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1.
J Appl Clin Med Phys ; 25(2): e14158, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-37722769

RESUMEN

Optimizing the positional accuracy of multileaf collimators (MLC) for radiotherapy is important for dose accuracy and for reducing doses delivered to normal tissues. This study investigates dose sensitivity variations and complexity metrics of MLC positional error in volumetric modulated arc therapy and determines the acceptable ranges of MLC positional accuracy in several clinical situations. Treatment plans were generated for four treatment sites (prostate cancer, lung cancer, spinal, and brain metastases) using different treatment planning systems (TPSs) and fraction sizes. Each treatment plan introduced 0.25-2.0 mm systematic or random MLC leaf bank errors. The generalized equivalent uniform dose (gEUD) sensitivity and complexity metrics (MU/Gy and plan irregularity) were calculated, and the correlation coefficients were assessed. Furthermore, the required tolerances for MLC positional accuracy control were calculated. The gEUD sensitivity showed the highest dependence of systematic positional error on the treatment site, followed by TPS and fraction size. The gEUD sensitivities were 6.7, 4.5, 2.5, and 1.7%/mm for Monaco and 8.9, 6.2, 3.4, and 2.3%/mm (spinal metastasis, lung cancer, prostate cancer, and brain metastasis, respectively) for RayStation. The gEUD sensitivity was strongly correlated with the complexity metrics (r = 0.88-0.93). The minimum allowable positional error for MLC was 0.63, 0.34, 1.02, and 0.28 mm (prostate, lung, brain, and spinal metastasis, respectively). The acceptable range of MLC positional accuracy depends on the treatment site, and an appropriate tolerance should be set for each treatment site with reference to the complexity metric. It is expected to enable easier and more detailed MLC positional accuracy control than before by reducing dose errors to patients at the treatment planning stage and by controlling MLC quality based on complexity metrics, such as MU/Gy.


Asunto(s)
Neoplasias Encefálicas , Neoplasias Pulmonares , Neoplasias de la Próstata , Radioterapia de Intensidad Modulada , Neoplasias de la Columna Vertebral , Masculino , Humanos , Planificación de la Radioterapia Asistida por Computador , Neoplasias de la Próstata/radioterapia , Dosificación Radioterapéutica , Neoplasias Pulmonares/radioterapia
2.
Molecules ; 28(4)2023 Feb 16.
Artículo en Inglés | MEDLINE | ID: mdl-36838885

RESUMEN

Targeting cancer cells that are highly dependent on the nicotinamide adenine dinucleotide (NAD+) metabolite is a promising therapeutic strategy. Nicotinamide phosphoribosyltransferase (NAMPT) is the rate-limiting enzyme catalyzing NAD+ production. Despite the high efficacy of several developed NAMPT inhibitors (i.e., FK866 (APO866)) in preclinical studies, their clinical activity was proven to be limited. Here, we report the synthesis of new NAMPT Inhibitors, JJ08, FEI191 and FEI199, which exhibit a broad anticancer activity in vitro. Results show that these compounds are potent NAMPT inhibitors that deplete NAD+ and NADP(H) after 24 h of drug treatment, followed by an increase in reactive oxygen species (ROS) accumulation. The latter event leads to ATP loss and mitochondrial depolarization with induction of apoptosis and necrosis. Supplementation with exogenous NAD+ precursors or catalase (ROS scavenger) abrogates the cell death induced by the new compounds. Finally, in vivo administration of the new NAMPT inhibitors in a mouse xenograft model of human Burkitt lymphoma delays tumor growth and significantly prolongs mouse survival. The most promising results are collected with JJ08, which completely eradicates tumor growth. Collectively, our findings demonstrate the efficient anticancer activity of the new NAMPT inhibitor JJ08 and highlight a strong interest for further evaluation of this compound in hematological malignancies.


Asunto(s)
Inhibidores Enzimáticos , Neoplasias Hematológicas , Nicotinamida Fosforribosiltransferasa , Animales , Humanos , Ratones , Línea Celular Tumoral , Citocinas/metabolismo , Inhibidores Enzimáticos/farmacología , Neoplasias Hematológicas/tratamiento farmacológico , NAD/metabolismo , Nicotinamida Fosforribosiltransferasa/antagonistas & inhibidores , Especies Reactivas de Oxígeno
3.
Anal Chem ; 94(20): 7400-7407, 2022 05 24.
Artículo en Inglés | MEDLINE | ID: mdl-35535999

RESUMEN

Hydration around nucleic acids, such as DNA and RNA, is an important factor not only for the stability of nucleic acids but also for their interaction with binding molecules. Thus, it is necessary to quantitatively elucidate the hydration properties of nucleic acids around a certain structure. In this study, volumetric changes in G-quadruplex (G4) RNA formation were investigated by systematically changing the number of G-quartet stacks under high pressure. The volumetric contribution at the level of each G4 structural unit revealed that the core G4 helix was significantly more dehydrated than the other parts, including the edges of G-quartets and loops. These findings will help in predicting the binding of G4 ligands on the surface of G4, depending on the chemical structure of the ligand and solution environment. Therefore, the preset volumetric parameter provides information that can predict molecular interactions in G4 formations during molecular crowding in cells.


Asunto(s)
G-Cuádruplex , ADN/química , Ligandos , ARN
4.
Metab Eng ; 66: 259-267, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-33984513

RESUMEN

With the increasing demand for blood transfusions, the production of human hemoglobin (Hb) from sustainable sources is increasingly studied. Microbial production is an attractive option, as it may provide a cheap, safe, and reliable source of this protein. To increase the production of human hemoglobin by the yeast Saccharomyces cerevisiae, the degradation of Hb was reduced through several approaches. The deletion of the genes HMX1 (encoding heme oxygenase), VPS10 (encoding receptor for vacuolar proteases), PEP4 (encoding vacuolar proteinase A), ROX1 (encoding heme-dependent repressor of hypoxic genes) and the overexpression of the HEM3 (encoding porphobilinogen deaminase) and the AHSP (encoding human alpha-hemoglobin-stabilizing protein) genes - these changes reduced heme and Hb degradation and improved heme and Hb production. The reduced hemoglobin degradation was validated by a bilirubin biosensor. During glucose fermentation, the engineered strains produced 18% of intracellular Hb relative to the total yeast protein, which is the highest production of human hemoglobin reported in yeast. This increased hemoglobin production was accompanied with an increased oxygen consumption rate and an increased glycerol yield, which (we speculate) is the yeast's response to rebalance its NADH levels under conditions of oxygen limitation and increased protein-production.


Asunto(s)
Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Proteínas Sanguíneas , Fermentación , Proteínas Fúngicas , Hemo , Hemoglobinas/genética , Hemoglobinas/metabolismo , Humanos , Chaperonas Moleculares , Peroxidasas , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
5.
Biochemistry ; 59(28): 2640-2649, 2020 07 21.
Artículo en Inglés | MEDLINE | ID: mdl-32578417

RESUMEN

G-Quadruplexes are noncanonical structures formed by guanine-rich regions of not only DNA but also RNA. RNA G-quadruplexes are widely present in the transcriptome as mRNAs and noncoding RNAs and take part in various essential functions in cells. Furthermore, stable RNA G-quadruplexes control the extent of biological functions, such as mRNA translation and antigen presentation. To understand and regulate the functions controlled by RNA G-quadruplexes in cellular environments, which are molecularly crowded, we would be required to investigate the stability of G-quadruplexes in molecular crowding. Here, we systematically investigated the thermodynamic stability of RNA G-quadruplexes with different numbers of G-quartets and lengths of loops. The molecular crowding conditions of polyethylene glycol with an average molecular weight of 200 (PEG200) were found to stabilize RNA G-quadruplexes with three and four G-quartets, while G-quadruplexes with two G-quartets did not exhibit any stabilization upon addition of PEG200. On the other hand, no difference in stabilization by PEG200 was observed among the G-quadruplexes with different loop lengths. Thermodynamic analysis of the RNA G-quadruplexes revealed more appropriate motifs for identifying G-quadruplex-forming sequences. The informatics analysis with new motifs demonstrated that the distributions of G-quadruplexes in human noncoding RNAs differed depending on the number of G-quartets. Therefore, RNA G-quadruplexes with different numbers of G-quartets may play different roles in response to environmental changes in cells.


Asunto(s)
G-Cuádruplex , ARN/química , Secuencia de Bases , Conformación de Ácido Nucleico , Polietilenglicoles/química , Estabilidad del ARN , Termodinámica
6.
Artículo en Inglés | MEDLINE | ID: mdl-32081425

RESUMEN

Telomeric G-quadruplex topology has the ability to regulate telomerase activity, which counteracts the shortening of telomere with successive cell divisions, thereby causing genomic longevity. However, the detailed mechanism of G-quadruplexes topologies formed by telomeric sequences requires further investigation. In this study, we quantitatively investigated the effect of cosolutes, particularly the varying number of hydroxyl groups, on the structural transition between hybrid type and parallel G-quadruplexes formed by telomeric DNA sequences. Cosolutes with one or no hydroxyl groups in the vicinal position more efficiently induced the transition to parallel G-quadruplex from hybrid G-quadruplex than those with more hydroxyl groups. We also examined the effect of cosolute structures on the hydration of G-quadruplex formation; the results indicated that cosolutes with fewer hydroxyl groups lead to the release of greater amount of water during G-quadruplex formation. Molecular dynamics results showed that the parallel G-quadruplex was more dehydrated than the hybrid type G-quadruplex. Generally, a dehydrated structure is favored under crowding condition. Thus, depending on the surrounding cosolutes, the G-quadruplex topology can be controlled by the G-quadruplex hydration state.

7.
J Hum Genet ; 65(12): 1075-1082, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32699345

RESUMEN

The coronavirus disease 2019 (COVID-19) outbreak, caused by SARS-CoV-2, has rapidly expanded to a global pandemic. However, numbers of infected cases, deaths, and mortality rates related to COVID-19 vary from country to country. Although many studies were conducted, the reasons of these differences have not been clarified. In this study, we comprehensively investigated 12,343 SARS-CoV-2 genome sequences isolated from patients/individuals in six geographic areas and identified a total of 1234 mutations by comparing with the reference SARS-CoV-2 sequence. Through a hierarchical clustering based on the mutant frequencies, we classified the 28 countries into three clusters showing different fatality rates of COVID-19. In correlation analyses, we identified that ORF1ab 4715L and S protein 614G variants, which are in a strong linkage disequilibrium, showed significant positive correlations with fatality rates (r = 0.41, P = 0.029 and r = 0.43, P = 0.022, respectively). We found that BCG-vaccination status significantly associated with the fatality rates as well as number of infected cases. In BCG-vaccinated countries, the frequency of the S 614G variant had a trend of association with the higher fatality rate. We also found that the frequency of several HLA alleles, including HLA-A*11:01, were significantly associated with the fatality rates, although these factors were associated with number of infected cases and not an independent factor to affect fatality rate in each country. Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19.


Asunto(s)
Betacoronavirus/genética , Infecciones por Coronavirus/genética , Infecciones por Coronavirus/mortalidad , Neumonía Viral/genética , Neumonía Viral/mortalidad , Factores de Edad , Vacuna BCG/genética , Vacuna BCG/uso terapéutico , Betacoronavirus/clasificación , Betacoronavirus/inmunología , Betacoronavirus/aislamiento & purificación , COVID-19 , Infecciones por Coronavirus/inmunología , Infecciones por Coronavirus/virología , Epítopos/genética , Genoma Viral , Salud Global , Antígenos HLA-A/genética , Antígenos HLA-A/inmunología , Antígenos HLA-B/genética , Antígenos HLA-B/inmunología , Humanos , Mutación , Pandemias , Neumonía Viral/inmunología , Neumonía Viral/virología , SARS-CoV-2 , Glicoproteína de la Espiga del Coronavirus/genética
8.
Nucleic Acids Res ; 46(16): 8079-8089, 2018 09 19.
Artículo en Inglés | MEDLINE | ID: mdl-30085309

RESUMEN

Programmed -1 ribosomal frameshifting (-1PRF) is a recoding mechanism to make alternative proteins from a single mRNA transcript. -1PRF is stimulated by cis-acting signals in mRNA, a seven-nucleotide slippery sequence and a downstream secondary structure element, which is often a pseudoknot. In this study we engineered the frameshifting pseudoknot from the mouse mammary tumor virus to respond to a rationally designed small molecule naphthyridine carbamate tetramer (NCTn). We demonstrate that NCTn can stabilize the pseudoknot structure in mRNA and activate -1PRF both in vitro and in human cells. The results illustrate how NCTn-inducible -1PRF may serve as an important component of the synthetic biology toolbox for the precise control of gene expression using small synthetic molecules.


Asunto(s)
Sistema de Lectura Ribosómico/genética , Regulación de la Expresión Génica/efectos de los fármacos , ARN/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , Animales , Secuencia de Bases/genética , Carbamatos/síntesis química , Carbamatos/química , Virus del Tumor Mamario del Ratón/genética , Ratones , Naftiridinas/síntesis química , Naftiridinas/química , Conformación de Ácido Nucleico/efectos de los fármacos , Biosíntesis de Proteínas/efectos de los fármacos , Biosíntesis de Proteínas/genética , Isoformas de Proteínas/genética , ARN/química , ARN Mensajero/genética , ARN Viral/genética , Bibliotecas de Moléculas Pequeñas/síntesis química , Bibliotecas de Moléculas Pequeñas/química , Biología Sintética
9.
Biotechnol Lett ; 42(12): 2595-2605, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32902709

RESUMEN

OBJECTIVES: To establish a technique for efficient fatty acid production through enhancement of coenzyme A (CoA) biosynthesis and malonyl-CoA supply by introducing exogenous pantothenate kinase (coaA) and acetyl-CoA carboxylase (acc) in Escherichia coli. RESULTS: The expression of acc, obtained from Corynebacterium glutamicum, accumulated 2.2-fold more fatty acids in E. coli. The addition of coaA from Pseudomonas putaida or fatty acid synthase (fasA) from C. glutamicum resulted in a 3.1- and 3.6-fold increase in fatty acid synthesis in E. coli cells, which expressed acc and coaA, or acc and fasA, respectively. The transformants, simultaneously possessing all three genes, produced 5.6-fold more fatty acids. The strain possessing acc, coaA, and fasA stored 691 mg/L of fatty acids, primarily as phospholipids, inside the inner membrane after 72-h cultivation. In addition, 19% of the total CoA pool was occupied by malonyl-CoA. CONCLUSIONS: Increased malonyl-CoA significantly contributed to fatty acid production, and the effect was boosted by the expanded total CoA pool. Manipulation of the intracellular CoA species is effective for fatty acid production in E. coli.


Asunto(s)
Acetil-CoA Carboxilasa/genética , Escherichia coli/genética , Ácidos Grasos/biosíntesis , Fosfotransferasas (Aceptor de Grupo Alcohol)/genética , Acetil-CoA Carboxilasa/química , Corynebacterium glutamicum/enzimología , Ácidos Grasos/genética
10.
J Cell Sci ; 129(16): 3189-202, 2016 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-27451356

RESUMEN

The mitogen-activated protein kinase (MAPK) cascade is a highly conserved signaling module composed of MAPK kinase kinases (MAPKKKs), MAPK kinases (MAPKK) and MAPKs. The MAPKKK Mkh1 is an initiating kinase in Pmk1 MAPK signaling, which regulates cell integrity in fission yeast (Schizosaccharomyces pombe). Our genetic screen for regulators of Pmk1 signaling identified Shk1 kinase binding protein 5 (Skb5), an SH3-domain-containing adaptor protein. Here, we show that Skb5 serves as an inhibitor of Pmk1 MAPK signaling activation by downregulating Mkh1 localization to cell tips through its interaction with the SH3 domain. Consistent with this, the Mkh1(3PA) mutant protein, with impaired Skb5 binding, remained in the cell tips, even when Skb5 was overproduced. Intriguingly, Skb5 needs Mkh1 to localize to the growing ends as Mkh1 deletion and disruption of Mkh1 binding impairs Skb5 localization. Deletion of Pck2, an upstream activator of Mkh1, impaired the cell tip localization of Mkh1 and Skb5 as well as the Mkh1-Skb5 interaction. Interestingly, both Pck2 and Mkh1 localized to the cell tips at the G1/S phase, which coincided with Pmk1 MAPK activation. Taken together, Mkh1 localization to cell tips is important for transmitting upstream signaling to Pmk1, and Skb5 spatially regulates this process.


Asunto(s)
Péptidos y Proteínas de Señalización Intracelular/metabolismo , Espacio Intracelular/metabolismo , Quinasas Quinasa Quinasa PAM/metabolismo , Sistema de Señalización de MAP Quinasas , Proteínas Quinasas Activadas por Mitógenos/metabolismo , Proteínas de Schizosaccharomyces pombe/metabolismo , Schizosaccharomyces/enzimología , Regulación hacia Abajo , Fase G1 , Eliminación de Gen , Fosforilación , Unión Proteica , Transporte de Proteínas , Fase S , Schizosaccharomyces/citología
11.
Bioorg Med Chem Lett ; 27(15): 3391-3394, 2017 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-28610980

RESUMEN

A naphthyridine carbamate tetramer (NCT8) is a synthetic compound, which selectively binds to nucleic acids containing CGG/CGG sequence. Although NCT8 is a promising compound for a wide range of DNA and RNA based biotechnology such as modulation of specific gene expression, little is known about its behavior in human cells. In the present study, we investigated the changes induced in gene expression by NCT8. Genes differentially expressed in the presence of NCT8 in HeLa cells were identified by whole-transcriptome analysis. The whole-transcriptome analysis showed that NCT8 significantly induced up-regulation of specific genes, whose promoter region has GC-rich sequence.


Asunto(s)
Carbamatos/farmacología , Secuencia Rica en GC/genética , Naftiridinas/farmacología , Regiones Promotoras Genéticas/efectos de los fármacos , Regiones Promotoras Genéticas/genética , Regulación hacia Arriba/efectos de los fármacos , Carbamatos/síntesis química , Carbamatos/química , Relación Dosis-Respuesta a Droga , Células HeLa , Humanos , Ligandos , Estructura Molecular , Naftiridinas/síntesis química , Naftiridinas/química , Relación Estructura-Actividad
12.
Chemistry ; 20(18): 5282-7, 2014 Apr 25.
Artículo en Inglés | MEDLINE | ID: mdl-24644006

RESUMEN

The hairpin structure is one of the most common secondary structures in RNA and holds a central position in the stream of RNA folding from a non-structured RNA to structurally complex and functional ribonucleoproteins. Since the RNA secondary structure is strongly correlated to the function and can be modulated by the binding of small molecules, we have investigated the modulation of RNA folding by a ligand-assisted formation of loop-loop complexes of two RNA hairpin loops. With a ligand (NCT6), designed based on the ligand binding to the G-G mismatches in double-stranded DNA, we successfully demonstrated the formation of both inter- and intra-molecular NCT6-assisted complex of two RNA hairpin loops. NCT6 selectively bound to the two hairpin loops containing (CGG)3 in the loop region. Native polyacrylamide gel electrophoresis analysis of two doubly-labeled RNA hairpin loops clearly showed the formation of intermolecular NCT6-assisted loop-loop complex. Förster resonance energy-transfer studies of RNA constructs containing two hairpin loops, in which each hairpin was labeled with Alexa488 and Cy3 fluorophores, showed the conformational change of the RNA constructs upon binding of NCT6. These experimental data showed that NCT6 simultaneously bound to two hairpin RNAs at the loop region, and can induce the conformational change of the RNA molecule. These data strongly support that NCT6 functions as molecular glue for two hairpin RNAs.


Asunto(s)
Conformación de Ácido Nucleico/efectos de los fármacos , ARN/química , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/farmacología , Secuencia de Bases , Sitios de Unión , Transferencia Resonante de Energía de Fluorescencia , Ligandos , Datos de Secuencia Molecular
13.
Oncoimmunology ; 13(1): 2373530, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38979545

RESUMEN

TCRαß+ CD4- CD8- double-negative T (DNT) cells are minor populations in peripheral blood, and their roles have mostly been discussed in inflammation and autoimmunity. However, the functions of DNT cells in tumor microenvironment remain to be elucidated. We investigated their characteristics, possible origins and functions in colorectal cancer tissues as well as their corresponding tumor-draining lymph nodes. We found a significant enrichment of DNT cells in tumor tissues compared with their corresponding lymph nodes, especially in tumors with lower T cell infiltration. T cell receptor (TCR) sequence analysis of CD4+ T, CD8+ T and DNT cells indicated that TCR sequences detected in DNT cells were found in CD8+ T cells, but rarely in CD4+ T cells, suggesting that a part of DNT cells was likely to be originated from CD8+ T cells. Through a single-cell transcriptomic analysis of DNT cells, we found that a DNT cell cluster, which showed similar phenotypes to central memory CD8+ T cells with low expression of effector and exhaustion markers, revealed some specific gene expression patterns, including higher GZMK expression. Moreover, in flow cytometry analysis, we found that DNT cells lost production of cytotoxic mediators. These findings imply that DNT cells might function as negative regulators of anti-tumor immune responses in tumor microenvironment.


Asunto(s)
Neoplasias Colorrectales , Ganglios Linfáticos , Microambiente Tumoral , Humanos , Neoplasias Colorrectales/inmunología , Neoplasias Colorrectales/patología , Ganglios Linfáticos/inmunología , Ganglios Linfáticos/patología , Microambiente Tumoral/inmunología , Linfocitos T CD8-positivos/inmunología , Linfocitos T CD8-positivos/metabolismo , Linfocitos Infiltrantes de Tumor/inmunología , Linfocitos Infiltrantes de Tumor/metabolismo , Masculino , Femenino , Linfocitos T CD4-Positivos/inmunología , Linfocitos T CD4-Positivos/metabolismo , Anciano , Receptores de Antígenos de Linfocitos T/metabolismo , Receptores de Antígenos de Linfocitos T/genética , Subgrupos de Linfocitos T/inmunología , Subgrupos de Linfocitos T/metabolismo , Persona de Mediana Edad
14.
PLoS One ; 19(8): e0308330, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39116074

RESUMEN

The immunogenicity of cancer cells is influenced by several factors, including the expression of the major histocompatibility complex class I (MHC-I), antigen expression, and the repertoire of proteasome-produced epitope peptides. The malignant pleural mesothelioma cell line ACC-MEOS-4 (MESO-4) expresses high levels of MHC-I and Wilms tumor 1 (WT1) tumor antigens. Using a functional T cell reporter assay specific for the HLA-A*24:02 restricted WT1 epitope (WT1235, CMTWNQMNL), we searched for factors that augmented the immunogenicity of MESO-4, focusing on proteasomes, which have a central role in the antigen processing machinery. ONX-0914, a selective inhibitor of the immunoproteasome subunit ß5i, enhanced immunogenicity dose-dependently at low concentrations without cytotoxicity. In addition, CD8+ T lymphocytes recognizing WT1 showed greater cytotoxicity against MESO-4 pre-treated with ONX-0914. MESO-4 expresses a standard proteasome (SP) and immunoproteasome (IP). Notably, IP has distinct catalytic activity from SP, favoring the generation of antigenic peptides with high affinity for MHC-I in antigen-presenting cells and cancer cells. In vitro, immunoproteasome digestion assay and mass spectrometry analysis showed that IP cleaved WT1235 internally after the hydrophobic residues. Importantly, this internal cleavage of the WT1235 epitope was mitigated by ONX-0914. These results suggest that ONX-0914 prevents the internal destructive cleavage of WT1235 by IP, thereby promoting the specific presentation of the WT1 epitope by MESO-4. In conclusion, selective IP inhibitors might offer a means to modulate cancer cell immunogenicity by directing the presentation of particular tumor epitopes.


Asunto(s)
Mesotelioma , Complejo de la Endopetidasa Proteasomal , Inhibidores de Proteasoma , Proteínas WT1 , Humanos , Línea Celular Tumoral , Proteínas WT1/inmunología , Inhibidores de Proteasoma/farmacología , Complejo de la Endopetidasa Proteasomal/metabolismo , Complejo de la Endopetidasa Proteasomal/inmunología , Mesotelioma/inmunología , Mesotelioma/tratamiento farmacológico , Epítopos/inmunología , Linfocitos T CD8-positivos/inmunología , Linfocitos T CD8-positivos/efectos de los fármacos , Antígeno HLA-A24/inmunología , Mesotelioma Maligno/inmunología , Mesotelioma Maligno/tratamiento farmacológico , Epítopos de Linfocito T/inmunología , Oligopéptidos
15.
Bioorg Med Chem Lett ; 23(12): 3539-41, 2013 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-23664873

RESUMEN

Here, we demonstrate that a series of naphthyridine derivatives, naphthyridine carbamate tetramer (NCTn), can bind to the RNA CGG/CGG triad comprised of two single-stranded regions of a hairpin loop and a tail. Complete suppression of the binding by a single mutation indicated simultaneous binding of NCTn between hairpin loop and single stranded tail, leading to the formation of NCTn-induced pseudoknot.


Asunto(s)
Carbamatos/química , Naftiridinas/química , ARN/química , Repeticiones de Trinucleótidos , Secuencia de Bases , Reparación de la Incompatibilidad de ADN , Ligandos , Modelos Moleculares , Conformación de Ácido Nucleico , ARN/genética , ARN/metabolismo
16.
Cancers (Basel) ; 15(3)2023 Jan 27.
Artículo en Inglés | MEDLINE | ID: mdl-36765744

RESUMEN

Targeting NAD depletion in cancer cells has emerged as an attractive therapeutic strategy for cancer treatment, based on the higher reliance of malignant vs. healthy cells on NAD to sustain their aberrant proliferation and altered metabolism. NAD depletion is exquisitely observed when NAMPT, a key enzyme for the biosynthesis of NAD, is inhibited. Growing evidence suggests that alternative NAD sources present in a tumor environment can bypass NAMPT and render its inhibition ineffective. Here, we report the identification of nicotinaldehyde as a novel precursor that can be used for NAD biosynthesis by human leukemia cells. Nicotinaldehyde supplementation replenishes the intracellular NAD level in leukemia cells treated with NAMPT inhibitor APO866 and prevents APO866-induced oxidative stress, mitochondrial dysfunction and ATP depletion. We show here that NAD biosynthesis from nicotinaldehyde depends on NAPRT and occurs via the Preiss-Handler pathway. The availability of nicotinaldehyde in a tumor environment fully blunts the antitumor activity of APO866 in vitro and in vivo. This is the first study to report the role of nicotinaldehyde in the NAD-targeted anti-cancer treatment, highlighting the importance of the tumor metabolic environment in modulating the efficacy of NAD-lowering cancer therapy.

17.
Cancers (Basel) ; 15(4)2023 Feb 06.
Artículo en Inglés | MEDLINE | ID: mdl-36831375

RESUMEN

Immunotherapies, including immune checkpoint blockades, play a critically important role in cancer treatments. For immunotherapies, neoantigens, which are generated by somatic mutations in cancer cells, are thought to be good targets due to their tumor specificity. Because neoantigens are unique in individual cancers, it is challenging to develop personalized immunotherapy targeting neoantigens. In this study, we screened "shared neoantigens", which are specific types of neoantigens derived from mutations observed commonly in a subset of cancer patients. Using exome sequencing data in the Cancer Genome Atlas (TCGA), we predicted shared neoantigen peptides and performed in vitro screening of shared neoantigen-reactive CD8+ T cells using peripheral blood from healthy donors. We examined the functional activity of neoantigen-specific T cell receptors (TCRs) by generating TCR-engineered T cells. Among the predicted shared neoantigens from TCGA data, we found that the mutated FGFR3Y373C peptide induced antigen-specific CD8+ T cells from the donor with HLA-A*02:06 via an ELISPOT assay. Subsequently, we obtained FGFR3Y373C-specific CD8+ T cell clones and identified two different sets of TCRs specifically reactive to FGFR3Y373C. We found that the TCR-engineered T cells expressing FGFR3Y373C-specific TCRs recognized the mutated FGFR3Y373C peptide but not the corresponding wild-type peptide. These two FGFR3Y373C-specific TCR-engineered T cells showed cytotoxic activity against mutated FGFR3Y373C-loaded cells. These results imply the possibility of strategies of immunotherapies targeting shared neoantigens, including cancer vaccines and TCR-engineered T cell therapies.

18.
Chem Commun (Camb) ; 58(89): 12459-12462, 2022 Nov 08.
Artículo en Inglés | MEDLINE | ID: mdl-36263745

RESUMEN

Since DNA methylation alters the chromatin state and regulates gene expression, elucidating the regulatory mechanisms of DNA methylation in response to environmental changes in the cell is crucial and urgent in understanding and regulating DNA methylation. G-quadruplex (G4) regulates transcription, translation and replication. Although it has recently been suggested that G4 regulates methylation, the detailed regulatory mechanism remains unclear. Here, we systematically analysed the effect of G4 formation on DNA methylation using G4s with various stabilities and topologies. The methylation efficiency decreased as the stability of G4 increased. Moreover, the degree of methylation suppression can be also controlled by G4 topology. Furthermore, our results showed the possibility of regulating methylation by modulating G4 stability and topology.


Asunto(s)
Metilación de ADN , G-Cuádruplex
19.
Sci Rep ; 12(1): 1149, 2022 01 21.
Artículo en Inglés | MEDLINE | ID: mdl-35064200

RESUMEN

In biological systems, the synthesis of nucleic acids, such as DNA and RNA, is catalyzed by enzymes in various aqueous solutions. However, substrate specificity is derived from the chemical properties of the residues, which implies that perturbations of the solution environment may cause changes in the fidelity of the reaction. Here, we investigated non-promoter-based synthesis of RNA using T7 RNA polymerase (T7 RNAP) directed by an RNA template in the presence of polyethylene glycol (PEG) of various molecular weights, which can affect polymerization fidelity by altering the solution properties. We found that the mismatch extensions of RNA propagated downstream polymerization. Furthermore, PEG promoted the polymerization of non-complementary ribonucleoside triphosphates, mainly due to the decrease in the dielectric constant of the solution. These results indicate that the mismatch extension of RNA-dependent RNA polymerization by T7 RNAP is driven by the stacking interaction of bases of the primer end and the incorporated nucleotide triphosphates (NTP) rather than base pairing between them. Thus, proteinaceous RNA polymerase may display different substrate specificity with changes in dielectricity caused by molecular crowding conditions, which can result in increased genetic diversity without proteinaceous modification.


Asunto(s)
ARN Polimerasas Dirigidas por ADN/química , ARN/biosíntesis , Proteínas Virales/química , Emparejamiento Base , ARN Polimerasas Dirigidas por ADN/metabolismo , Variación Genética , Polimerizacion , ARN/genética , Ribonucleósidos/química , Ribonucleósidos/metabolismo , Soluciones , Especificidad por Sustrato , Proteínas Virales/metabolismo
20.
Abdom Radiol (NY) ; 47(2): 891-902, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34914007

RESUMEN

PURPOSE: In contrast-enhanced abdominopelvic CT (CE-APCT) for oncologic follow-up, ultrahigh-resolution CT (UHRCT) may improve depiction of fine lesions and low-dose scans are desirable for minimizing the potential adverse effects by ionizing radiation. We compared image quality and radiologists' acceptance of model-based iterative (MBIR) and deep learning (DLR) reconstructions of low-dose CE-APCT by UHRCT. METHODS: Using our high-resolution (matrix size: 1024) and low-dose (tube voltage 100 kV; noise index: 20-40 HU) protocol, we scanned phantoms to compare the modulation transfer function and noise power spectrum between MBIR and DLR and assessed findings in 36 consecutive patients who underwent CE-APCT (noise index: 35 HU; mean CTDIvol: 4.2 ± 1.6 mGy) by UHRCT. We used paired t-test to compare objective noise and contrast-to-noise ratio (CNR) and Wilcoxon signed-rank test to compare radiologists' subjective acceptance regarding noise, image texture and appearance, and diagnostic confidence between MBIR and DLR using our routine protocol (matrix size: 512; tube voltage: 120 kV; noise index: 15 HU) for reference. RESULTS: Phantom studies demonstrated higher spatial resolution and lower low-frequency noise by DLR than MBIR at equal doses. Clinical studies indicated significantly worse objective noise, CNR, and subjective noise by DLR than MBIR, but other subjective characteristics were better (P < 0.001 for all). Compared with the routine protocol, subjective noise was similar or better by DLR, and other subjective characteristics were similar or worse by MBIR. CONCLUSION: Image quality, except regarding noise characteristics, and acceptance by radiologists were better by DLR than MBIR in low-dose CE-APCT by UHRCT.


Asunto(s)
Aprendizaje Profundo , Algoritmos , Humanos , Proyectos Piloto , Dosis de Radiación , Interpretación de Imagen Radiográfica Asistida por Computador/métodos , Radiólogos , Tomografía Computarizada por Rayos X/métodos
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