electric conductivity, catalytic ability, and recyclability. High rhodamine B (RhB) removal efficiency in the 3DER was observed through a physical modelling experiment. The optimal operating condition was determined through a single-factor experiment in which 5.0 g·L-1 CPE and 3 mM peroxymonosulfate (PMS) were added to a 200 mL solution of 10 mM RhB under a current intensity of 0.5 A and a 1.5 to 2.0 cm distance between the 2D electrodes. When the initial pH value of the simulated solution was 3 to 9, the RhB removal rate exceeded 96% after 20 min reaction. In addition, the main reactive oxidation species in the 3DER were determined. The results illustrated that HO• and SO4•- both existed, but that the contribution of SO4•- to RhB removal was much lower than that of HO• in the 3DER. In summary, this research provides information on the potential of the 3DER for removing refractory organics from water.

5.
IEEE Trans Pattern Anal Mach Intell ; 45(8): 9426-9438, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37028045

ABSTRACT

To enable effective learning of new tasks with only a few examples, meta-learning acquires common knowledge from the existing tasks with a globally shared meta-learner. To further address the problem of task heterogeneity, recent developments balance between customization and generalization by incorporating task clustering to generate task-aware modulation to be applied to the global meta-learner. However, these methods learn task representation mostly from the features ofinput data, while the task-specific optimization process with respect to the base-learner is often neglected. In this work, we propose a Clustered Task-Aware Meta-Learning (CTML) framework with task representation learned from both features and learning paths. We first conduct rehearsed task learning from the common initialization, and collect a set of geometric quantities that adequately describes this learning path. By inputting this set of values into a meta path learner, we automatically abstract path representation optimized for downstream clustering and modulation. Aggregating the path and feature representations results in an improved task representation. To further improve inference efficiency, we devise a shortcut tunnel to bypass the rehearsed learning process at a meta-testing time. Extensive experiments on two real-world application domains: few-shot image classification and cold-start recommendation demonstrate the superiority of CTML compared to state-of-the-art methods. We provide our code at https://github.com/didiya0825.


Subject(s)
Algorithms , Cluster Analysis
6.
Semin Cancer Biol ; 85: 52-68, 2022 10.
Article in English | MEDLINE | ID: mdl-33862221

ABSTRACT

The intrinsic mechanisms sensing the imbalance of energy in cells are pivotal for cell survival under various environmental insults. AMP-activated protein kinase (AMPK) serves as a central guardian maintaining energy homeostasis by orchestrating diverse cellular processes, such as lipogenesis, glycolysis, TCA cycle, cell cycle progression and mitochondrial dynamics. Given that AMPK plays an essential role in the maintenance of energy balance and metabolism, managing AMPK activation is considered as a promising strategy for the treatment of metabolic disorders such as type 2 diabetes and obesity. Since AMPK has been attributed to aberrant activation of metabolic pathways, mitochondrial dynamics and functions, and epigenetic regulation, which are hallmarks of cancer, targeting AMPK may open up a new avenue for cancer therapies. Although AMPK is previously thought to be involved in tumor suppression, several recent studies have unraveled its tumor promoting activity. The double-edged sword characteristics for AMPK as a tumor suppressor or an oncogene are determined by distinct cellular contexts. In this review, we will summarize recent progress in dissecting the upstream regulators and downstream effectors for AMPK, discuss the distinct roles of AMPK in cancer regulation and finally offer potential strategies with AMPK targeting in cancer therapy.


Subject(s)
AMP-Activated Protein Kinases , Neoplasms , Signal Transduction , Humans , AMP-Activated Protein Kinases/metabolism , Energy Metabolism , Epigenesis, Genetic , Neoplasms/drug therapy , Neoplasms/metabolism
7.
Cell Stress ; 4(12): 273-277, 2020 Nov 25.
Article in English | MEDLINE | ID: mdl-33336150

ABSTRACT

Cancer represents the leading public health problem throughout the world. Globally, about one out of six deaths is related to cancer, which is largely due to the metastatic lesions. However, there are no effective strategies for targeting cancer metastasis. Identification of the key druggable targets maintaining metastasis is crucial for cancer treatment. In our recent study (Cai et al. (2020), Mol Cell, doi: 10.1016/j.molcel.2020.09.018), we found that activity of AMPK was enriched in metastatic tumors compared to primary tumors. Depletion of AMPK rendered cancer cells more sensitive to metabolic and oxidative stress, leading to the impairment of breast cancer lung metastasis. Activation of AMPK rewired cancer metabolism towards TCA cycle, which protects disseminated cancer cells from both metabolic and oxidative stress-induced cell death, and facilitates cancer metastasis. Further, AMPK critically maintained the activity of pyruvate dehydrogenase complex (PDH), the rate limiting enzyme involved in TCA cycle, thus favoring the pyruvate metabolism towards TCA cycle rather than converting it to lactate. Mechanistically, AMPK was shown to co-localize with PDHA, the catalytic subunit of PDH, in the mitochondrial matrix and directly triggered the phosphorylation of PDHA on Ser295 and Ser314. Hyper-phosphorylation of Ser295 and Ser314 of PDHA promotes lung metastasis through elevating activity of PDH. Of note, PDHA Ser314 phosphorylation abrogated the interaction between PDHA and PDHKs leading to the dephosphorylation on previously reported S293 site, whose phosphorylation serves as a negative signal for PDH activation, while S295 phosphorylation serves as an intrinsic catalytic site required for pyruvate metabolism. Our study presented the first evidence for the pro-metastatic property of the AMPK-PDH axis and advance our current understanding of how PDH is activated under physiological and pathological conditions.

8.
Mol Cell ; 80(2): 263-278.e7, 2020 10 15.
Article in English | MEDLINE | ID: mdl-33022274

ABSTRACT

Cancer metastasis accounts for the major cause of cancer-related deaths. How disseminated cancer cells cope with hostile microenvironments in secondary site for full-blown metastasis is largely unknown. Here, we show that AMPK (AMP-activated protein kinase), activated in mouse metastasis models, drives pyruvate dehydrogenase complex (PDHc) activation to maintain TCA cycle (tricarboxylic acid cycle) and promotes cancer metastasis by adapting cancer cells to metabolic and oxidative stresses. This AMPK-PDHc axis is activated in advanced breast cancer and predicts poor metastasis-free survival. Mechanistically, AMPK localizes in the mitochondrial matrix and phosphorylates the catalytic alpha subunit of PDHc (PDHA) on two residues S295 and S314, which activates the enzymatic activity of PDHc and alleviates an inhibitory phosphorylation by PDHKs, respectively. Importantly, these phosphorylation events mediate PDHc function in cancer metastasis. Our study reveals that AMPK-mediated PDHA phosphorylation drives PDHc activation and TCA cycle to empower cancer cells adaptation to metastatic microenvironments for metastasis.


Subject(s)
AMP-Activated Protein Kinases/metabolism , Breast Neoplasms/enzymology , Breast Neoplasms/pathology , Citric Acid Cycle , Pyruvate Dehydrogenase Complex/metabolism , Animals , Catalytic Domain , Cell Line, Tumor , Cell Survival , Enzyme Activation , Female , Humans , Mice, Inbred BALB C , Mice, Nude , Neoplasm Metastasis , Phosphorylation , Phosphoserine/metabolism , Signal Transduction , Stress, Physiological , Survival Analysis
9.
Cell Discov ; 6: 15, 2020.
Article in English | MEDLINE | ID: mdl-32218989

ABSTRACT

Liver metastasis, characterized by the spread of tumors to the liver from other areas, represents a deadly disease with poor prognosis. Currently, there is no effective therapeutic strategies and/or agents to combat liver metastasis primarily due to the insufficient understanding of liver metastasis. To develop a promising strategy for targeting liver metastasis, understanding of a cell origin responsible for liver metastasis and how this cell can be pharmacologically eliminated are therefore crucial. Using diverse tumor models including p53 -/- genetic mouse model and syngeneic tumor models, we identified primordial germ cell (PGC)-like tumor cells, which are enriched in earliest liver micro-metastasis (up to 99%), as a cell origin of liver metastasis. PGC-like tumor cells formed earliest micro-metastasis in liver and gradually differentiated into non-PGC-like tumor cells to constitute late macro-metastasis in the course of tumor metastasis. The liver metastasis-initiating cells (PGC-like tumor cells) display cell renewal and differentiation capabilities, resemble primordial germ cells (PGCs) in morphology and PGC marker gene expression, and express higher level of the genes linked to metastasis and immune escape compared with non-PGC-like tumor cells. Of note, Stellarhigh PGC-like tumor cells, but not Stellarlow non-PGC-like cells, sorted from primary tumors of p53 -/- mice readily form liver metastasis. Depletion of PGC-like tumor cells through genetic depletion of any of key germ cell genes impairs liver metastasis, while increased PGC-like tumor cells by SMAD2 knockout is correlated with markedly enhanced liver metastasis. Finally, we present the proof of principle evidence that pharmacologically targeting BMP pathways serves as a promising strategy to eliminate PGC-like tumor cells leading to abrogating liver metastasis. Collectively, our study identifies PGC-like tumor cells as a cell origin of liver metastasis, whose depletion by genetically targeting core PGC developmental genes or pharmacologically inhibiting BMP pathways serves a promising strategy for targeting liver metastasis.

10.
Semin Cancer Biol ; 67(Pt 2): 16-33, 2020 12.
Article in English | MEDLINE | ID: mdl-32014608

ABSTRACT

Strictly regulated protein degradation by ubiquitin-proteasome system (UPS) is essential for various cellular processes whose dysregulation is linked to serious diseases including cancer. Skp2, a well characterized component of Skp2-SCF E3 ligase complex, is able to conjugate both K48-linked ubiquitin chains and K63-linked ubiquitin chains on its diverse substrates, inducing proteasome mediated proteolysis or modulating the function of tagged substrates respectively. Overexpression of Skp2 is observed in various human cancers associated with poor survival and adverse therapeutic outcomes, which in turn suggests that Skp2 engages in tumorigenic activity. To that end, the oncogenic properties of Skp2 are demonstrated by various genetic mouse models, highlighting the potential of Skp2 as a target for tackling cancer. In this article, we will describe the downstream substrates of Skp2 as well as upstream regulators for Skp2-SCF complex activity. We will further summarize the comprehensive oncogenic functions of Skp2 while describing diverse strategies and therapeutic platforms currently available for developing Skp2 inhibitors.


Subject(s)
Drug Resistance, Neoplasm/genetics , Molecular Targeted Therapy/methods , Neoplasms/pathology , S-Phase Kinase-Associated Proteins/metabolism , Animals , Carcinogens , Female , Gene Expression Regulation , Humans , Male , Metabolic Networks and Pathways , Mice , Neoplasms/drug therapy , Neoplasms/genetics , S-Phase Kinase-Associated Proteins/genetics , Ubiquitination
11.
Cell Discov ; 4: 54, 2018.
Article in English | MEDLINE | ID: mdl-30302273

ABSTRACT

The century-old embryonal/gametogenesis hypothesis of tumors could link diverse tumors' malignant features together likely representing the real "stemness" of tumors. However, the genetic evidence to validate abnormal gametogenesis in tumors remains lacking. Here we show that p53 deficiency elicits abnormal gametogenesis from primordial germ cell-like stage to late oocyte-like stage and subsequent parthenogenetic activation. The similar upregulation of abnormal gametogenesis by p53 deficiency is observed both in p53-/- mouse model and cultured cancer cells. Notably, germ cell-like cells isolated from distinct tumors from p53-/- mice and cancer cell lines display potent tumorigenicity potential. Abnormal oogenesis induced by p53 deficiency and then spontaneous parthenogenetic activation endow tumors with imitated embryonic development, life cycle, and therapeutic resistance. Our study establishes the genetic evidence to support embryonal/gametogenesis theory of tumors and reveals a pivotal role of p53 in restricting abnormal gametogenesis that may represent a novel aspect for p53's tumor suppression.

12.
Nat Commun ; 9(1): 3759, 2018 09 14.
Article in English | MEDLINE | ID: mdl-30217978

ABSTRACT

Recognition of histones by epigenetic readers is a fundamental mechanism for the regulation of chromatin and transcription. Most reader modules target specific post-translational modifications on histones. Here, we report the identification of a reader of histone H3, the ZZ-type zinc finger (ZZ) domain of ZZZ3, a subunit of the Ada-two-A-containing (ATAC) histone acetyltransferase complex. The solution NMR structure of the ZZ in complex with the H3 peptide reveals a unique binding mechanism involving caging of the N-terminal Alanine 1 of histone H3 in an acidic cavity of the ZZ domain, indicating a specific recognition of H3 versus other histones. Depletion of ZZZ3 or disruption of the ZZ-H3 interaction dampens ATAC-dependent promoter histone H3K9 acetylation and target gene expression. Overall, our study identifies the ZZ domain of ZZZ3 as a histone H3 reader that is required for the ATAC complex-mediated maintenance of histone acetylation and gene activation.


Subject(s)
DNA-Binding Proteins/metabolism , Histone Acetyltransferases/genetics , Histone Code/genetics , Histones/metabolism , Transcription Factors/metabolism , Transcriptional Activation/genetics , Acetylation , DNA-Binding Proteins/genetics , Epigenesis, Genetic , HEK293 Cells , Histone Acetyltransferases/metabolism , Humans , Magnetic Resonance Spectroscopy , Protein Processing, Post-Translational , Spectrometry, Fluorescence , Transcription Factors/genetics , Zinc Fingers
13.
Cell Discov ; 4: 28, 2018.
Article in English | MEDLINE | ID: mdl-29900004

ABSTRACT

The histone variant H2A.Z is essential for maintaining embryonic stem cell (ESC) identity in part by keeping developmental genes in a poised bivalent state. However, how H2A.Z is deposited into the bivalent domains remains unknown. In mammals, two chromatin remodeling complexes, Tip60/p400 and SRCAP, exchange the canonical histone H2A for H2A.Z in the chromatin. Here we show that Glioma Amplified Sequence 41 (Gas41), a shared subunit of the two H2A.Z-depositing complexes, functions as a reader of histone lysine acetylation and recruits Tip60/p400 and SRCAP to deposit H2A.Z into specific chromatin regions including bivalent domains. The YEATS domain of Gas41 bound to acetylated histone H3K27 and H3K14 both in vitro and in cells. The crystal structure of the Gas41 YEATS domain in complex with the H3K27ac peptide revealed that, similar to the AF9 and ENL YEATS domains, Gas41 YEATS forms a serine-lined aromatic cage for acetyllysine recognition. Consistently, mutations in the aromatic residues of the Gas41 YEATS domain abrogated the interaction. In mouse ESCs, knockdown of Gas41 led to flattened morphology of ESC colonies, as the result of derepression of differentiation genes. Importantly, the abnormal morphology was rescued by expressing wild-type Gas41, but not the YEATS domain mutated counterpart that does not recognize histone acetylation. Mechanically, we found that Gas41 depletion led to reduction of H2A.Z levels and a concomitant reduction of H3K27me3 levels on bivalent domains. Together, our study reveals an essential role of the Gas41 YEATS domain in linking histone acetylation to H2A.Z deposition and maintenance of ESC identity.

14.
Nat Commun ; 7: 10810, 2016 Mar 10.
Article in English | MEDLINE | ID: mdl-26960573

ABSTRACT

The euchromatin histone methyltransferase 2 (also known as G9a) methylates histone H3K9 to repress gene expression, but it also acts as a coactivator for some nuclear receptors. The molecular mechanisms underlying this activation remain elusive. Here we show that G9a functions as a coactivator of the endogenous oestrogen receptor α (ERα) in breast cancer cells in a histone methylation-independent manner. G9a dimethylates ERα at K235 both in vitro and in cells. Dimethylation of ERαK235 is recognized by the Tudor domain of PHF20, which recruits the MOF histone acetyltransferase (HAT) complex to ERα target gene promoters to deposit histone H4K16 acetylation promoting active transcription. Together, our data suggest the molecular mechanism by which G9a functions as an ERα coactivator. Along with the PHF20/MOF complex, G9a links the crosstalk between ERα methylation and histone acetylation that governs the epigenetic regulation of hormonal gene expression.


Subject(s)
Antigens, Neoplasm/genetics , Biomarkers, Tumor/genetics , Breast Neoplasms/genetics , Epigenesis, Genetic , Estrogen Receptor alpha/genetics , Gene Expression Regulation, Neoplastic , Histocompatibility Antigens/genetics , Histone Acetyltransferases/genetics , Histone-Lysine N-Methyltransferase/genetics , Acetylation , Antigens, Neoplasm/metabolism , Biomarkers, Tumor/metabolism , Cell Line, Tumor , DNA-Binding Proteins , Estrogen Receptor alpha/metabolism , Female , Fluorescent Antibody Technique , HEK293 Cells , Histocompatibility Antigens/metabolism , Histone Acetyltransferases/metabolism , Histone-Lysine N-Methyltransferase/metabolism , Humans , Immunoprecipitation , In Vitro Techniques , MCF-7 Cells , Magnetic Resonance Spectroscopy , Nuclear Receptor Coactivator 2 , Promoter Regions, Genetic , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Transcription Factors
15.
Cell ; 159(3): 558-71, 2014 Oct 23.
Article in English | MEDLINE | ID: mdl-25417107

ABSTRACT

The recognition of modified histones by "reader" proteins constitutes a key mechanism regulating gene expression in the chromatin context. Compared with the great variety of readers for histone methylation, few protein modules that recognize histone acetylation are known. Here, we show that the AF9 YEATS domain binds strongly to histone H3K9 acetylation and, to a lesser extent, H3K27 and H3K18 acetylation. Crystal structural studies revealed that AF9 YEATS adopts an eight-stranded immunoglobin fold and utilizes a serine-lined aromatic "sandwiching" cage for acetyllysine readout, representing a novel recognition mechanism that is distinct from that of known acetyllysine readers. ChIP-seq experiments revealed a strong colocalization of AF9 and H3K9 acetylation genome-wide, which is important for the chromatin recruitment of the H3K79 methyltransferase DOT1L. Together, our studies identified the evolutionarily conserved YEATS domain as a novel acetyllysine-binding module and established a direct link between histone acetylation and DOT1L-mediated H3K79 methylation in transcription control.


Subject(s)
Histone Code , Methyltransferases/chemistry , Methyltransferases/metabolism , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Acetylation , Amino Acid Sequence , Gene Expression Regulation , Histone Acetyltransferases/chemistry , Histone Acetyltransferases/metabolism , Histone-Lysine N-Methyltransferase , Histones/metabolism , Humans , Methylation , Models, Molecular , Molecular Sequence Data , Protein Processing, Post-Translational , Protein Structure, Tertiary , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Sequence Alignment , Transcription, Genetic
16.
Nature ; 508(7495): 263-8, 2014 Apr 10.
Article in English | MEDLINE | ID: mdl-24590075

ABSTRACT

Recognition of modified histones by 'reader' proteins plays a critical role in the regulation of chromatin. H3K36 trimethylation (H3K36me3) is deposited onto the nucleosomes in the transcribed regions after RNA polymerase II elongation. In yeast, this mark in turn recruits epigenetic regulators to reset the chromatin to a relatively repressive state, thus suppressing cryptic transcription. However, much less is known about the role of H3K36me3 in transcription regulation in mammals. This is further complicated by the transcription-coupled incorporation of the histone variant H3.3 in gene bodies. Here we show that the candidate tumour suppressor ZMYND11 specifically recognizes H3K36me3 on H3.3 (H3.3K36me3) and regulates RNA polymerase II elongation. Structural studies show that in addition to the trimethyl-lysine binding by an aromatic cage within the PWWP domain, the H3.3-dependent recognition is mediated by the encapsulation of the H3.3-specific 'Ser 31' residue in a composite pocket formed by the tandem bromo-PWWP domains of ZMYND11. Chromatin immunoprecipitation followed by sequencing shows a genome-wide co-localization of ZMYND11 with H3K36me3 and H3.3 in gene bodies, and its occupancy requires the pre-deposition of H3.3K36me3. Although ZMYND11 is associated with highly expressed genes, it functions as an unconventional transcription co-repressor by modulating RNA polymerase II at the elongation stage. ZMYND11 is critical for the repression of a transcriptional program that is essential for tumour cell growth; low expression levels of ZMYND11 in breast cancer patients correlate with worse prognosis. Consistently, overexpression of ZMYND11 suppresses cancer cell growth in vitro and tumour formation in mice. Together, this study identifies ZMYND11 as an H3.3-specific reader of H3K36me3 that links the histone-variant-mediated transcription elongation control to tumour suppression.


Subject(s)
Breast Neoplasms/genetics , Breast Neoplasms/pathology , Carrier Proteins/metabolism , Histones/metabolism , Lysine/metabolism , RNA Polymerase II/metabolism , Transcription Elongation, Genetic , Amino Acid Sequence , Animals , Breast Neoplasms/metabolism , Carrier Proteins/chemistry , Cell Cycle Proteins , Chromatin/genetics , Chromatin/metabolism , Co-Repressor Proteins/chemistry , Co-Repressor Proteins/metabolism , Crystallography, X-Ray , DNA-Binding Proteins , Disease-Free Survival , Female , Gene Expression Regulation, Neoplastic/genetics , Histones/chemistry , Humans , Methylation , Mice , Mice, Nude , Models, Molecular , Molecular Sequence Data , Oncogenes/genetics , Prognosis , Protein Binding , Protein Conformation , Protein Structure, Tertiary , Substrate Specificity
17.
Cell Rep ; 6(2): 325-35, 2014 Jan 30.
Article in English | MEDLINE | ID: mdl-24412361

ABSTRACT

The histone lysine demethylase KDM5B regulates gene transcription and cell differentiation and is implicated in carcinogenesis. It contains multiple conserved chromatin-associated domains, including three PHD fingers of unknown function. Here, we show that the first and third, but not the second, PHD fingers of KDM5B possess histone binding activities. The PHD1 finger is highly specific for unmodified histone H3 (H3K4me0), whereas the PHD3 finger shows preference for the trimethylated histone mark H3K4me3. RNA-seq analysis indicates that KDM5B functions as a transcriptional repressor for genes involved in inflammatory responses, cell proliferation, adhesion, and migration. Biochemical analysis reveals that KDM5B associates with components of the nucleosome remodeling and deacetylase (NuRD) complex and may cooperate with the histone deacetylase 1 (HDAC1) in gene repression. KDM5B is downregulated in triple-negative breast cancer relative to estrogen-receptor-positive breast cancer. Overexpression of KDM5B in the MDA-MB 231 breast cancer cells suppresses cell migration and invasion, and the PHD1-H3K4me0 interaction is essential for inhibiting migration. These findings highlight tumor-suppressive functions of KDM5B in triple-negative breast cancer cells and suggest a multivalent mechanism for KDM5B-mediated transcriptional regulation.


Subject(s)
Gene Expression Regulation, Neoplastic , Histones/metabolism , Jumonji Domain-Containing Histone Demethylases/metabolism , Nuclear Proteins/metabolism , Repressor Proteins/metabolism , Amino Acid Sequence , Binding Sites , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Cell Line, Tumor , Chromatin Assembly and Disassembly , Histone Deacetylase 1/metabolism , Humans , Jumonji Domain-Containing Histone Demethylases/chemistry , Jumonji Domain-Containing Histone Demethylases/genetics , Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism , Molecular Sequence Data , Nuclear Proteins/chemistry , Nuclear Proteins/genetics , Protein Binding , Repressor Proteins/chemistry , Repressor Proteins/genetics
18.
J Mol Biol ; 426(8): 1661-76, 2014 Apr 17.
Article in English | MEDLINE | ID: mdl-24333487

ABSTRACT

The monocytic leukemic zinc finger (MOZ) histone acetyltransferase (HAT) acetylates free histones H3, H4, H2A, and H2B in vitro and is associated with up-regulation of gene transcription. The MOZ HAT functions as a quaternary complex with the bromodomain-PHD finger protein 1 (BRPF1), inhibitor of growth 5 (ING5), and hEaf6 subunits. BRPF1 links the MOZ catalytic subunit to the ING5 and hEaf6 subunits, thereby promoting MOZ HAT activity. Human BRPF1 contains multiple effector domains with known roles in gene transcription, as well as chromatin binding and remodeling. However, the biological function of the BRPF1 bromodomain remains unknown. Our findings reveal novel interactions of the BRPF1 bromodomain with multiple acetyllysine residues on the N-terminus of histones and show that it preferentially selects for H2AK5ac, H4K12ac, and H3K14ac. We used chemical shift perturbation data from NMR titration experiments to map the BRPF1 bromodomain ligand binding pocket and identified key residues responsible for coordination of the post-translationally modified histones. Extensive molecular dynamics simulations were used to generate structural models of bromodomain-histone ligand complexes, to analyze hydrogen bonding and other interactions, and to calculate the binding free energies. Our results outline the molecular mechanism driving binding specificity of the BRPF1 bromodomain for discrete acetyllysine residues on the N-terminal histone tails. Together, these data provide insights into how histone recognition by the bromodomain directs the biological function of BRPF1, ultimately targeting the MOZ HAT complex to chromatin substrates.


Subject(s)
Adaptor Proteins, Signal Transducing/chemistry , Histones/chemistry , Nuclear Proteins/chemistry , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Amino Acid Sequence , Binding Sites , DNA-Binding Proteins , Histones/metabolism , Humans , Hydrogen Bonding , Lysine/chemistry , Macromolecular Substances/chemistry , Models, Molecular , Molecular Dynamics Simulation , Molecular Sequence Data , Nuclear Magnetic Resonance, Biomolecular , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Protein Binding , Protein Interaction Domains and Motifs , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid
19.
Proc Natl Acad Sci U S A ; 110(43): 17284-9, 2013 Oct 22.
Article in English | MEDLINE | ID: mdl-24101509

ABSTRACT

Estrogen receptor alpha (ERα) is a ligand-activated transcription factor. Upon estrogen stimulation, ERα recruits a number of coregulators, including both coactivators and corepressors, to the estrogen response elements, modulating gene activation or repression. Most coregulator complexes contain histone-modifying enzymes to control ERα target gene expression in an epigenetic manner. In addition to histones, these epigenetic modifiers can modify nonhistone proteins including ERα, thereby constituting another layer of transcriptional regulation. Here we show that SET and MYND domain containing 2 (SMYD2), a histone H3K4 and H3K36 methyltransferase, directly methylates ERα protein at lysine 266 (K266) both in vitro and in cells. In breast cancer MCF7 cells, SMYD2 attenuates the chromatin recruitment of ERα to prevent ERα target gene activation under an estrogen-depleted condition. Importantly, the SMYD2-mediated repression of ERα target gene expression is mediated by the methylation of ERα at K266 in the nucleus, but not the methylation of histone H3K4. Upon estrogen stimulation, ERα-K266 methylation is diminished, thereby enabling p300/cAMP response element-binding protein-binding protein to acetylate ERα at K266, which is known to promote ERα transactivation activity. Our study identifies a previously undescribed inhibitory methylation event on ERα. Our data suggest that the dynamic cross-talk between SMYD2-mediated ERα protein methylation and p300/cAMP response element-binding protein-binding protein-dependent ERα acetylation plays an important role in fine-tuning the functions of ERα at chromatin and the estrogen-induced gene expression profiles.


Subject(s)
Estrogen Receptor alpha/metabolism , Gene Expression Regulation, Neoplastic/genetics , Histone-Lysine N-Methyltransferase/metabolism , Lysine/metabolism , Acetylation , Amino Acid Sequence , Blotting, Western , Cell Line, Tumor , Chromatin/genetics , Chromatin/metabolism , Estradiol/pharmacology , Estrogen Receptor alpha/genetics , Estrogens/pharmacology , Gene Expression Regulation, Neoplastic/drug effects , Histone Demethylases/metabolism , Histone-Lysine N-Methyltransferase/genetics , Humans , Lysine/genetics , MCF-7 Cells , Methylation/drug effects , Mutation , RNA Interference , Reverse Transcriptase Polymerase Chain Reaction , Sequence Homology, Amino Acid , p300-CBP Transcription Factors/metabolism
20.
Mol Cell Proteomics ; 9(12): 2617-28, 2010 Dec.
Article in English | MEDLINE | ID: mdl-20699381

ABSTRACT

Gastric cardia cancer (GCC), which occurs at the gastric-esophageal boundary, is one of the most malignant tumors. Despite its high mortality and morbidity, the molecular mechanism of initiation and progression of this disease is largely unknown. In this study, using proteomics and metabolomics approaches, we found that the level of several enzymes and their related metabolic intermediates involved in glucose metabolism were deregulated in GCC. Among these enzymes, two subunits controlling pyruvic acid efflux, lactate dehydrogenase A (LDHA) and pyruvate dehydrogenase B (PDHB), were further analyzed in vitro. Either down-regulation of LDH subunit LDHA or overexpression of PDH subunit PDHB could force pyruvic acid into the Krebs cycle rather than the glycolysis process in AGS gastric cancer cells, which inhibited cell growth and cell migration. Our results reflect an important glucose metabolic signature, especially the dysregulation of pyruvic acid efflux in the development of GCC. Forced transition from glycolysis to the Krebs cycle had an inhibitory effect on GCC progression, providing potential therapeutic targets for this disease.


Subject(s)
Glucose/metabolism , Metabolomics , Proteomics , Stomach Neoplasms/metabolism , Base Sequence , Cell Line, Tumor , Chromatography, High Pressure Liquid , Citric Acid Cycle , DNA Primers , Electrophoresis, Gel, Two-Dimensional , Female , Glycolysis , Humans , L-Lactate Dehydrogenase/genetics , Male , Middle Aged , Polymerase Chain Reaction , Pyruvate Dehydrogenase Complex/genetics , RNA Interference , Stomach Neoplasms/enzymology , Stomach Neoplasms/pathology
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