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1.
Int Microbiol ; 2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38777925

RESUMEN

INTRODUCTION: The emergence of multidrug-resistant bacteria and biofilms requires discovering new antimicrobial agents from unexplored environments. OBJECTIVES: This study aims to isolate and characterize a new actinobacterial strain from the Hoggar Mountains in southern Algeria and evaluate its ability to produce bioactive molecules with potential antibacterial and antibiofilm activities. METHODS: A novel halotolerant actinobacterial strain, designated HG-17, was isolated from the Hoggar Mountains, and identified based on phenotypic characterizations, 16S rDNA sequence analysis, and phylogenetic analysis. The antibacterial and antibiofilm activities of the strain were assessed, and the presence of biosynthetic genes (PKS-I and NRPS) was confirmed. Two active compounds, HG-7 and HG-9, were extracted butanol solvent, purified by HPLC, and their chemical structures were elucidated using ESI mass spectrometry and NMR spectroscopy. RESULTS: The strain HG-17 was identified as Streptomyces purpureus NBRC with 98.8% similarity. It exhibited strong activity against multidrug-resistant and biofilm-forming bacteria. The two purified active compounds, HG-7 and HG-9, were identified as cyclo-(d-cis-hydroxyproline-l-phenylalanine) and cyclo-(l-prolone-l-tyrosine), respectively. The minimum inhibitory concentrations (MICs) of HG-7 and HG-9 ranged from 3 to 15 µg/mL, comparable to the MICs of tetracycline (8 to 15 µg/mL). Their minimum biofilm inhibitory concentration (MBIC 50%) showed good inhibition from 48.0 to 52.0% at concentrations of 1 to 7 µg/mL against the tested bacteria. CONCLUSION: This is the first report of cyclo-(d-cis-hydroxyproline-l-phenylalanine) and cyclo-(l-prolone-l-tyrosine) antibiotics from S. purpureus and their anti-multi-drug-resistant and biofilm-forming bacteria. These results indicate that both antibiotics could be used as effective therapeutics to control infections associated with multidrug-resistant bacteria.

2.
Cancer Res ; 84(7): 1013-1028, 2024 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-38294491

RESUMEN

Cytidine deaminase (CDA) functions in the pyrimidine salvage pathway for DNA and RNA syntheses and has been shown to protect cancer cells from deoxycytidine-based chemotherapies. In this study, we observed that CDA was overexpressed in pancreatic adenocarcinoma from patients at baseline and was essential for experimental tumor growth. Mechanistic investigations revealed that CDA localized to replication forks where it increased replication speed, improved replication fork restart efficiency, reduced endogenous replication stress, minimized DNA breaks, and regulated genetic stability during DNA replication. In cellular pancreatic cancer models, high CDA expression correlated with resistance to DNA-damaging agents. Silencing CDA in patient-derived primary cultures in vitro and in orthotopic xenografts in vivo increased replication stress and sensitized pancreatic adenocarcinoma cells to oxaliplatin. This study sheds light on the role of CDA in pancreatic adenocarcinoma, offering insights into how this tumor type modulates replication stress. These findings suggest that CDA expression could potentially predict therapeutic efficacy and that targeting CDA induces intolerable levels of replication stress in cancer cells, particularly when combined with DNA-targeted therapies. SIGNIFICANCE: Cytidine deaminase reduces replication stress and regulates DNA replication to confer resistance to DNA-damaging drugs in pancreatic cancer, unveiling a molecular vulnerability that could enhance treatment response.


Asunto(s)
Adenocarcinoma , Citidina Desaminasa , Inhibidores de la Síntesis del Ácido Nucleico , Neoplasias Pancreáticas , Humanos , Adenocarcinoma/tratamiento farmacológico , Adenocarcinoma/metabolismo , Adenocarcinoma/patología , Citidina Desaminasa/metabolismo , ADN , Neoplasias Pancreáticas/tratamiento farmacológico , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/patología , Replicación del ADN , Inhibidores de la Síntesis del Ácido Nucleico/uso terapéutico
3.
Cell Rep ; 42(3): 112211, 2023 03 28.
Artículo en Inglés | MEDLINE | ID: mdl-36884350

RESUMEN

Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate their immune functions under regulatory mechanisms involving SGs and PBs. However, the impact of T cell activation on such complexes in terms of formation, constitution, and relationship remains unknown. Here, by combining proteomic, transcriptomic, and immunofluorescence approaches, we simultaneously characterized the SGs and PBs from primary human T lymphocytes pre and post stimulation. The identification of the proteomes and transcriptomes of SGs and PBs indicate an unanticipated molecular and functional complementarity. Notwithstanding, these granules keep distinct spatial organizations and abilities to interact with mRNAs. This comprehensive characterization of the RNP granule proteomic and transcriptomic landscapes provides a unique resource for future investigations on SGs and PBs in T lymphocytes.


Asunto(s)
Activación de Linfocitos , Cuerpos de Procesamiento , Proteoma , Gránulos de Estrés , Linfocitos T , Transcriptoma , Gránulos de Estrés/metabolismo , Linfocitos T/citología , Linfocitos T/inmunología , Linfocitos T/metabolismo , Cuerpos de Procesamiento/metabolismo , Proteoma/metabolismo , Transcriptoma/genética , Proteómica , Perfilación de la Expresión Génica , Humanos , Masculino , Femenino , Adulto , Células Cultivadas , ARN/análisis , Biosíntesis de Proteínas , Transcripción Genética , Fraccionamiento Celular
4.
BMC Bioinformatics ; 24(1): 30, 2023 Jan 27.
Artículo en Inglés | MEDLINE | ID: mdl-36707753

RESUMEN

BACKGROUND: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called 'spatial transcriptomics'. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. RESULTS: Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies. CONCLUSIONS: Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.


Asunto(s)
Programas Informáticos , Transcriptoma , Humanos , Animales , Ratones , Perfilación de la Expresión Génica , Análisis Espacial , Análisis de la Célula Individual
5.
Metabolites ; 12(9)2022 Sep 11.
Artículo en Inglés | MEDLINE | ID: mdl-36144257

RESUMEN

Tyrosine kinase inhibitors pazopanib and sunitinib are both used to treat advanced renal cell carcinoma but expose patients to an increased risk of hepatotoxicity. We have previously identified two aldehyde derivatives for pazopanib and sunitinib (P-CHO and S-CHO, respectively) in liver microsomes. In this study, we aimed to decipher their role in hepatotoxicity by treating HepG2 and HepaRG hepatic cell lines with these derivatives and evaluating cell viability, mitochondrial dysfunction, and oxidative stress accumulation. Additionally, plasma concentrations of P-CHO were assessed in a cohort of patients treated with pazopanib. Results showed that S-CHO slightly decreased the viability of HepG2, but to a lesser extent than sunitinib, and affected the maximal respiratory capacity of the mitochondrial chain. P-CHO decreased viability and ATP production in HepG2. Traces of P-CHO were detected in the plasma of patients treated with pazopanib. Overall, these results showed that P-CHO and S-CHO affect hepatocyte integrity and could be involved in the pazopanib and sunitinib hepatotoxicity.

6.
Curr Microbiol ; 79(10): 298, 2022 Aug 24.
Artículo en Inglés | MEDLINE | ID: mdl-36002540

RESUMEN

Multi-resistant bacterial pathogens are a major public health problem for treating nosocomial infections owing to their high resistance to antibiotics. The objective of this research was to characterize the bioactive molecules secreted by a novel moderately halophilic actinobacterium strain, designated GSB-11, exhibiting a strong antagonistic activity against several multidrug-resistant pathogenic bacteria. This potential strain was identified by phenotypic, genotypic (16S rRNA), and phylogenetic analyses. GSB-11 was related to "Streptomyces acrimycini" NBRC 12736 T with 99.59% similarity. Molecular screening by PCR assay demonstrated that the strain possesses two biosynthetic genes coding for NRPS and PKS-II. Two active compounds GSB11-6 and GSB11-7 were extracted from the cell-free culture supernatant of Bennett medium and purified using reversed-phase HPLC. According to spectrometric (mass spectrum) and spectroscopic (1H NMR, 13C NMR, 1H-1H COSY, and 1H-13C HMBC) spectra analyses, the compounds GSB11-6 and GSB11-7 were identified to be maculosin and N-acetyltyramine, respectively. Their minimum inhibitory concentrations (MIC) revealed interesting values against certain multidrug-resistant pathogenic bacteria. They were between 5 and 15 mg/mL for GSB11-6, 10 and 30 mg/mL for GSB11-7. To our best knowledge, this is the first study of these active substances isolated from "Streptomyces acrimycini" showing an interesting antibacterial activity. Therefore, these essential compounds could be candidates for future research against multidrug-resistant bacteria.


Asunto(s)
Microbiología del Suelo , Streptomyces , Antibacterianos/química , Pruebas de Sensibilidad Microbiana , Péptidos Cíclicos , Filogenia , Piperazinas , ARN Ribosómico 16S/genética , Tiramina/análogos & derivados
7.
Viruses ; 13(11)2021 11 03.
Artículo en Inglés | MEDLINE | ID: mdl-34835019

RESUMEN

The detailed characterization of human γδ T lymphocyte differentiation at the single-cell transcriptomic (scRNAseq) level in tumors and patients with coronavirus disease 2019 (COVID-19) requires both a reference differentiation trajectory of γδ T cells and a robust mapping method for additional γδ T lymphocytes. Here, we incepted such a method to characterize thousands of γδ T lymphocytes from (n = 95) patients with cancer or adult and pediatric COVID-19 disease. We found that cancer patients with human papillomavirus-positive head and neck squamous cell carcinoma and Epstein-Barr virus-positive Hodgkin's lymphoma have γδ tumor-infiltrating T lymphocytes that are more prone to recirculate from the tumor and avoid exhaustion. In COVID-19, both TCRVγ9 and TCRVγnon9 subsets of γδ T lymphocytes relocalize from peripheral blood mononuclear cells (PBMC) to the infected lung tissue, where their advanced differentiation, tissue residency, and exhaustion reflect T cell activation. Although severe COVID-19 disease increases both recruitment and exhaustion of γδ T lymphocytes in infected lung lesions but not blood, the anti-IL6R therapy with Tocilizumab promotes γδ T lymphocyte differentiation in patients with COVID-19. PBMC from pediatric patients with acute COVID-19 disease display similar γδ T cell lymphopenia to that seen in adult patients. However, blood γδ T cells from children with the COVID-19-related multisystem inflammatory syndrome are not lymphodepleted, but they are differentiated as in healthy PBMC. These findings suggest that some virus-induced memory γδ T lymphocytes durably persist in the blood of adults and could subsequently infiltrate and recirculate in tumors.


Asunto(s)
COVID-19/inmunología , Linfocitos Infiltrantes de Tumor/inmunología , Neoplasias/inmunología , RNA-Seq , Receptores de Antígenos de Linfocitos T gamma-delta/inmunología , Subgrupos de Linfocitos T/inmunología , Subgrupos de Linfocitos T/metabolismo , Adulto , Líquido del Lavado Bronquioalveolar/inmunología , COVID-19/complicaciones , Diferenciación Celular , Niño , Neoplasias de Cabeza y Cuello/inmunología , Neoplasias de Cabeza y Cuello/virología , Herpesvirus Humano 4/aislamiento & purificación , Enfermedad de Hodgkin/inmunología , Enfermedad de Hodgkin/virología , Humanos , Pulmón/inmunología , Activación de Linfocitos , Recuento de Linfocitos , Linfocitos Infiltrantes de Tumor/metabolismo , Linfocitos Infiltrantes de Tumor/fisiología , Neoplasias/virología , Papillomaviridae/aislamiento & purificación , Índice de Severidad de la Enfermedad , Análisis de la Célula Individual , Síndrome de Respuesta Inflamatoria Sistémica/inmunología , Subgrupos de Linfocitos T/fisiología
8.
Oncoimmunology ; 10(1): 1939518, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34721945

RESUMEN

γδ T lymphocytes diverge from conventional T CD8 lymphocytes for ontogeny, homing, and antigen specificity, but whether their differentiation in tumors also deviates was unknown. Using innovative analyses of our original and ~150 published single-cell RNA sequencing datasets validated by phenotyping of human tumors and murine models, here we present the first high-resolution view of human γδ T cell differentiation in cancer. While γδ T lymphocytes prominently encompass TCRVγ9 cells more differentiated than T CD8 in healthy donor's blood, a different scenario is unveiled in tumors. Solid tumors and lymphomas are infiltrated by a majority of TCRVγnon9 γδ T cells which are quantitatively correlated and remarkably aligned with T CD8 for differentiation, exhaustion, gene expression profile, and response to immune checkpoint therapy. This cancer-wide association is critical for developing cancer immunotherapies.


Asunto(s)
Neoplasias , Transcriptoma , Animales , Linfocitos T CD8-positivos , Diferenciación Celular , Humanos , Linfocitos Infiltrantes de Tumor , Ratones , Neoplasias/genética , Receptores de Antígenos de Linfocitos T gamma-delta/genética , Subgrupos de Linfocitos T
9.
Mol Cancer Ther ; 20(12): 2433-2445, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34552006

RESUMEN

The PI3K pathway is highly active in human cancers. The four class I isoforms of PI3K are activated by distinct mechanisms leading to a common downstream signaling. Their downstream redundancy is thought to be responsible for treatment failures of PI3K inhibitors. We challenged this concept, by mapping the differential phosphoproteome evolution in response to PI3K inhibitors with different isoform-selectivity patterns in pancreatic cancer, a disease currently without effective therapy. In this cancer, the PI3K signal was shown to control cell proliferation. We compared the effects of LY294002 that inhibit with equal potency all class I isoenzymes and downstream mTOR with the action of inhibitors with higher isoform selectivity toward PI3Kα, PI3Kß, or PI3Kγ (namely, A66, TGX-221 and AS-252424). A bioinformatics global pathway analysis of phosphoproteomics data allowed us to identify common and specific signals activated by PI3K inhibitors supported by the biological data. AS-252424 was the most effective treatment and induced apoptotic pathway activation as well as the highest changes in global phosphorylation-regulated cell signal. However, AS-252424 treatment induced reactivation of Akt, therefore decreasing the treatment outcome on cell survival. Reversely, AS-252424 and A66 combination treatment prevented p-Akt reactivation and led to synergistic action in cell lines and patient organoids. The combination of clinically approved α-selective BYL-719 with γ-selective IPI-549 was more efficient than single-molecule treatment on xenograft growth. Mapping unique adaptive signaling responses to isoform-selective PI3K inhibition will help to design better combinative treatments that prevent the induction of selective compensatory signals.


Asunto(s)
Neoplasias Pancreáticas/tratamiento farmacológico , Inhibidores de las Quinasa Fosfoinosítidos-3/uso terapéutico , Proteómica/métodos , Animales , Línea Celular Tumoral , Resistencia a Medicamentos , Humanos , Ratones , Neoplasias Pancreáticas/patología , Inhibidores de las Quinasa Fosfoinosítidos-3/farmacología
10.
Front Immunol ; 12: 597651, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33732232

RESUMEN

High-definition transcriptomic studies through single-cell RNA sequencing (scRNA-Seq) have revealed the heterogeneity and functionality of the various microenvironments across numerous solid tumors. Those pioneer studies have highlighted different cellular signatures correlated with clinical response to immune checkpoint inhibitors. scRNA-Seq offers also a unique opportunity to unravel the intimate heterogeneity of the ecosystems across different lymphoma entities. In this review, we will first cover the basics and future developments of the technology, and we will discuss its input in the field of translational lymphoma research, from determination of cell-of-origin and functional diversity, to monitoring of anti-cancer targeted drugs response and toxicities, and how new improvements in both data collection and interpretation will further foster precision medicine in the upcoming years.


Asunto(s)
Perfilación de la Expresión Génica , Linfoma/genética , Análisis de la Célula Individual , Transcriptoma , Biomarcadores de Tumor , Terapia Combinada , Biología Computacional/métodos , Perfilación de la Expresión Génica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Linfoma/diagnóstico , Linfoma/patología , Linfoma/terapia , Anotación de Secuencia Molecular , Medicina de Precisión , Pronóstico , Análisis de la Célula Individual/métodos , Resultado del Tratamiento
11.
Redox Biol ; 40: 101861, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33548859

RESUMEN

Preeclampsia (PE) is a multifactorial pregnancy disease, characterized by new-onset gestational hypertension with (or without) proteinuria or end-organ failure, exclusively observed in humans. It is a leading cause of maternal morbidity affecting 3-7% of pregnant women worldwide. PE pathophysiology could result from abnormal placentation due to a defective trophoblastic invasion and an impaired remodeling of uterine spiral arteries, leading to a poor adaptation of utero-placental circulation. This would be associated with hypoxia/reoxygenation phenomena, oxygen gradient fluctuations, altered antioxidant capacity, oxidative stress, and reduced nitric oxide (NO) bioavailability. This results in part from the reaction of NO with the radical anion superoxide (O2•-), which produces peroxynitrite ONOO-, a powerful pro-oxidant and inflammatory agent. Another mechanism is the progressive inhibition of the placental endothelial nitric oxide synthase (eNOS) by oxidative stress, which results in eNOS uncoupling via several events such as a depletion of the eNOS substrate L-arginine due to increased arginase activity, an oxidation of the eNOS cofactor tetrahydrobiopterin (BH4), or eNOS post-translational modifications (for instance by S-glutathionylation). The uncoupling of eNOS triggers a switch of its activity from a NO-producing enzyme to a NADPH oxidase-like system generating O2•-, thereby potentiating ROS production and oxidative stress. Moreover, in PE placentas, eNOS could be post-translationally modified by lipid peroxidation-derived aldehydes such as 4-oxononenal (ONE) a highly bioreactive agent, able to inhibit eNOS activity and NO production. This review summarizes the dysfunction of placental eNOS evoked by oxidative stress and lipid peroxidation products, and the potential consequences on PE pathogenesis.


Asunto(s)
Óxido Nítrico Sintasa de Tipo III , Preeclampsia , Endotelio Vascular/metabolismo , Femenino , Humanos , Óxido Nítrico/metabolismo , Óxido Nítrico Sintasa de Tipo III/metabolismo , Estrés Oxidativo , Placenta/metabolismo , Preeclampsia/metabolismo , Embarazo
12.
JCI Insight ; 6(2)2021 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-33332284

RESUMEN

Tumor antigen-specific CD4 T cells accumulate at tumor sites, evoking their involvement in antitumor effector functions in situ. Contrary to CD8 cytotoxic T lymphocyte exhaustion, that of CD4 T cells remains poorly appreciated. Here, using phenotypic, transcriptomic, and functional approaches, we characterized CD4 T cell exhaustion in patients with head and neck, cervical, and ovarian cancer. We identified a CD4 tumor-infiltrating lymphocyte (TIL) population, defined by high PD-1 and CD39 expression, which contained high proportions of cytokine-producing cells, although the quantity of cytokines produced by these cells was low, evoking an exhausted state. Terminal exhaustion of CD4 TILs was instated regardless of TIM-3 expression, suggesting divergence with CD8 T cell exhaustion. scRNA-Seq and further phenotypic analyses uncovered similarities with the CD8 T cell exhaustion program. In particular, PD-1hiCD39+ CD4 TILs expressed the exhaustion transcription factor TOX and the chemokine CXCL13 and were tumor antigen specific. In vitro, PD-1 blockade enhanced CD4 TIL activation, as evidenced by increased CD154 expression and cytokine secretion, leading to improved dendritic cell maturation and consequently higher tumor-specific CD8 T cell proliferation. Our data identify exhausted CD4 TILs as players in responsiveness to immune checkpoint blockade.


Asunto(s)
Linfocitos Infiltrantes de Tumor/inmunología , Receptor de Muerte Celular Programada 1/antagonistas & inhibidores , Linfocitos T Colaboradores-Inductores/inmunología , Antígenos de Neoplasias/inmunología , Apirasa/inmunología , Linfocitos T CD8-positivos/inmunología , Femenino , Expresión Génica , Neoplasias de Cabeza y Cuello/genética , Neoplasias de Cabeza y Cuello/inmunología , Humanos , Tolerancia Inmunológica/genética , Inmunidad Celular/genética , Técnicas In Vitro , Activación de Linfocitos/genética , Cooperación Linfocítica/genética , Masculino , Neoplasias Ováricas/genética , Neoplasias Ováricas/inmunología , Receptor de Muerte Celular Programada 1/inmunología , ARN Mensajero/genética , ARN Mensajero/metabolismo , Escape del Tumor/genética , Neoplasias del Cuello Uterino/genética , Neoplasias del Cuello Uterino/inmunología
13.
Biomark Res ; 8(1): 72, 2020 Dec 09.
Artículo en Inglés | MEDLINE | ID: mdl-33298182

RESUMEN

BACKGROUND: Ibrutinib, an irreversible Bruton Tyrosine Kinase (BTK) inhibitor, has revolutionized Chronic Lymphocytic Leukemia (CLL) treatment, but resistances to ibrutinib have emerged, whether related or not to BTK mutations. Patterns of CLL evolution under ibrutinib therapy are well characterized for the leukemic cells but not for their microenvironment. METHODS: Here, we addressed this question at the single cell level of both transcriptome and immune-phenotype. The PBMCs from a CLL patient were monitored during ibrutinib treatment using Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-Seq) technology. RESULTS: This unveiled that the short clinical relapse of this patient driven by BTK mutation is associated with intraclonal heterogeneity in B leukemic cells and up-regulation of common signaling pathways induced by ibrutinib in both B leukemic cells and immune cells. This approach also pinpointed a subset of leukemic cells present before treatment and highly enriched during progression under ibrutinib. These latter exhibit an original gene signature including up-regulated BCR, MYC-activated, and other targetable pathways. Meanwhile, although ibrutinib differentially affected the exhaustion of T lymphocytes, this treatment enhanced the T cell cytotoxicity even during disease progression. CONCLUSIONS: These results could open new alternative of therapeutic strategies for ibrutinib-refractory CLL patients, based on immunotherapy or targeting B leukemic cells themselves.

14.
Cancer Immunol Res ; 8(7): 869-882, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32295784

RESUMEN

Although understanding of T-cell exhaustion is widely based on mouse models, its analysis in patients with cancer could provide clues indicating tumor sensitivity to immune checkpoint blockade (ICB). Data suggest a role for costimulatory pathways, particularly CD28, in exhausted T-cell responsiveness to PD-1/PD-L1 blockade. Here, we used single-cell transcriptomic, phenotypic, and functional approaches to dissect the relation between CD8+ T-cell exhaustion, CD28 costimulation, and tumor specificity in head and neck, cervical, and ovarian cancers. We found that memory tumor-specific CD8+ T cells, but not bystander cells, sequentially express immune checkpoints once they infiltrate tumors, leading, in situ, to a functionally exhausted population. Exhausted T cells were nonetheless endowed with effector and tumor residency potential but exhibited loss of the costimulatory receptor CD28 in comparison with their circulating memory counterparts. Accordingly, PD-1 inhibition improved proliferation of circulating tumor-specific CD8+ T cells and reversed functional exhaustion of specific T cells at tumor sites. In agreement with their tumor specificity, high infiltration of tumors by exhausted cells was predictive of response to therapy and survival in ICB-treated patients with head and neck cancer. Our results showed that PD-1 blockade-mediated proliferation/reinvigoration of circulating memory T cells and local reversion of exhaustion occur concurrently to control tumors.


Asunto(s)
Antineoplásicos Inmunológicos/farmacología , Antígenos CD28/inmunología , Linfocitos T CD8-positivos/inmunología , Neoplasias Glandulares y Epiteliales/tratamiento farmacológico , Neoplasias Glandulares y Epiteliales/inmunología , Receptor de Muerte Celular Programada 1/antagonistas & inhibidores , Animales , Antígenos CD28/metabolismo , Linfocitos T CD8-positivos/efectos de los fármacos , Proliferación Celular/fisiología , Femenino , Humanos , Activación de Linfocitos , Ratones , Ratones Endogámicos C57BL , Neoplasias Glandulares y Epiteliales/metabolismo , Neoplasias Glandulares y Epiteliales/patología , Análisis de la Célula Individual/métodos , Tasa de Supervivencia , Transcriptoma
15.
NAR Genom Bioinform ; 2(2): lqaa025, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33575582

RESUMEN

The development of single-cell transcriptomic technologies yields large datasets comprising multimodal informations, such as transcriptomes and immunophenotypes. Despite the current explosion of methods for pre-processing and integrating multimodal single-cell data, there is currently no user-friendly software to display easily and simultaneously both immunophenotype and transcriptome-based UMAP/t-SNE plots from the pre-processed data. Here, we introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of pre-processed multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and epitopes of functional maturation in human peripheral T lymphocytes. So this free and open-source algorithm constitutes a unique resource for biologists seeking for a user-friendly analytic tool for multimodal single cell datasets.

16.
Free Radic Biol Med ; 141: 416-425, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31323312

RESUMEN

Preeclampsia (PE) is a leading cause of pregnancy complications, affecting 3-7% of pregnant women worldwide. The pathophysiology of preeclampsia involves a redox imbalance, oxidative stress and a reduced nitric oxide (NO) bioavailability. The molecular and cellular mechanisms leading to the dysfunction of the placental endothelial NO synthase (eNOS) are not clarified. This study was designed to investigate whether aldehydes generated by lipid peroxidation products (LPP), may contribute to placental eNOS dysfunction in PE. The analysis of placentas from PE-affected patients and normal pregnancies, showed a significant increase in protein carbonyl content, indicative of oxidative stress-induced protein modification, as shown by the accumulation of acrolein, 4-hydroxynonenal (HNE), and 4-oxo-2(E)-nonenal (ONE) adducts in PE placentas. In contrast, the levels of these LPP-adducts were low in placentas from normal pregnancies. Immunofluorescence and confocal experiments pointed out a colocalization of eNOS with ONE-Lys adducts, whereas eNOS was not modified in normal placentas. LC-MS/MS analysis of recombinant eNOS preincubated with ONE, allowed to identify several ONE-modified Lys-containing peptides, confirming that eNOS may undergo post-translational modification by LPP. The preincubation of HTR-8/SVneo human trophoblasts (HTR8) with ONE, resulted in ONE-Lys modification of eNOS and a reduced generation of NO. ONE inhibited the migration of HTR8 trophoblasts in the wound closure model, and this was partly restored by the NO donor, NOC-18, which confirmed the important role of NO in the invasive potential of trophoblasts. In conclusion, placental eNOS is modified by ONE in PE placentas, which emphasizes the sensitivity of this protein to oxidative stress in the disturbed redox environment of preeclamptic pregnancies.


Asunto(s)
Óxido Nítrico Sintasa de Tipo III/genética , Óxido Nítrico/metabolismo , Preeclampsia/tratamiento farmacológico , Acroleína/antagonistas & inhibidores , Acroleína/metabolismo , Adulto , Aldehídos/antagonistas & inhibidores , Técnicas de Cultivo de Célula , Supervivencia Celular/efectos de los fármacos , Cromatografía Liquida , Femenino , Humanos , Peroxidación de Lípido/efectos de los fármacos , Óxido Nítrico/genética , Óxido Nítrico Sintasa de Tipo III/antagonistas & inhibidores , Estrés Oxidativo/efectos de los fármacos , Placenta/efectos de los fármacos , Placenta/patología , Preeclampsia/genética , Preeclampsia/patología , Embarazo , Espectrometría de Masas en Tándem , Trofoblastos/efectos de los fármacos , Trofoblastos/patología
17.
Nucleic Acids Res ; 47(21): e133, 2019 12 02.
Artículo en Inglés | MEDLINE | ID: mdl-31294801

RESUMEN

The momentum of scRNA-seq datasets prompts for simple and powerful tools exploring their meaningful signatures. Here we present Single-Cell_Signature_Explorer (https://sites.google.com/site/fredsoftwares/products/single-cell-signature-explorer), the first method for qualitative and high-throughput scoring of any gene set-based signature at the single cell level and its visualization using t-SNE or UMAP. By scanning datasets for single or combined signatures, it rapidly maps any multi-gene feature, exemplified here with signatures of cell lineages, biological hallmarks and metabolic pathways in large scRNAseq datasets of human PBMC, melanoma, lung cancer and adult testis.


Asunto(s)
ARN Citoplasmático Pequeño/genética , Análisis de Secuencia de ARN , Análisis de la Célula Individual , Programas Informáticos , Biología Computacional , Bases de Datos Genéticas , Humanos
18.
Proc Natl Acad Sci U S A ; 116(24): 11906-11915, 2019 06 11.
Artículo en Inglés | MEDLINE | ID: mdl-31118283

RESUMEN

γδ T lymphocytes represent ∼1% of human peripheral blood mononuclear cells and even more cells in most tissues of vertebrates. Although they have important anticancer functions, most current single-cell RNA sequencing (scRNA-seq) studies do not identify γδ T lymphocytes because their transcriptomes at the single-cell level are unknown. Here we show that high-resolution clustering of large scRNA-seq datasets and a combination of gene signatures allow the specific detection of human γδ T lymphocytes and identification of their T cell receptor (TCR)Vδ1 and TCRVδ2 subsets in large datasets from complex cell mixtures. In t-distributed stochastic neighbor embedding plots from blood and tumor samples, the few γδ T lymphocytes appear collectively embedded between cytotoxic CD8 T and NK cells. Their TCRVδ1 and TCRVδ2 subsets form close yet distinct subclusters, respectively neighboring NK and CD8 T cells because of expression of shared and distinct cytotoxic maturation genes. Similar pseudotime maturation trajectories of TCRVδ1 and TCRVδ2 γδ T lymphocytes were discovered, unveiling in both subsets an unattended pool of terminally differentiated effector memory cells with preserved proliferative capacity, a finding confirmed by in vitro proliferation assays. Overall, the single-cell transcriptomes of thousands of individual γδ T lymphocytes from different CMV+ and CMV- donors reflect cytotoxic maturation stages driven by the immunological history of donors. This landmark study establishes the rationale for identification, subtyping, and deep characterization of human γδ T lymphocytes in further scRNA-seq studies of complex tissues in physiological and disease conditions.


Asunto(s)
Receptores de Antígenos de Linfocitos T gamma-delta/inmunología , Subgrupos de Linfocitos T/inmunología , Adulto , Secuencia de Bases , Linfocitos T CD8-positivos/inmunología , Proliferación Celular/fisiología , Células Cultivadas , Humanos , Memoria Inmunológica/inmunología , Células Asesinas Naturales/inmunología , Leucocitos Mononucleares/inmunología , Análisis de Secuencia de ARN/métodos , Transcriptoma/inmunología
19.
Sci Rep ; 9(1): 4181, 2019 03 12.
Artículo en Inglés | MEDLINE | ID: mdl-30862887

RESUMEN

Discovery of protein modification sites relies on protein digestion by proteases and mass spectrometry (MS) identification of the modified peptides. Depending on proteases used and target protein sequence, this method yields highly variable coverage of modification sites. We introduce PTMselect, a digestion-simulating software which tailors the optimal set of proteases for discovery of global or targeted modification from any single or multiple proteins.


Asunto(s)
Procesamiento Proteico-Postraduccional , Programas Informáticos , Espectrometría de Masas en Tándem , Algoritmos , Animales , Cromatografía Liquida , Ratones , Péptidos/metabolismo
20.
Saudi Pharm J ; 27(1): 56-65, 2019 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-30662307

RESUMEN

The actinobacterium strain ABH26 closely related to Saccharothrix xinjiangensis, isolated from an Algerian Saharan soil sample, exhibited highly antagonist activity against Gram-positive bacteria, yeasts and filamentous fungi. Its ability to produce antimicrobial compounds was investigated using several solid culture media. The highest antimicrobial activity was obtained on Bennett medium. The antibiotics secreted by strain ABH26 on Bennett medium were extracted by methanol and purified by reverse-phase HPLC using a C18 column. The chemical structures of the compounds were determined after spectroscopic (1H NMR, 13C NMR, 1H-1H COSY and 1H-13C HMBC spectra), and spectrometric (mass spectrum) analyses. Two new cyanogriside antibiotics named cyanogriside I (1) and cyanogriside J (2), were characterized along with three known caerulomycins, caerulomycin A (3), caerulomycin F (4) and caerulomycinonitrile (5). This is the first report of cyanogrisides and caerulomycins production by a member of the Saccharothrix genus. The minimum inhibitory concentrations (MIC) of these antibiotics were determined against pathogenic microorganisms.

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