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Molecular Metabolism Feb 2021Live kinase B1 (LKB1) is a tumor suppressor that is mutated in Peutz-Jeghers syndrome (PJS) and a variety of cancers. Lkb1 encodes serine-threonine kinase (STK) 11 that... (Review)
Review
BACKGROUND
Live kinase B1 (LKB1) is a tumor suppressor that is mutated in Peutz-Jeghers syndrome (PJS) and a variety of cancers. Lkb1 encodes serine-threonine kinase (STK) 11 that activates AMP-activated protein kinase (AMPK) and its 13 superfamily members, regulating multiple biological processes, such as cell polarity, cell cycle arrest, embryo development, apoptosis, and bioenergetics metabolism. Increasing evidence has highlighted that deficiency of LKB1 in cancer cells induces extensive metabolic alterations that promote tumorigenesis and development. LKB1 also participates in the maintenance of phenotypes and functions of normal cells through metabolic regulation.
SCOPE OF REVIEW
Given the important role of LKB1 in metabolic regulation, we provide an overview of the association of metabolic alterations in glycolysis, aerobic oxidation, the pentose phosphate pathway (PPP), gluconeogenesis, glutamine, lipid, and serine induced by aberrant LKB1 signals in tumor progression, non-neoplastic diseases, and functions of immune cells.
MAJOR CONCLUSIONS
In this review, we summarize layers of evidence demonstrating that disordered metabolisms in glucose, glutamine, lipid, and serine caused by LKB1 deficiency promote carcinogenesis and non-neoplastic diseases. The metabolic reprogramming resulting from the loss of LKB1 confers cancer cells with growth or survival advantages. Nevertheless, it also causes a metabolic frangibility for LKB1-deficient cancer cells. The metabolic regulation of LKB1 also plays a vital role in maintaining cellular phenotype in the progression of non-neoplastic diseases. In addition, lipid metabolic regulation of LKB1 plays an important role in controlling the function, activity, proliferation, and differentiation of several types of immune cells. We conclude that in-depth knowledge of metabolic pathways regulated by LKB1 is conducive to identifying therapeutic targets and developing drug combinations to treat cancers and metabolic diseases and achieve immunoregulation.
Topics: AMP-Activated Protein Kinase Kinases; AMP-Activated Protein Kinases; Animals; Apoptosis; Carcinogenesis; Energy Metabolism; Glucose; Glutamine; Humans; Lipid Metabolism; Lipids; Metabolic Engineering; Metabolic Networks and Pathways; Mutation; Neoplasms; Peutz-Jeghers Syndrome; Protein Serine-Threonine Kinases; Serine; Signal Transduction
PubMed: 33278637
DOI: 10.1016/j.molmet.2020.101131 -
Accounts of Chemical Research Aug 2022There is a continuous demand to improve our understanding of fundamental processes that underlie human health and disease. Therefore, novel strategies that can assist in...
There is a continuous demand to improve our understanding of fundamental processes that underlie human health and disease. Therefore, novel strategies that can assist in these efforts are required. For example, molecular biology and genetic approaches have revolutionized our understanding of protein-mediated processes by facilitating their direct visualization and analyses in living cells. Despite these developments, genetic manipulation has limitations in controlling events that occur after translation such as posttranslational modifications (PTMs), which are imperative regulatory elements. As a result, developing new methods to study PTMs in live cells is a major bottleneck in deciphering their exact roles in the myriad cellular processes.Synthetic and semisynthetic proteins are prepared by combining solid phase peptide synthesis (SPPS) and chemoselective ligation approaches with synthetic or recombinant peptides. Employing protein synthesis allows chemists to incorporate natural and unnatural modifications with virtually unlimited number of functional groups into the protein's sequence, such as PTMs and their mimics. In addition, synthetic proteins can include additional elements such as fluorescent tags, reactive groups, caged units, and enrichment handles. Therefore, harnessing the power of chemical protein synthesis offers great opportunities to study fundamental biological processes.Unfortunately, the low cell permeability of proteins limits their applications mainly to settings, excluding live cell studies. As a result, chemical biologists have been attempting to overcome these limitations by developing protein delivery methods that would enable the study of custom-made proteins in a biological context. Success with these strategies should enable accurate determination of protein localization, degradation, folding, interactions, and involvement in the assembly of membrane-less organelles formed by liquid-liquid phase separation inside cells. Importantly, protein delivery approaches are complementary to genetic manipulations, and combining these approaches should pave the way to new discoveries.In this Account, we describe recent developments in protein delivery methods, with emphasis on those most compatible with synthetic proteins. We highlight experimental approaches and conceptual adaptations required to design and study synthetic proteins in live cells, with or without genetic manipulation. In addition, we highlight the strength and weakness of these approaches for both the delivery and the subsequent studies. We also describe our endeavors to deliver synthetic proteins to cells via cell penetrating peptides (CPPs) and multiplexed bead loading (MBL), as showcases of the applications of these methods to shed light on biological processes. Lastly, we contemplate other future applications of synthetic proteins to answer questions that are currently unapproachable.
Topics: Cell-Penetrating Peptides; Humans; Protein Processing, Post-Translational; Protein Transport; Proteins; Solid-Phase Synthesis Techniques
PubMed: 35833291
DOI: 10.1021/acs.accounts.2c00236 -
Drug Metabolism and Disposition: the... Dec 2023Drug-metabolizing enzymes and transporters (DMETs) are key regulators of the pharmacokinetics, efficacy, and toxicity of therapeutics. Over the past two decades,...
Drug-metabolizing enzymes and transporters (DMETs) are key regulators of the pharmacokinetics, efficacy, and toxicity of therapeutics. Over the past two decades, significant advancements in in vitro methodologies, targeted proteomics, in vitro to in vivo extrapolation methods, and integrated computational approaches such as physiologically based pharmacokinetic modeling have unequivocally contributed to improving our ability to quantitatively predict the role of DMETs in absorption, distribution, metabolism, and excretion and drug-drug interactions. However, the paucity of data regarding alterations in DMET activity in specific populations such as pregnant individuals, lactation, pediatrics, geriatrics, organ impairment, and disease states such as, cancer, kidney, and liver diseases and inflammation has restricted our ability to realize the full potential of these recent advancements. We envision that a series of carefully curated articles in a special supplementary issue of will summarize the latest progress in in silico, in vitro, and in vivo approaches to characterize alteration in DMET activity and quantitatively predict drug disposition in specific populations. In addition, the supplementary issue will underscore the current scientific knowledge gaps that present formidable barriers to fully understand the clinical implications of altered DMET activity in specific populations and highlight opportunities for multistakeholder collaboration to advance our collective understanding of this rapidly emerging area. SIGNIFICANCE STATEMENT: This commentary highlights current knowledge and identifies gaps and key challenges in understanding the role of drug-metabolizing enzymes and transporters (DMETs) in drug disposition in specific populations. With this commentary for the special issue in , the authors intend to increase interest and invite potential contributors whose research is focused or has aided in expanding the understanding around the role and impact of DMETs in drug disposition in specific populations.
Topics: Pregnancy; Female; Humans; Child; Membrane Transport Proteins; Liver Diseases; Drug Interactions; Inflammation; Metabolic Clearance Rate
PubMed: 37775331
DOI: 10.1124/dmd.123.001453 -
Biochemical Society Transactions Dec 2020In fluctuating environmental conditions, organisms must modulate their bioenergetic production in order to maintain cellular homeostasis for optimal fitness.... (Review)
Review
In fluctuating environmental conditions, organisms must modulate their bioenergetic production in order to maintain cellular homeostasis for optimal fitness. Mitochondria are hubs for metabolite and energy generation. Mitochondria are also highly dynamic in their function: modulating their composition, size, density, and the network-like architecture in relation to the metabolic demands of the cell. Here, we review the recent research on the post-transcriptional regulation of mitochondrial composition focusing on mRNA localization, mRNA translation, protein import, and the role that dynamic mitochondrial structure may have on these gene expression processes. As mitochondrial structure and function has been shown to be very important for age-related processes, including cancer, metabolic disorders, and neurodegeneration, understanding how mitochondrial composition can be affected in fluctuating conditions can lead to new therapeutic directions to pursue.
Topics: Animals; Cell Cycle; Cell Respiration; Cricetinae; Environment; Fermentation; Fungal Proteins; Gene Expression Regulation; Genes, Fungal; HeLa Cells; Homeostasis; Humans; Mitochondria; Mitochondrial Proteins; Myocardium; Neoplasms; Osteosarcoma; Oxygen Consumption; Protein Transport; RNA, Messenger; Saccharomyces cerevisiae
PubMed: 33245320
DOI: 10.1042/BST20200250 -
Archives of Toxicology May 2021The review presents metabolic properties of Ivermectin (IVM) as substrate and inhibitor of human P450 (P450, CYP) enzymes and drug transporters. IVM is metabolized, both... (Review)
Review
The review presents metabolic properties of Ivermectin (IVM) as substrate and inhibitor of human P450 (P450, CYP) enzymes and drug transporters. IVM is metabolized, both in vivo and in vitro, by C-hydroxylation and O-demethylation reactions catalyzed by P450 3A4 as the major enzyme, with a contribution of P450 3A5 and 2C9. In samples from both in vitro and in vivo metabolism, a number of metabolites were detected and as major identified metabolites were 3″-O-demethylated, C4-methyl hydroxylated, C25 isobutyl-/isopropyl-hydroxylated, and products of oxidation reactions. Ivermectin inhibited P450 2C9, 2C19, 2D6, and CYP3A4 with IC values ranging from 5.3 μM to no inhibition suggesting that it is no or weak inhibitor of the enzymes. It is suggested that P-gp (MDR1) transporter participate in IVM efflux at low drug concentration with a slow transport rate. At the higher, micromolar concentration range, which saturates MDR1 (P-gp), MRP1, and to a lesser extent, MRP2 and MRP3 participate in IVM transport across physiological barriers. IVM exerts a potent inhibition of P-gp (ABCB1), MRP1 (ABCC1), MRP2 (ABCC2), and BCRP1 (ABCG2), and medium to weak inhibition of OATP1B1 (SLC21A6) and OATP1B3 (SLCOB3) transport activity. The metabolic and transport properties of IVM indicate that when IVM is co-administered with other drugs/chemicals that are potent inhibitors/inducers P4503A4 enzyme and of MDR1 (P-gp), BCRP or MRP transporters, or when polymorphisms of the drug transporters and P450 3A4 exist, drug-drug or drug-toxic chemical interactions might result in suboptimal response to the therapy or to toxic effects.
Topics: ATP Binding Cassette Transporter, Subfamily B; ATP Binding Cassette Transporter, Subfamily G, Member 2; Biological Transport; Cells, Cultured; Cytochrome P-450 CYP3A; Cytochrome P-450 Enzyme Inhibitors; Cytochrome P-450 Enzyme System; Drug Interactions; Humans; Hydroxylation; Insecticides; Ivermectin; Membrane Transport Proteins; Microsomes, Liver; Multidrug Resistance-Associated Protein 2; Multidrug Resistance-Associated Proteins; Neoplasm Proteins; Pharmaceutical Preparations
PubMed: 33719007
DOI: 10.1007/s00204-021-03025-z -
Nature Communications Feb 2022When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource...
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation-known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells.
Topics: Fermentation; Gene Expression Regulation, Fungal; Glucose; Metabolic Networks and Pathways; Mitochondria; Proteome; Proteomics; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Yeasts
PubMed: 35145105
DOI: 10.1038/s41467-022-28467-6 -
IET Systems Biology Jul 2021The minimum dominating set (MDSet) comprises the smallest number of graph nodes, where other graph nodes are connected with at least one MDSet node. The MDSet has been...
The minimum dominating set (MDSet) comprises the smallest number of graph nodes, where other graph nodes are connected with at least one MDSet node. The MDSet has been successfully applied to extract proteins that control protein-protein interaction (PPI) networks and to reveal the correlation between structural analysis and biological functions. Although the PPI network contains many MDSets, the identification of multiple MDSets is an NP-complete problem, and it is difficult to determine the best MDSets, enriched with biological functions. Therefore, the MDSet model needs to be further expanded and validated to find constrained solutions that differ from those generated by the traditional models. Moreover, by identifying the critical set of the network, the set of nodes common to all MDSets can be time-consuming. Herein, the authors adopted the minimisation of metabolic adjustment (MOMA) algorithm to develop a new framework, called maximisation of interaction adjustment (MOIA). In MOIA, they provide three models; the first one generates two MDSets with a minimum number of shared proteins, the second model generates constrained multiple MDSets ( -MDSets), and the third model generates user-defined MDSets, containing the maximum number of essential genes and/or other important genes of the PPI network. In practice, these models significantly reduce the cost of finding the critical set and classifying the graph nodes. Herein, the authors termed the critical set as the -critical set, where is the number of MDSets generated by the proposed model. Then, they defined a new set of proteins called the -critical set, where each node belongs to MDSets. This set has been shown to be as important as the -critical set and contains many essential genes, transcription factors, and protein kinases as the -critical set. The -critical set can be used to extend the search for drug target proteins. Based on the performance of the MOIA models, the authors believe the proposed methods contribute to answering key questions about the MDSets of PPI networks, and their results and analysis can be extended to other network types.
Topics: Algorithms; Protein Interaction Maps; Proteins
PubMed: 34048146
DOI: 10.1049/syb2.12021 -
Cells Jan 2022Pregnane X receptor (PXR) is a member of the nuclear receptor superfamily that is activated by a variety of endogenous metabolites or xenobiotics. Its downstream target...
Pregnane X receptor (PXR) is a member of the nuclear receptor superfamily that is activated by a variety of endogenous metabolites or xenobiotics. Its downstream target genes are involved in metabolism, inflammation and processes closely related to cancer. However, the stability regulation of PXR protein resulting from post-translational modification is still largely undefined. In the present study, primary mouse hepatocytes, hepatoma HepG2 cells and HEK 293T cells were used to investigate gene expression and protein interactions. The role of kinases was evaluated by RNA interference and overexpression constructs with or without PXR phosphorylation site mutations. The activity of CYP3A4 and P-gp was determined by enzymatic and substrate accumulation assays. It was found that E3 ubiquitin ligase TRIM21 mediates the ubiquitination and degradation of PXR and plays an important role in regulating the activity of PXR. On this basis, PXR phosphorylation-associated kinases were evaluated regarding regulation of the stability of PXR. We found cyclin dependent kinase 2 (CDK2) exclusively phosphorylates PXR at Ser350, promotes its disassociation with Hsp90/DNAJC7, and leads to subsequent TRIM21-mediated PXR ubiquitination and degradation. As well-known CDK inhibitors, dinaciclib and kenpaullone stabilize PXR and result in elevated expression and activity of PXR-targeted DMETs, including carboxylesterases, CYP3A4 and P-gp. The suppressed degradation of PXR by CDK2 inhibitors denotes dinaciclib-induced promotion of PXR-targeted genes. The findings of CDK2-mediated PXR degradation indicate a wide range of potential drug-drug interactions during clinical cancer therapy using CDK inhibitors and imply an alternative direction for the development of novel PXR antagonists.
Topics: Cyclic N-Oxides; Cyclin-Dependent Kinase 2; Gene Expression Regulation; HEK293 Cells; HSP90 Heat-Shock Proteins; Heat-Shock Proteins; Hep G2 Cells; Hepatocytes; Humans; Indolizines; Molecular Chaperones; Phosphorylation; Phosphoserine; Pregnane X Receptor; Proteasome Endopeptidase Complex; Protein Binding; Protein Kinase Inhibitors; Protein Stability; Proteolysis; Pyridinium Compounds; Ribonucleoproteins; Signal Transduction; Ubiquitin; Ubiquitination
PubMed: 35053380
DOI: 10.3390/cells11020264 -
A cut above (and below): Protein cleavage in the regulation of polycystin trafficking and signaling.Cellular Signalling Aug 2020The polycystin-1 and 2 proteins, encoded by the genes mutated in Autosomal Dominant Polycystic Kidney Disease, are connected to a large number of biological pathways.... (Review)
Review
The polycystin-1 and 2 proteins, encoded by the genes mutated in Autosomal Dominant Polycystic Kidney Disease, are connected to a large number of biological pathways. While the nature of these connections and their relevance to the primary functions of the polycystin proteins have yet to be fully elucidated, it is clear that many of them are mediated by or depend upon cleavage of the polycystin-1 protein. Cleavage of polycystin-1 at its G protein coupled receptor proteolytic site is an obligate step in the protein's maturation and in aspects of its trafficking. This cleavage may also serve to prime polycystin-1 to play a role as a non-canonical G protein coupled receptor. Cleavage of the cytoplasmic polycystin-1C terminal tail releases fragments that are able to enter the nucleus and the mitochondria and to influence their activities. Understanding the nature of these cleavages, their regulation and their consequences is likely to provide valuable insights into both the physiological functions served by the polycystin proteins and the pathological consequences of their absence.
Topics: Animals; Cell Adhesion; Humans; Osteogenesis; Protein Transport; Proteolysis; Signal Transduction; TRPP Cation Channels
PubMed: 32283256
DOI: 10.1016/j.cellsig.2020.109634 -
International Journal of Molecular... Dec 2022Despite numerous therapies, cancer remains one of the leading causes of death worldwide due to the lack of markers for early detection and response to treatment in many... (Review)
Review
Despite numerous therapies, cancer remains one of the leading causes of death worldwide due to the lack of markers for early detection and response to treatment in many patients. Technological advances in tumor screening and renewed interest in energy metabolism have allowed us to identify new cellular players in order to develop personalized treatments. Among the metabolic actors, the mitochondrial transporter uncoupling protein 2 (UCP2), whose expression is increased in many cancers, has been identified as an interesting target in tumor metabolic reprogramming. Over the past decade, a better understanding of its biochemical and physiological functions has established a role for UCP2 in (1) protecting cells from oxidative stress, (2) regulating tumor progression through changes in glycolytic, oxidative and calcium metabolism, and (3) increasing antitumor immunity in the tumor microenvironment to limit cancer development. With these pleiotropic roles, UCP2 can be considered as a potential tumor biomarker that may be interesting to target positively or negatively, depending on the type, metabolic status and stage of tumors, in combination with conventional chemotherapy or immunotherapy to control tumor development and increase response to treatment. This review provides an overview of the latest published science linking mitochondrial UCP2 activity to the tumor context.
Topics: Humans; Uncoupling Protein 2; Oxidative Stress; Energy Metabolism; Oxidation-Reduction; Neoplasms; Mitochondrial Proteins; Reactive Oxygen Species; Tumor Microenvironment
PubMed: 36499405
DOI: 10.3390/ijms232315077