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Proceedings of the National Academy of... Nov 2019If the genome contains outlier sequences extraordinarily sensitive to environmental agents, these would be sentinels for monitoring personal carcinogen exposure and...
If the genome contains outlier sequences extraordinarily sensitive to environmental agents, these would be sentinels for monitoring personal carcinogen exposure and might drive direct changes in cell physiology rather than acting through rare mutations. New methods, adductSeq and freqSeq, provided statistical resolution to quantify rare lesions at single-base resolution across the genome. Primary human melanocytes, but not fibroblasts, carried spontaneous apurinic sites and TG sequence lesions more frequent than ultraviolet (UV)-induced cyclobutane pyrimidine dimers (CPDs). UV exposure revealed hyperhotspots acquiring CPDs up to 170-fold more frequently than the genomic average; these sites were more prevalent in melanocytes. Hyperhotspots were disproportionately located near genes, particularly for RNA-binding proteins, with the most-recurrent hyperhotspots at a fixed position within 2 motifs. One motif occurs at ETS family transcription factor binding sites, known to be UV targets and now shown to be among the most sensitive in the genome, and at sites of mTOR/5' terminal oligopyrimidine-tract translation regulation. The second occurs at ATTCTY, which developed "dark CPDs" long after UV exposure, repaired CPDs slowly, and had accumulated CPDs prior to the experiment. Motif locations active as hyperhotspots differed between cell types. Melanocyte CPD hyperhotspots aligned precisely with recurrent UV signature mutations in individual gene promoters of melanomas and with known cancer drivers. At sunburn levels of UV exposure, every cell would have a hyperhotspot CPD in each of the ∼20 targeted cell pathways, letting hyperhotspots act as epigenetic marks that create phenome instability; high prevalence favors cooccurring mutations, which would allow tumor evolution to use weak drivers.
Topics: 5' Untranslated Regions; Cells, Cultured; DNA Damage; Fibroblasts; Gene Expression Regulation; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Melanocytes; Melanoma; Mutation; Promoter Regions, Genetic; Protein Biosynthesis; Pyrimidine Dimers; Pyrimidine Nucleotides; Skin Neoplasms; TOR Serine-Threonine Kinases; Ultraviolet Rays
PubMed: 31723047
DOI: 10.1073/pnas.1907860116 -
Ciencia & Saude Coletiva Aug 2022The development of new drugs depends on several scientific steps, which culminate in clinical trials. The clinical trials pharmacy (CTP) is the place for receiving,... (Review)
Review
The development of new drugs depends on several scientific steps, which culminate in clinical trials. The clinical trials pharmacy (CTP) is the place for receiving, preparing, storing and dispensing the investigational product or study drug. Therefore, it must have infrastructure and procedures that guarantee participant safety and quality of research data. This study aimed to systematize guidelines for CTP in Brazil. We conducted a scope review and organized the results using the Ishikawa Method (6Ms). In total, 51 publications were selected for each "M", 39 laws, regulations or guidelines and 12 scientific articles: 25 publications for pharmaceutical services (pharmacy procedures to ensure participant safety from investigational product ordering to final disposition), 14 for Quality Indicators, 12 for Human Resources, 11 for Infrastructure, 11 for Material Resources and 5 for Investigational Product. Our results synthesize information for the organization, operation and evaluation of CTP in Brazil, emphasizes the inclusion of the pharmacist within the clinical trials context, and contributes to preparation for monitoring, auditing, and inspections conducted by regulatory agencies.
Topics: Brazil; Cytidine Triphosphate; Humans; Pharmaceutical Services; Pharmacies; Pharmacists
PubMed: 35894322
DOI: 10.1590/1413-81232022278.04052022 -
Cancer Letters Feb 2020Cancer is a disease of uncontrolled cell growth and a major cause of death worldwide. Many molecular events characterize tumor initiation and progression. Global gene... (Review)
Review
Cancer is a disease of uncontrolled cell growth and a major cause of death worldwide. Many molecular events characterize tumor initiation and progression. Global gene expression analyses using next-generation sequencing, proteomics and metabolomics show genomic, epigenetic, and metabolite concentration changes in various tumors. Molecular alterations identified include multiple cancer-driving mutations, gene fusions, amplifications, deletions, and post-translational modifications. Data integration from many high-throughput platforms unraveled dysregulation in many metabolic pathways in cancer. Since cancer cells are fast-growing, their metabolic needs are enhanced, hence the requirement for de novo synthesis of essential metabolites. One critical requirement of fast-growing cells and a historically important pathway in cancer is the nucleotide biosynthetic pathway and its enzymes are valuable targets for small molecule inhibition. Purines and pyrimidines are building blocks of DNA synthesis and due to their excessive growth, cancer cells extensively utilize de novo pathways for nucleotide biosynthesis. Methotrexate, one of the early chemotherapeutic agents, targets dihydrofolate reductase of the folate metabolic pathway that is involved in nucleotide biosynthesis. In this review, we discuss the nucleotide biosynthetic pathways in cancer and targeting opportunities.
Topics: Antimetabolites, Antineoplastic; Biosynthetic Pathways; Cell Proliferation; Energy Metabolism; Enzyme Inhibitors; Folic Acid Antagonists; Humans; Methotrexate; Neoplasms; Protein Processing, Post-Translational; Purine Nucleotides; Pyrimidine Nucleotides; S-Adenosylmethionine; Tetrahydrofolate Dehydrogenase; Tetrahydrofolates
PubMed: 31733288
DOI: 10.1016/j.canlet.2019.11.013 -
Blood Advances Mar 2024Adult T-cell leukemia/lymphoma (ATL) is triggered by infection with human T-cell lymphotropic virus-1 (HTLV-1). Here, we describe the reprogramming of pyrimidine...
Adult T-cell leukemia/lymphoma (ATL) is triggered by infection with human T-cell lymphotropic virus-1 (HTLV-1). Here, we describe the reprogramming of pyrimidine biosynthesis in both normal T cells and ATL cells through regulation of uridine-cytidine kinase 2 (UCK2), which supports vigorous proliferation. UCK2 catalyzes the monophosphorylation of cytidine/uridine and their analogues during pyrimidine biosynthesis and drug metabolism. We found that UCK2 was overexpressed aberrantly in HTLV-1-infected T cells but not in normal T cells. T-cell activation via T-cell receptor (TCR) signaling induced expression of UCK2 in normal T cells. Somatic alterations and epigenetic modifications in ATL cells activate TCR signaling. Therefore, we believe that expression of UCK2 in HTLV-1-infected cells is induced by dysregulated TCR signaling. Recently, we established azacitidine-resistant (AZA-R) cells showing absent expression of UCK2. AZA-R cells proliferated normally in vitro, whereas UCK2 knockdown inhibited ATL cell growth. Although uridine and cytidine accumulated in AZA-R cells, possibly because of dysfunction of pyrimidine salvage biosynthesis induced by loss of UCK2 expression, the amount of UTP and CTP was almost the same as in parental cells. Furthermore, AZA-R cells were more susceptible to an inhibitor of dihydroorotic acid dehydrogenase, which performs the rate-limiting enzyme of de novo pyrimidine nucleotide biosynthesis, and more resistant to dipyridamole, an inhibitor of pyrimidine salvage biosynthesis, suggesting that AZA-R cells adapt to UCK2 loss by increasing de novo pyrimidine nucleotide biosynthesis. Taken together, the data suggest that fine-tuning pyrimidine biosynthesis supports vigorous cell proliferation of both normal T cells and ATL cells.
Topics: Adult; Humans; Pyrimidines; Uridine; Cell Proliferation; Cytidine; Human T-lymphotropic virus 1; Pyrimidine Nucleotides; Receptors, Antigen, T-Cell; T-Lymphocytes
PubMed: 38190613
DOI: 10.1182/bloodadvances.2023011131 -
International Journal of Molecular... Nov 2022The activity of phosphate groups of phosphoethanolamine and pyrimidine nucleotides (thymidine 5-monophosphate, cytidine 5-monophosphate and uridine 5'monophosphate) in...
The activity of phosphate groups of phosphoethanolamine and pyrimidine nucleotides (thymidine 5-monophosphate, cytidine 5-monophosphate and uridine 5'monophosphate) in the process of complexation metal ions in aqueous solution was studied. Using the potentiometric method with computer calculation of the data and spectroscopic methods such as UV-Vis, EPR, C and P NMR as well as FT-IR, the overall stability constants of the complexes as well as coordination modes were obtained. At lower pH, copper(II) ions are complexed only by phosphate groups, whereas the endocyclic nitrogen atom of nucleotides has been identified as a negative center interacting with the -NH groups of phosphoethanolamine.
Topics: Pyrimidine Nucleotides; Copper; Phosphates; Spectroscopy, Fourier Transform Infrared; Ions; Cytidine Monophosphate
PubMed: 36430195
DOI: 10.3390/ijms232213718 -
Science (New York, N.Y.) Oct 2019Theories about the origin of life require chemical pathways that allow formation of life's key building blocks under prebiotically plausible conditions. Complex...
Theories about the origin of life require chemical pathways that allow formation of life's key building blocks under prebiotically plausible conditions. Complex molecules like RNA must have originated from small molecules whose reactivity was guided by physico-chemical processes. RNA is constructed from purine and pyrimidine nucleosides, both of which are required for accurate information transfer, and thus Darwinian evolution. Separate pathways to purines and pyrimidines have been reported, but their concurrent syntheses remain a challenge. We report the synthesis of the pyrimidine nucleosides from small molecules and ribose, driven solely by wet-dry cycles. In the presence of phosphate-containing minerals, 5'-mono- and diphosphates also form selectively in one-pot reactions. The pathway is compatible with purine synthesis, allowing the concurrent formation of all Watson-Crick bases.
Topics: Chemical Phenomena; Hydroxylamine; Purine Nucleosides; Purine Nucleotides; Pyrimidine Nucleosides; Pyrimidine Nucleotides; RNA; Ribonucleotides; Ribose
PubMed: 31604305
DOI: 10.1126/science.aax2747 -
Acta Crystallographica. Section F,... Apr 2020Human O-phosphoethanolamine phospho-lyase (hEtnppl; EC 4.2.3.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the degradation of O-phosphoethanolamine...
Human O-phosphoethanolamine phospho-lyase (hEtnppl; EC 4.2.3.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the degradation of O-phosphoethanolamine (PEA) into acetaldehyde, phosphate and ammonia. Physiologically, the enzyme is involved in phospholipid metabolism, as PEA is the precursor of phosphatidylethanolamine in the CDP-ethanolamine (Kennedy) pathway. Here, the crystal structure of hEtnppl in complex with pyridoxamine 5'-phosphate was determined at 2.05 Å resolution by molecular replacement using the structure of A1RDF1 from Arthrobacter aurescens TC1 (PDB entry 5g4i) as the search model. Structural analysis reveals that the two proteins share the same general fold and a similar arrangement of active-site residues. These results provide novel and useful information for the complete characterization of the human enzyme.
Topics: Carbon-Oxygen Lyases; Catalytic Domain; Crystallography, X-Ray; Cytidine Diphosphate; Ethanolamines; Humans; Models, Molecular; Protein Structure, Quaternary; Pyridoxal Phosphate
PubMed: 32254049
DOI: 10.1107/S2053230X20002988 -
Southern Medical Journal Jan 2015
Topics: Antiviral Agents; Cost-Benefit Analysis; Costs and Cost Analysis; Drug Costs; Drug Industry; Drug Therapy, Combination; Hepatitis C, Chronic; Humans; Practice Patterns, Physicians'; Public Health; Sofosbuvir; United States; Uridine Monophosphate
PubMed: 25580761
DOI: 10.14423/SMJ.0000000000000229 -
Pharmacology & Therapeutics Dec 2019The UDP glycosyltransferase (UGT) superfamily of enzymes is responsible for the metabolism and clearance of thousands of lipophilic chemicals including drugs, toxins and... (Review)
Review
The UDP glycosyltransferase (UGT) superfamily of enzymes is responsible for the metabolism and clearance of thousands of lipophilic chemicals including drugs, toxins and endogenous signaling molecules. They provide a protective interface between the organism and its chemical-rich environment, as well as controlling critical signaling pathways to maintain healthy tissue function. UGTs are associated with drug responses and interactions, as well as a wide range of diseases including cancer. The human genome contains 22 UGT genes; however as befitting their exceptionally diverse substrate ranges and biological activities, the output of these UGT genes is functionally diversified by multiple processes including alternative splicing, post-translational modification, homo- and hetero-oligomerization, and interactions with other proteins. All UGT genes are subject to extensive alternative splicing generating variant/truncated UGT proteins with altered functions including the capacity to dominantly modulate/inhibit cognate full-length forms. Heterotypic oligomerization of different UGTs can alter kinetic properties relative to monotypic complexes, and potentially produce novel substrate specificities. Moreover, the recently profiled interactions of UGTs with non-UGT proteins may facilitate coordination between different metabolic processes, as well as providing opportunities for UGTs to engage in novel 'moonlighting' functions. Herein we provide a detailed and comprehensive review of all known modes of UGT functional diversification and propose a UGTome model to describe the resulting expansion of metabolic capacity and its potential to modulate drug/xenobiotic responses and cell behaviours in normal and disease contexts.
Topics: Animals; Glycosyltransferases; Humans; Metabolic Networks and Pathways; Uridine Diphosphate
PubMed: 31647974
DOI: 10.1016/j.pharmthera.2019.107414 -
Eye & Contact Lens Feb 2024
Topics: Humans; Dry Eye Syndromes; Keratoconjunctivitis Sicca; Polyphosphates; Uracil Nucleotides
PubMed: 38284907
DOI: 10.1097/ICL.0000000000001071