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1.
Proc Natl Acad Sci U S A ; 120(36): e2303859120, 2023 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-37639593

RESUMO

Recurrent chromosomal rearrangements found in rhabdomyosarcoma (RMS) produce the PAX3-FOXO1 fusion protein, which is an oncogenic driver and a dependency in this disease. One important function of PAX3-FOXO1 is to arrest myogenic differentiation, which is linked to the ability of RMS cells to gain an unlimited proliferation potential. Here, we developed a phenotypic screening strategy for identifying factors that collaborate with PAX3-FOXO1 to block myo-differentiation in RMS. Unlike most genes evaluated in our screen, we found that loss of any of the three subunits of the Nuclear Factor Y (NF-Y) complex leads to a myo-differentiation phenotype that resembles the effect of inactivating PAX3-FOXO1. While the transcriptomes of NF-Y- and PAX3-FOXO1-deficient RMS cells bear remarkable similarity to one another, we found that these two transcription factors occupy nonoverlapping sites along the genome: NF-Y preferentially occupies promoters, whereas PAX3-FOXO1 primarily binds to distal enhancers. By integrating multiple functional approaches, we map the PAX3 promoter as the point of intersection between these two regulators. We show that NF-Y occupies CCAAT motifs present upstream of PAX3 to function as a transcriptional activator of PAX3-FOXO1 expression in RMS. These findings reveal a critical upstream role of NF-Y in the oncogenic PAX3-FOXO1 pathway, highlighting how a broadly essential transcription factor can perform tumor-specific roles in governing cellular state.


Assuntos
Rabdomiossarcoma , Fator de Ligação a CCAAT/genética , Diferenciação Celular/genética , Aberrações Cromossômicas , Rabdomiossarcoma/genética , Fatores de Transcrição
2.
Biochem Cell Biol ; 2024 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-38306631

RESUMO

Currently used lung disease screening tools are expensive in terms of money and time. Therefore, chest radiograph images (CRIs) are employed for prompt and accurate COVID-19 identification. Recently, many researchers have applied Deep learning (DL) based models to detect COVID-19 automatically. However, their model could have been more computationally expensive and less robust, i.e., its performance degrades when evaluated on other datasets. This study proposes a trustworthy, robust, and lightweight network (ChestCovidNet) that can detect COVID-19 by examining various CRIs datasets. The ChestCovidNet model has only 11 learned layers, eight convolutional (Conv) layers, and three fully connected (FC) layers. The framework employs both the Conv and group Conv layers, Leaky Relu activation function, shufflenet unit, Conv kernels of 3×3 and 1×1 to extract features at different scales, and two normalization procedures that are cross-channel normalization and batch normalization. We used 9013 CRIs for training whereas 3863 CRIs for testing the proposed ChestCovidNet approach. Furthermore, we compared the classification results of the proposed framework with hybrid methods in which we employed DL frameworks for feature extraction and support vector machines (SVM) for classification. The study's findings demonstrated that the embedded low-power ChestCovidNet model worked well and achieved a classification accuracy of 98.12% and recall, F1-score, and precision of 95.75%.

3.
Proc Biol Sci ; 291(2025): 20232557, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38889794

RESUMO

Hyperoxia has been shown to expand the aerobic capacity of some fishes, although there have been very few studies examining the underlying mechanisms and how they vary across different exposure durations. Here, we investigated the cardiorespiratory function of yellowtail kingfish (Seriola lalandi) acutely (~20 h) and chronically (3-5 weeks) acclimated to hyperoxia (~200% air saturation). Our results show that the aerobic performance of kingfish is limited in normoxia and increases with environmental hyperoxia. The aerobic scope was elevated in both hyperoxia treatments driven by a ~33% increase in maximum O2 uptake (MO2max), although the mechanisms differed across treatments. Fish acutely transferred to hyperoxia primarily elevated tissue O2 extraction, while increased stroke volume-mediated maximum cardiac output was the main driving factor in chronically acclimated fish. Still, an improved O2 delivery to the heart in chronic hyperoxia was not the only explanatory factor as such. Here, maximum cardiac output only increased in chronic hyperoxia compared with normoxia when plastic ventricular growth occurred, as increased stroke volume was partly enabled by an ~8%-12% larger relative ventricular mass. Our findings suggest that hyperoxia may be used long term to boost cardiorespiratory function potentially rendering fish more resilient to metabolically challenging events and stages in their life cycle.


Assuntos
Consumo de Oxigênio , Perciformes , Animais , Perciformes/fisiologia , Hiperóxia/fisiopatologia , Aclimatação , Oxigênio/metabolismo , Débito Cardíaco
4.
J Mol Recognit ; 37(4): e3086, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38686702

RESUMO

Organophosphorus are typically hazardous chemicals used in the pharmaceutical, agricultural, and other industries. They pose a serious risk to human life and can be fatal upon direct exposure. Hence, studying the interaction between such compounds with proteins is crucial for environmental, health, and food safety. In this study, we investigated the interaction mechanism between azinphos-methyl (AZM) and ß-lactoglobulin (BLG) at pH 7.4 using a combination of biophysical techniques. Intrinsic fluorescence investigations revealed that BLG fluorescence was quenched in the presence of increasing AZM concentrations. The quenching mechanism was identified as static, as evidenced by a decrease in the fluorescence quenching constant (1.25 × 104, 1.18 × 104, and 0.86 × 104 M-1) with an increase in temperatures. Thermodynamic calculations (ΔH > 0; ΔS > 0) affirmed the formation of a complex between AZM and BLG through hydrophobic interactions. The BLG's secondary structure was found to be increased due to AZM interaction. Ultraviolet -visible spectroscopy data showed alterations in BLG conformation in the presence of AZM. Molecular docking highlighted the significant role of hydrophobic interactions involving residues such as Val43, Ile56, Ile71, Val92, Phe105, and Met107 in the binding between BLG and AZM. A docking energy of -6.9 kcal mol-1, and binding affinity of 1.15 × 105 M-1 suggest spontaneous interaction between AZM and BLG with moderate to high affinity. These findings underscore the potential health risks associated with the entry of AZM into the food chain, emphasizing the need for further consideration of its impact on human health.


Assuntos
Azinfos-Metil , Lactoglobulinas , Simulação de Acoplamento Molecular , Praguicidas , Termodinâmica , Lactoglobulinas/química , Lactoglobulinas/metabolismo , Bovinos , Animais , Azinfos-Metil/química , Praguicidas/química , Praguicidas/metabolismo , Espectrometria de Fluorescência , Interações Hidrofóbicas e Hidrofílicas , Ligação Proteica , Estrutura Secundária de Proteína
5.
Cytotherapy ; 26(7): 757-768, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38625071

RESUMO

With investigators looking to expand engineered T cell therapies such as CAR-T to new tumor targets and patient populations, a variety of cell manufacturing platforms have been developed to scale manufacturing capacity using closed and/or automated systems. Such platforms are particularly useful for solid tumor targets, which typically require higher CAR-T cell doses. Although T cell phenotype and function are key attributes that often correlate with therapeutic efficacy, how manufacturing platforms influence the final CAR-T cell product is currently unknown. We compared 4 commonly used T cell manufacturing platforms (CliniMACS Prodigy, Xuri W25 rocking platform, G-Rex gas-permeable bioreactor, static bag culture) using identical media, stimulation, culture length, and donor starting material. Selected CD4+CD8+ cells were transduced with lentiviral vector incorporating a CAR targeting FGFR4, a promising target for pediatric sarcoma. We observed significant differences in overall expansion over the 14-day culture; bag cultures had the highest capacity for expansion while the Prodigy had the lowest (481-fold versus 84-fold, respectively). Strikingly, we also observed considerable differences in the phenotype of the final product, with the Prodigy significantly enriched for CCR7+CD45RA+ naïve/stem central memory (Tn/scm)-like cells at 46% compared to bag and G-Rex with 16% and 13%, respectively. Gene expression analysis also showed that Prodigy CAR-Ts are more naïve, less cytotoxic and less exhausted than bag, G-Rex, and Xuri CAR-Ts, and pointed to differences in cell metabolism that were confirmed via metabolic assays. We hypothesized that dissolved oxygen level, which decreased substantially during the final 3 days of the Prodigy culture, may contribute to the observed differences in T cell phenotype. By culturing bag and G-Rex cultures in 1% O2 from day 5 onward, we could generate >60% Tn/scm-like cells, with longer time in hypoxia correlating with a higher percentage of Tn/scm-like cells. Intriguingly, our results suggest that oxygenation is responsible, at least in part, for observed differences in T cell phenotype among bioreactors and suggest hypoxic culture as a potential strategy prevent T cell differentiation during expansion. Ultimately, our study demonstrates that selection of bioreactor system may have profound effects not only on the capacity for expansion, but also on the differentiation state of the resulting CAR-T cells.


Assuntos
Diferenciação Celular , Imunoterapia Adotiva , Receptores de Antígenos Quiméricos , Humanos , Imunoterapia Adotiva/métodos , Receptores de Antígenos Quiméricos/genética , Receptores de Antígenos Quiméricos/metabolismo , Proliferação de Células , Linfócitos T/metabolismo , Linfócitos T/citologia , Reatores Biológicos , Técnicas de Cultura de Células/métodos , Linfócitos T CD8-Positivos/imunologia
6.
J Nat Prod ; 87(2): 332-339, 2024 02 23.
Artigo em Inglês | MEDLINE | ID: mdl-38294825

RESUMO

Neopetrotaurines A-C (1-3), unusual alkaloids possessing two isoquinoline-derived moieties that are linked via a unique taurine bridge, were isolated from a Neopetrosia sp. marine sponge. These new compounds have proton-deficient structural scaffolds that are difficult to unambiguously assign using only conventional 2- and 3-bond 1H-13C and 1H-15N heteronuclear correlation data. Thus, the application of LR-HSQMBC and HMBC NMR experiments optimized to detect 4- and 5-bond long-range 1H-13C heteronuclear correlations facilitated the structure elucidation of these unusual taurine-bridged marine metabolites. Neopetrotaurines A-C (1-3) showed significant inhibition of transcription driven by the oncogenic fusion protein PAX3-FOXO1, which is associated with alveolar rhabdomyosarcoma, and cytotoxic activity against PAX3-FOXO1-positive cell lines.


Assuntos
Alcaloides , Poríferos , Rabdomiossarcoma Alveolar , Animais , Rabdomiossarcoma Alveolar/metabolismo , Linhagem Celular , Alcaloides/farmacologia , Isoquinolinas/farmacologia
7.
BMC Pediatr ; 24(1): 545, 2024 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-39180069

RESUMO

BACKGROUND: Concurrent infections or co-infections caused by intestinal parasites and Helicobacter pylori are quite rampant in paediatrics living in endemic areas of sub-Saharan Africa, including Ethiopia, and if left untreated, can result in severe complications and hence must be addressed to ensure their health and well-being. OBJECTIVES: To determine the prevalence of intestinal parasitic and H. pylori co-infections and associated factors among paediatric patients with gastrointestinal symptoms who attended the Arba Minch General Hospital (AMGH), Arba Minch, southern Ethiopia, from September to November 2020. METHODS: A cross-sectional study was conducted among a study population of 299 paediatric patients with gastrointestinal symptoms who visited AMGH. Stool samples were collected and analysed to detect H. pylori and intestinal parasites. A rapid lateral flow chromatographic immunoassay was employed to identify the H. pylori copra antigen, whereas the latter was detected using wet mount saline preparation and formol-ether concentration method. Socio-demographic, clinical, behavioural and other factors were obtained by means of a pre-tested structured questionnaire. Descriptive statistics and logistic regression analysis were done by Statistical Package for Social Service (SPSS) version 25; P values < 0.05 were considered statistically significant. RESULTS: The prevalence of Helicobacter pylori and intestinal parasites was 14% (n = 42) and 37.1% (n = 111), respectively, whereas that of the co-infections with these pathogens was 6.4% (n = 19). Giardia lamblia was the most prevailing parasite, 21.4% (n = 64). Informal maternal education [AOR = 5.14; 95% CI: 1.98-15.70] and lack of hand washing practice were significantly associated with the extent of co-infections [AOR = 4.18; 95% CI: 1.36-12.80]. CONCLUSION: Nearly one in twenty pediatric patients with gastrointestinal symptoms had intestinal parasitic infections and H. pylori co-infections, representing a silent health problem that is to be addressed through effective control strategies. Health administrators should consider the importance of co-infections in clinical diagnosis and planning aimed at its prevention.


Assuntos
Coinfecção , Infecções por Helicobacter , Helicobacter pylori , Enteropatias Parasitárias , Humanos , Etiópia/epidemiologia , Infecções por Helicobacter/epidemiologia , Infecções por Helicobacter/complicações , Feminino , Masculino , Estudos Transversais , Helicobacter pylori/isolamento & purificação , Coinfecção/epidemiologia , Criança , Enteropatias Parasitárias/epidemiologia , Prevalência , Pré-Escolar , Adolescente , Hospitais Gerais , Lactente , Fezes/parasitologia , Fezes/microbiologia , Gastroenteropatias/epidemiologia , Gastroenteropatias/microbiologia , Gastroenteropatias/parasitologia
8.
Chem Biodivers ; 21(8): e202400920, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38818615

RESUMO

Parkinson's disease (PD) is a neurodegenerative condition characterized by both motor and non-motor symptoms. Although PD is commonly associated with a decline of dopaminergic neurons in the substantia nigra, other diagnostic criteria and biomarkers also exist. In the search for novel therapeutic agents, chromene and pyran derivatives have shown potential due to their diverse pharmacological activities. This study utilizes a comprehensive computational approach to investigate the viability of chromene/pyran compounds as potential treatments for PD. The drug-likeness characteristics of these molecules were analyzed using ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) studies. Molecular docking was performed against PDB ID: 2V5Z. The best three molecules chosen were compound 7, compound 24, and compound 67 have a binding energy of -6.7, -8.6, and -10.9 kcal/mol. Molecules demonstrating positive blood-brain barrier permeability, good solubility, and favorable binding affinity were further evaluated using Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations to assess their electronic structure and stability. DFT calculations indicated that molecule 82 has a dipole moment of 15.70 D. RMSD and RMSF results confirmed the stability of the complexes over a 100 ns simulation, with a maximum of 3 hydrogen bonds formed.


Assuntos
Benzopiranos , Teoria da Densidade Funcional , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Doença de Parkinson , Piranos , Doença de Parkinson/tratamento farmacológico , Doença de Parkinson/metabolismo , Piranos/química , Piranos/farmacologia , Piranos/metabolismo , Humanos , Benzopiranos/química , Benzopiranos/metabolismo , Benzopiranos/farmacologia , Estrutura Molecular , Barreira Hematoencefálica/metabolismo , Antiparkinsonianos/química , Antiparkinsonianos/farmacologia , Antiparkinsonianos/metabolismo
9.
Foodborne Pathog Dis ; 2024 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-39463274

RESUMO

Milk, a nutritious global important food commodity, serves as an excellent medium for microbial growth as well. The foodborne pathogen Staphylococcus aureus is a commensal member of human microflora that enters the food chain through poor hygienic practices and cross contamination and causes various clinical manifestations in humans. During this study, raw milk and swab samples (milker's hand, udder, towel, milking bucket, and farm floor) were collected from four middle-scale buffalo dairy farms. The results revealed S. aureus presence in 11.6% (n = 56/448) bucket raw milk samples and 2.6% (n = 12/448) udder raw milk samples. Contrarily, S. aureus prevalence was significantly higher in farm floors (100%, n = 84/84), towel (35.7%, n = 10/28), milking bucket (11.6%, n = 56/448), milker's hand (10.7%, n = 3/28), and udder swab samples (4.0%, n = 18/448). The chi-square test yielded p values of 0.000, 0.005, and 0.0011 for udder raw milk, udder swab, and milker's hand swab, respectively. The p values of the milking bucket (p = 0.048) and farm floors (p = 0.0183) confirmed their possible role in S. aureus cross contamination. Gene amplifications of nuclease and enterotoxin A indicate potential virulence of S. aureus isolates in collected samples. Antibiotic susceptibility testing revealed multidrug resistance in 44% (n = 239) of S. aureus isolates with the highest resistance of 61% against penicillin. Resistance against ampicillin, streptomycin, and lincomycin was observed. Fewer S. aureus isolates were resistant to kanamycin and erythromycin, whereas the lowest number of resistant isolates was observed against chloramphenicol. A high prevalence of S. aureus in the farm environment and milking equipment suggested the cross contamination of potentially enterotoxin-producing and multidrug-resistant S. aureus to raw milk. Therefore, good hygiene practices should be enforced to avoid foodborne and zoonotic infections.

10.
Genome Res ; 30(9): 1228-1242, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32796005

RESUMO

Neuroblastoma is a malignancy of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Like many childhood cancers, neuroblastoma shows a relative paucity of somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) compared to adult cancers. Here, we assessed the contribution of somatic structural variation (SV) in neuroblastoma using a combination of whole-genome sequencing (WGS) of tumor-normal pairs (n = 135) and single-nucleotide polymorphism (SNP) genotyping of primary tumors (n = 914). Our study design allowed for orthogonal validation and replication across platforms. SV frequency, type, and localization varied significantly among high-risk tumors. MYCN nonamplified high-risk tumors harbored an increased SV burden overall, including a significant excess of tandem duplication events across the genome. Genes disrupted by SV breakpoints were enriched in neuronal lineages and associated with phenotypes such as autism spectrum disorder (ASD). The postsynaptic adapter protein-coding gene, SHANK2, located on Chromosome 11q13, was disrupted by SVs in 14% of MYCN nonamplified high-risk tumors based on WGS and 10% in the SNP array cohort. Expression of SHANK2 was low across human-derived neuroblastoma cell lines and high-risk neuroblastoma tumors. Forced expression of SHANK2 in neuroblastoma cells resulted in significant growth inhibition (P = 2.6 × 10-2 to 3.4 × 10-5) and accelerated neuronal differentiation following treatment with all-trans retinoic acid (P = 3.1 × 10-13 to 2.4 × 10-30). These data further define the complex landscape of somatic structural variation in neuroblastoma and suggest that events leading to deregulation of neurodevelopmental processes, such as inactivation of SHANK2, are key mediators of tumorigenesis in this childhood cancer.


Assuntos
Genes Supressores de Tumor , Variação Estrutural do Genoma , Proteínas do Tecido Nervoso/genética , Neuroblastoma/genética , Neurogênese/genética , Linhagem Celular Tumoral , Cromotripsia , Estudos de Coortes , Quebras de DNA , Variações do Número de Cópias de DNA , Feminino , Humanos , Masculino , Proteína Proto-Oncogênica N-Myc/genética , Neuroblastoma/patologia , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , RNA Neoplásico , RNA-Seq , Medição de Risco , Telomerase/genética , Células Tumorais Cultivadas , Sequenciamento Completo do Genoma
11.
J Mol Recognit ; 36(6): e3009, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36841950

RESUMO

Several proteins and peptides tend to form an amyloid fibril, causing a range of unrelated diseases, from neurodegenerative to certain types of cancer. In the native state, these proteins are folded and soluble. However, these proteins acquired ß-sheet amyloid fibril due to unfolding and aggregation. The conversion mechanism from well-folded soluble into amorphous or amyloid fibril is not well understood yet. Here, we induced unfolding and aggregation of hen egg-white lysozyme (HEWL) by reducing agent dithiothreitol and applied mechanical sheering force by constant shaking (1000 rpm) on the thermostat for 7 days. Our turbidity results showed that reduced HEWL rapidly formed aggregates, and a plateau was attained in nearly 5 h of incubation in both shaking and non-shaking conditions. The turbidity was lower in the shaking condition than in the non-shaking condition. The thioflavin T binding and transmission electron micrographs showed that reduced HEWL formed amorphous aggregates in both conditions. Far-UV circular dichroism results showed that reduced HEWL lost nearly all alpha-helical structure, and ß-sheet secondary structure was not formed in both conditions. All the spectroscopic and microscopic results showed that reduced HEWL formed amorphous aggregates under both conditions.


Assuntos
Amiloide , Muramidase , Animais , Temperatura , Muramidase/química , Amiloide/química , Dicroísmo Circular , Concentração de Íons de Hidrogênio , Galinhas/metabolismo
12.
Arch Microbiol ; 205(3): 95, 2023 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-36807206

RESUMO

Biodesulfurization is emerging as a valuable technology for the desulfurization of dibenzothiophene (DBT) and its alkylated substitutes, which are otherwise regarded as refractory to other physical and chemical desulfurizing techniques. The inability of the currently identified pure cultures and artificial microbial consortia due to lower desulfurization rate and product inhibition issues has compelled the researcher to look for an alternative solution. Thus, in the present study, an indigenously isolated microbial consortium was employed to tackle the desulfurization issue. Herein, we isolated several kinds of DBT desulfurizing natural microbial consortia from hydrocarbon-contaminated soil samples by conventional enrichment technique. The most effective desulfurizing microbial consortium was sequenced through illumine sequencing technique. Finally, the effect of the products of the desulfurizing pathway (such as 2-hydroxybiphenyl (2-HBP) and sulfate (SO4-2) was evaluated on the growth and desulfurization capability of the isolated consortium. The outcomes of Gibb's assay analysis showed that six isolates followed the "4S" pathway and converted DBT to 2-HBP. Among the isolates, I5 showed maximum growth rate (1.078 g/L dry cell weight) and desulfurization activity (about 77% as indicated by HPLC analysis) and was considered for further in-depth experimentation. The analysis of 16S rRNA by high-throughput sequencing approach of the I5 isolate revealed five types of bacterial phyla including Proteobacteria, Bacteroidetes, Firmicutes, Patescibacteria, and Actinobacteria (in order of abundance). The isolate showed significant tolerance to the inhibitory effect of both 2-HBP and SO4-2 and maintained growth in the presence of even about 1.0 mM initial concentration of both products. This clearly suggests that the isolate can be an efficient candidate for future in-depth desulfurization studies of coal and other fossil fuels.


Assuntos
Bactérias , Tiofenos , RNA Ribossômico 16S/genética , Tiofenos/metabolismo , Bactérias/genética
13.
Bioorg Med Chem Lett ; 91: 129373, 2023 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-37315697

RESUMO

Efforts directed at improving potency and preparing structurally different TYK2 JH2 inhibitors from the first generation of compounds such as 1a led to the SAR study of new central pyridyl based analogs 2-4. The current SAR study resulted in the identification of 4h as a potent and selective TYK2 JH2 inhibitor with distinct structural differences from 1a. In this manuscript, the in vitro and in vivo profiles of 4h are described. The hWB IC50 of 4h was shown as 41 nM with 94% bioavailability in the mouse PK study.


Assuntos
Piridinas , TYK2 Quinase , Camundongos , Animais , Relação Estrutura-Atividade , Piridinas/farmacologia
14.
Mol Cell Proteomics ; 20: 100136, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34391887

RESUMO

Immune checkpoint inhibitors and adoptive lymphocyte transfer-based therapies have shown great therapeutic potential in cancers with high tumor mutational burden (TMB), such as melanoma, but not in cancers with low TMB, such as mutant epidermal growth factor receptor (EGFR)-driven lung adenocarcinoma. Precision immunotherapy is an unmet need for most cancers, particularly for cancers that respond inadequately to immune checkpoint inhibitors. Here, we employed large-scale MS-based proteogenomic profiling to identify potential immunogenic human leukocyte antigen (HLA) class I-presented peptides in melanoma and EGFR-mutant lung adenocarcinoma. Similar numbers of peptides were identified from both tumor types. Cell line and patient-specific databases (DBs) were constructed using variants identified from whole-exome sequencing. A de novo search algorithm was used to interrogate the HLA class I immunopeptidome MS data. We identified 12 variant peptides and several classes of tumor-associated antigen-derived peptides. We constructed a cancer germ line (CG) antigen DB with 285 antigens. This allowed us to identify 40 class I-presented CG antigen-derived peptides. The class I immunopeptidome comprised more than 1000 post-translationally modified (PTM) peptides representing 58 different PTMs, underscoring the critical role PTMs may play in HLA binding. Finally, leveraging de novo search algorithm and an annotated long noncoding RNA (lncRNA) DB, we developed a novel lncRNA-encoded peptide discovery pipeline to identify 44 lncRNA-derived peptides that are presented by class I. We validated tandem MS spectra of select variant, CG antigen, and lncRNA-derived peptides using synthetic peptides and performed HLA class I-binding assays to demonstrate binding to class I proteins. In summary, we provide direct evidence of HLA class I presentation of a large number of variant and tumor-associated peptides in both low and high TMB cancer. These results can potentially be useful for precision immunotherapies, such as vaccine or adoptive cell therapies in melanoma and EGFR-mutant lung cancers.


Assuntos
Adenocarcinoma de Pulmão/metabolismo , Antígenos de Neoplasias/metabolismo , Antígenos de Histocompatibilidade Classe I/metabolismo , Neoplasias Pulmonares/metabolismo , Melanoma/metabolismo , Peptídeos/metabolismo , Adenocarcinoma de Pulmão/genética , Idoso , Antígenos de Neoplasias/genética , Linhagem Celular Tumoral , Receptores ErbB/genética , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Neoplasias Pulmonares/genética , Masculino , Melanoma/genética , Mutação , Peptídeos/genética , Proteogenômica
15.
Curr Cardiol Rep ; 25(5): 411-420, 2023 05.
Artigo em Inglês | MEDLINE | ID: mdl-37074565

RESUMO

PURPOSE OF REVIEW: Heart failure is a highly prevalent condition caused by many different aetiologies and characterised by cardiac dysfunction and congestion. Once developed, congestion leads to signs (peripheral oedema) and symptoms (breathlessness on exertion), adverse cardiac remodelling, and an increased risk of hospitalisation and premature death. This review summarises strategies that could enable early identification and a more objective management of congestion in patients with heart failure. RECENT FINDINGS: For patients with suspected or diagnosed heart failure, combining an echocardiogram with assessment of great veins, lungs, and kidneys by ultrasound might facilitate recognition and quantification of congestion, the management of which is still difficult and highly subjective. Congestion is a one of the key drivers of morbidity and mortality in patients with heart failure and is often under-recognised. The use of ultrasound allows for a timely, simultaneous identification of cardiac dysfunction and multiorgan congestion; ongoing and future studies will clarify how to tailor diuretic treatments in those with or at risk of heart failure.


Assuntos
Cardiomiopatias , Insuficiência Cardíaca , Humanos , Diuréticos/uso terapêutico , Insuficiência Cardíaca/complicações , Insuficiência Cardíaca/tratamento farmacológico , Insuficiência Cardíaca/diagnóstico , Hospitalização , Pulmão
16.
Med Chem Res ; : 1-7, 2023 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-37362320

RESUMO

Adaptor protein 2-associated kinase 1 (AAK1) is a member of the Ark1/Prk1 family of serine/threonine kinases and plays a role in modulating receptor endocytosis. AAK1 was identified as a potential therapeutic target for the treatment of neuropathic pain when it was shown that AAK1 knock out (KO) mice had a normal response to the acute pain phase of the mouse formalin model, but a reduced response to the persistent pain phase. Herein we report our early work investigating a series of pyrrolo[2,1-f][1,2,4]triazines as part of our efforts to recapitulate this KO phenotype with a potent, small molecule inhibitor of AAK1. The synthesis, structure-activity relationships (SAR), and in vivo evaluation of these AAK1 inhibitors is described.

17.
Bioorg Med Chem ; 67: 116833, 2022 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-35605346

RESUMO

Allosteric integrase inhibitors (ALLINIs) of HIV-1 may hold promise as a novel mechanism for HIV therapeutics and cure. Scaffold modifications to the 4-(4,4-dimethylpiperidinyl) 2,6-dimethylpyridinyl class of ALLINIs provided a series of potent compounds with differentiated 5/6 fused ring systems. Notably, inhibitors containing the 1,2,4-triazolopyridine and imidazopyridine core exhibited single digit nM antiviral potency and low to moderate clearance after intravenous (IV) dosing in rat pharmacokinetic (PK) studies. The 1,2,4-triazolopyridines showed a higher oral exposure when compared to the imidazopyridines. Further modifications to the C5 substituent of the 1,2,4-triazolopyridines resulted in a new lead compound, which had improved rat IV/PO PK compared to the former lead compound GSK3739936, while maintaining antiviral potency. Structure-activity relationships (SAR) and rat pharmacokinetic profiles of this series are discussed.


Assuntos
Fármacos Anti-HIV , Inibidores de Integrase de HIV , Integrase de HIV , HIV-1 , Regulação Alostérica , Animais , Fármacos Anti-HIV/farmacologia , Integrase de HIV/metabolismo , Inibidores de Integrase de HIV/farmacologia , HIV-1/metabolismo , Ratos
18.
J Nat Prod ; 85(5): 1419-1427, 2022 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-35465663

RESUMO

Chemical investigation of the marine hydroid Dentitheca habereri led to the identification of eight new diacylated zoanthoxanthin alkaloids, named dentithecamides A-H (1-8), along with three previously reported analogues, zoamides B-D (9-11). The structures of compounds 1-11 were elucidated by spectroscopic and spectrometric analyses, including IR, HRESIMS, and NMR experiments, and by comparison with literature data. Compounds 1-11 are the first zoanthoxanthin alkaloids to be reported from a hydroid. Dentithecamides A (1) and B (2) along with zoamides B-D (9-11), which all share a conformationally mobile cycloheptadiene core, inhibited PAX3-FOXO1 regulated transcriptional activity and thus provided a structural framework for the potential development of more potent PAX3-FOXO1 inhibitors.


Assuntos
Alcaloides , Imidazóis , Alcaloides/química
19.
Proc Natl Acad Sci U S A ; 116(18): 9008-9013, 2019 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-30975761

RESUMO

Survival from malignant mesothelioma, particularly pleural mesothelioma, is very poor. For patients with breast, ovarian, or prostate cancers, overall survival is associated with increased sensitivity to platinum chemotherapy due to loss-of-function mutations in DNA repair genes. The goal of this project was to evaluate, in patients with malignant mesothelioma, the relationship between inherited loss-of-function mutations in DNA repair and other tumor suppressor genes and overall survival following platinum chemotherapy. Patients with histologically confirmed malignant mesothelioma were evaluated for inherited mutations in tumor suppressor genes. Survival was evaluated with respect to genotype and site of mesothelioma. Among 385 patients treated with platinum chemotherapy, median overall survival was significantly longer for patients with loss-of-function mutations in any of the targeted genes compared with patients with no such mutation (P = 0.0006). The effect of genotype was highly significant for patients with pleural mesothelioma (median survival 7.9 y versus 2.4 y, P = 0.0012), but not for patients with peritoneal mesothelioma (median survival 8.2 y versus 5.4 y, P = 0.47). Effect of patient genotype on overall survival, measured at 3 y, remained independently significant after adjusting for gender and age at diagnosis, two other known prognostic factors. Patients with pleural mesothelioma with inherited mutations in DNA repair and other tumor suppressor genes appear to particularly benefit from platinum chemotherapy compared with patients without inherited mutations. These patients may also benefit from other DNA repair targeted therapies such as poly-ADP ribose polymerase (PARP) inhibitors.


Assuntos
Mesotelioma/genética , Mesotelioma/mortalidade , Adulto , Idoso , Idoso de 80 Anos ou mais , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Reparo do DNA/genética , Feminino , Predisposição Genética para Doença/genética , Mutação em Linhagem Germinativa , Humanos , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/mortalidade , Masculino , Mesotelioma/tratamento farmacológico , Mesotelioma Maligno , Pessoa de Meia-Idade , Platina/uso terapêutico , Neoplasias Pleurais/genética , Neoplasias Pleurais/mortalidade , Análise de Sobrevida , Proteínas Supressoras de Tumor/genética , Ubiquitina Tiolesterase/genética , Adulto Jovem
20.
Eur Heart J ; 42(6): 684-696, 2021 02 11.
Artigo em Inglês | MEDLINE | ID: mdl-33215209

RESUMO

AIMS: To investigate the effects of spironolactone on fibrosis and cardiac function in people at increased risk of developing heart failure. METHODS AND RESULTS: Randomized, open-label, blinded-endpoint trial comparing spironolactone (50 mg/day) or control for up to 9 months in people with, or at high risk of, coronary disease and raised plasma B-type natriuretic peptides. The primary endpoint was the interaction between baseline serum galectin-3 and changes in serum procollagen type-III N-terminal pro-peptide (PIIINP) in participants assigned to spironolactone or control. Procollagen type-I C-terminal pro-peptide (PICP) and collagen type-1 C-terminal telopeptide (CITP), reflecting synthesis and degradation of type-I collagen, were also measured. In 527 participants (median age 73 years, 26% women), changes in PIIINP were similar for spironolactone and control [mean difference (mdiff): -0.15; 95% confidence interval (CI) -0.44 to 0.15 µg/L; P = 0.32] but those receiving spironolactone had greater reductions in PICP (mdiff: -8.1; 95% CI -11.9 to -4.3 µg/L; P < 0.0001) and PICP/CITP ratio (mdiff: -2.9; 95% CI -4.3 to -1.5; <0.0001). No interactions with serum galectin were observed. Systolic blood pressure (mdiff: -10; 95% CI -13 to -7 mmHg; P < 0.0001), left atrial volume (mdiff: -1; 95% CI -2 to 0 mL/m2; P = 0.010), and NT-proBNP (mdiff: -57; 95% CI -81 to -33 ng/L; P < 0.0001) were reduced in those assigned spironolactone. CONCLUSIONS: Galectin-3 did not identify greater reductions in serum concentrations of collagen biomarkers in response to spironolactone. However, spironolactone may influence type-I collagen metabolism. Whether spironolactone can delay or prevent progression to symptomatic heart failure should be investigated.


Assuntos
Insuficiência Cardíaca , Espironolactona , Idoso , Envelhecimento , Biomarcadores , Feminino , Fibrose , Insuficiência Cardíaca/tratamento farmacológico , Humanos , Masculino , Fragmentos de Peptídeos , Pró-Colágeno , Espironolactona/uso terapêutico
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