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1.
Cell ; 184(4): 1047-1063.e23, 2021 02 18.
Artículo en Inglés | MEDLINE | ID: mdl-33539780

RESUMEN

DNA has not been utilized to record temporal information, although DNA has been used to record biological information and to compute mathematical problems. Here, we found that indel generation by Cas9 and guide RNA can occur at steady rates, in contrast to typical dynamic biological reactions, and the accumulated indel frequency can be a function of time. By measuring indel frequencies, we developed a method for recording and measuring absolute time periods over hours to weeks in mammalian cells. These time-recordings were conducted in several cell types, with different promoters and delivery vectors for Cas9, and in both cultured cells and cells of living mice. As applications, we recorded the duration of chemical exposure and the lengths of elapsed time since the onset of biological events (e.g., heat exposure and inflammation). We propose that our systems could serve as synthetic "DNA clocks."


Asunto(s)
Proteína 9 Asociada a CRISPR/metabolismo , Animales , Secuencia de Bases , Microambiente Celular , Simulación por Computador , Células HEK293 , Semivida , Humanos , Mutación INDEL/genética , Inflamación/patología , Integrasas/metabolismo , Masculino , Ratones Desnudos , Regiones Promotoras Genéticas/genética , ARN Guía de Kinetoplastida/genética , Reproducibilidad de los Resultados , Factores de Tiempo
2.
Annu Rev Biochem ; 89: 529-555, 2020 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-32097570

RESUMEN

Protein folding in the cell is mediated by an extensive network of >1,000 chaperones, quality control factors, and trafficking mechanisms collectively termed the proteostasis network. While the components and organization of this network are generally well established, our understanding of how protein-folding problems are identified, how the network components integrate to successfully address challenges, and what types of biophysical issues each proteostasis network component is capable of addressing remains immature. We describe a chemical biology-informed framework for studying cellular proteostasis that relies on selection of interesting protein-folding problems and precise researcher control of proteostasis network composition and activities. By combining these methods with multifaceted strategies to monitor protein folding, degradation, trafficking, and aggregation in cells, researchers continue to rapidly generate new insights into cellular proteostasis.


Asunto(s)
Chaperonas Moleculares/genética , Técnicas de Sonda Molecular , Proteoma/genética , Deficiencias en la Proteostasis/genética , Proteostasis/genética , Animales , Sistemas CRISPR-Cas , Regulación de la Expresión Génica , Semivida , Respuesta al Choque Térmico/efectos de los fármacos , Humanos , Chaperonas Moleculares/metabolismo , Agregado de Proteínas , Ingeniería de Proteínas/métodos , Pliegue de Proteína/efectos de los fármacos , Transporte de Proteínas/efectos de los fármacos , Proteoma/química , Proteoma/metabolismo , Proteostasis/efectos de los fármacos , Deficiencias en la Proteostasis/metabolismo , Deficiencias en la Proteostasis/patología , Transducción de Señal , Bibliotecas de Moléculas Pequeñas/síntesis química , Bibliotecas de Moléculas Pequeñas/farmacología , Respuesta de Proteína Desplegada/efectos de los fármacos
3.
Nat Immunol ; 22(6): 746-756, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-34031618

RESUMEN

T cell exhaustion presents one of the major hurdles to cancer immunotherapy. Among exhausted CD8+ tumor-infiltrating lymphocytes, the terminally exhausted subset contributes directly to tumor cell killing owing to its cytotoxic effector function. However, this subset does not respond to immune checkpoint blockades and is difficult to be reinvigorated with restored proliferative capacity. Here, we show that a half-life-extended interleukin-10-Fc fusion protein directly and potently enhanced expansion and effector function of terminally exhausted CD8+ tumor-infiltrating lymphocytes by promoting oxidative phosphorylation, a process that was independent of the progenitor exhausted T cells. Interleukin-10-Fc was a safe and highly efficient metabolic intervention that synergized with adoptive T cell transfer immunotherapy, leading to eradication of established solid tumors and durable cures in the majority of treated mice. These findings show that metabolic reprogramming by upregulating mitochondrial pyruvate carrier-dependent oxidative phosphorylation can revitalize terminally exhausted T cells and enhance the response to cancer immunotherapy.


Asunto(s)
Inmunoterapia Adoptiva/métodos , Interleucina-10/farmacología , Neoplasias/terapia , Fosforilación Oxidativa/efectos de los fármacos , Linfocitos T Citotóxicos/efectos de los fármacos , Animales , Proteínas de Transporte de Anión/genética , Proteínas de Transporte de Anión/metabolismo , Línea Celular Tumoral , Terapia Combinada/métodos , Modelos Animales de Enfermedad , Sinergismo Farmacológico , Femenino , Células HEK293 , Semivida , Humanos , Inhibidores de Puntos de Control Inmunológico/farmacología , Inhibidores de Puntos de Control Inmunológico/uso terapéutico , Fragmentos Fc de Inmunoglobulinas/farmacología , Fragmentos Fc de Inmunoglobulinas/uso terapéutico , Interleucina-10/uso terapéutico , Ratones , Ratones Transgénicos , Mitocondrias/efectos de los fármacos , Mitocondrias/metabolismo , Proteínas de Transporte de Membrana Mitocondrial/genética , Proteínas de Transporte de Membrana Mitocondrial/metabolismo , Transportadores de Ácidos Monocarboxílicos/genética , Transportadores de Ácidos Monocarboxílicos/metabolismo , Neoplasias/inmunología , Neoplasias/patología , Receptores Quiméricos de Antígenos/inmunología , Receptores Quiméricos de Antígenos/metabolismo , Receptores de Interleucina-10/metabolismo , Proteínas Recombinantes de Fusión/farmacología , Proteínas Recombinantes de Fusión/uso terapéutico , Transducción de Señal/efectos de los fármacos , Transducción de Señal/inmunología , Linfocitos T Citotóxicos/citología , Linfocitos T Citotóxicos/inmunología , Linfocitos T Citotóxicos/metabolismo
4.
Cell ; 174(1): 231-244.e12, 2018 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-29804834

RESUMEN

The acetyltransferases CBP and p300 are multifunctional transcriptional co-activators. Here, we combined quantitative proteomics with CBP/p300-specific catalytic inhibitors, bromodomain inhibitor, and gene knockout to reveal a comprehensive map of regulated acetylation sites and their dynamic turnover rates. CBP/p300 acetylates thousands of sites, including signature histone sites and a multitude of sites on signaling effectors and enhancer-associated transcriptional regulators. Time-resolved acetylome analyses identified a subset of CBP/p300-regulated sites with very rapid (<30 min) acetylation turnover, revealing a dynamic balance between acetylation and deacetylation. Quantification of acetylation, mRNA, and protein abundance after CBP/p300 inhibition reveals a kinetically competent network of gene expression that strictly depends on CBP/p300-catalyzed rapid acetylation. Collectively, our in-depth acetylome analyses reveal systems attributes of CBP/p300 targets, and the resource dataset provides a framework for investigating CBP/p300 functions and for understanding the impact of small-molecule inhibitors targeting its catalytic and bromodomain activities.


Asunto(s)
Acetiltransferasas/metabolismo , Factores de Transcripción p300-CBP/metabolismo , Acetilación/efectos de los fármacos , Acetiltransferasas/antagonistas & inhibidores , Animales , Línea Celular , Técnicas de Inactivación de Genes , Semivida , Compuestos Heterocíclicos de 4 o más Anillos/química , Compuestos Heterocíclicos de 4 o más Anillos/metabolismo , Compuestos Heterocíclicos de 4 o más Anillos/farmacología , Histonas/metabolismo , Humanos , Marcaje Isotópico , Cinética , Espectrometría de Masas , Ratones , Péptidos/análisis , Receptores de Hidrocarburo de Aril/genética , Receptores de Hidrocarburo de Aril/metabolismo , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Transducción de Señal , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/metabolismo , Bibliotecas de Moléculas Pequeñas/farmacología , Transcriptoma/efectos de los fármacos , Factores de Transcripción p300-CBP/antagonistas & inhibidores , Factores de Transcripción p300-CBP/genética
5.
Cell ; 164(4): 757-69, 2016 Feb 11.
Artículo en Inglés | MEDLINE | ID: mdl-26871635

RESUMEN

Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remain controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ∼ 590 nt, and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs.


Asunto(s)
Biosíntesis de Proteínas , Ribosomas/metabolismo , Saccharomyces cerevisiae/metabolismo , Semivida , Degradación de ARNm Mediada por Codón sin Sentido , Polirribosomas/metabolismo , ARN Mensajero/metabolismo , Saccharomyces cerevisiae/citología
6.
Cell ; 167(1): 122-132.e9, 2016 Sep 22.
Artículo en Inglés | MEDLINE | ID: mdl-27641505

RESUMEN

A major determinant of mRNA half-life is the codon-dependent rate of translational elongation. How the processes of translational elongation and mRNA decay communicate is unclear. Here, we establish that the DEAD-box protein Dhh1p is a sensor of codon optimality that targets an mRNA for decay. First, we find mRNAs whose translation elongation rate is slowed by inclusion of non-optimal codons are specifically degraded in a Dhh1p-dependent manner. Biochemical experiments show Dhh1p is preferentially associated with mRNAs with suboptimal codon choice. We find these effects on mRNA decay are sensitive to the number of slow-moving ribosomes on an mRNA. Moreover, we find Dhh1p overexpression leads to the accumulation of ribosomes specifically on mRNAs (and even codons) of low codon optimality. Lastly, Dhh1p physically interacts with ribosomes in vivo. Together, these data argue that Dhh1p is a sensor for ribosome speed, targeting an mRNA for repression and subsequent decay.


Asunto(s)
Codón/metabolismo , ARN Helicasas DEAD-box/metabolismo , Biosíntesis de Proteínas , Estabilidad del ARN , ARN Mensajero/metabolismo , Ribosomas/metabolismo , Codón/genética , ARN Helicasas DEAD-box/genética , Semivida
7.
Nat Rev Mol Cell Biol ; 18(2): 102-114, 2017 02.
Artículo en Inglés | MEDLINE | ID: mdl-27847391

RESUMEN

A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.


Asunto(s)
MicroARNs , Procesamiento Postranscripcional del ARN , Empalme del ARN , Regulación de la Expresión Génica , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Variación Genética , Semivida , Humanos , Poliadenilación , Precursores del ARN/genética , Estabilidad del ARN
8.
Cell ; 156(4): 812-24, 2014 Feb 13.
Artículo en Inglés | MEDLINE | ID: mdl-24529382

RESUMEN

We measured half-lives of 21,248 mRNA 3' isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A)-binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilizing and stabilizing elements are linked to the propensity of the poly(A) tail to engage in double-stranded structures. Isoforms engineered to fold into 3' stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at 3' ends are a major determinant of mRNA stability.


Asunto(s)
Estabilidad del ARN , Saccharomyces cerevisiae/genética , Secuencia de Bases , Genoma Fúngico , Estudio de Asociación del Genoma Completo , Semivida , Motivos de Nucleótidos , ARN de Hongos/química , ARN de Hongos/metabolismo , ARN Mensajero/química , ARN Mensajero/metabolismo , Saccharomyces cerevisiae/metabolismo , Alineación de Secuencia
9.
Nature ; 622(7984): 802-809, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-37853123

RESUMEN

Ketamine, an N-methyl-D-aspartate receptor (NMDAR) antagonist1, has revolutionized the treatment of depression because of its potent, rapid and sustained antidepressant effects2-4. Although the elimination half-life of ketamine is only 13 min in mice5, its antidepressant activities can last for at least 24 h6-9. This large discrepancy poses an interesting basic biological question and has strong clinical implications. Here we demonstrate that after a single systemic injection, ketamine continues to suppress burst firing and block NMDARs in the lateral habenula (LHb) for up to 24 h. This long inhibition of NMDARs is not due to endocytosis but depends on the use-dependent trapping of ketamine in NMDARs. The rate of untrapping is regulated by neural activity. Harnessing the dynamic equilibrium of ketamine-NMDAR interactions by activating the LHb and opening local NMDARs at different plasma ketamine concentrations, we were able to either shorten or prolong the antidepressant effects of ketamine in vivo. These results provide new insights into the causal mechanisms of the sustained antidepressant effects of ketamine. The ability to modulate the duration of ketamine action based on the biophysical properties of ketamine-NMDAR interactions opens up new opportunities for the therapeutic use of ketamine.


Asunto(s)
Antidepresivos , Depresión , Habénula , Ketamina , Receptores de N-Metil-D-Aspartato , Animales , Ratones , Antidepresivos/administración & dosificación , Antidepresivos/metabolismo , Antidepresivos/farmacocinética , Antidepresivos/farmacología , Depresión/tratamiento farmacológico , Depresión/metabolismo , Habénula/efectos de los fármacos , Habénula/metabolismo , Semivida , Ketamina/administración & dosificación , Ketamina/metabolismo , Ketamina/farmacocinética , Ketamina/farmacología , Neuronas/fisiología , Receptores de N-Metil-D-Aspartato/antagonistas & inhibidores , Receptores de N-Metil-D-Aspartato/metabolismo , Factores de Tiempo , Unión Proteica
10.
Nature ; 621(7978): 396-403, 2023 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37130545

RESUMEN

Messenger RNA (mRNA) vaccines are being used to combat the spread of COVID-19 (refs. 1-3), but they still exhibit critical limitations caused by mRNA instability and degradation, which are major obstacles for the storage, distribution and efficacy of the vaccine products4. Increasing secondary structure lengthens mRNA half-life, which, together with optimal codons, improves protein expression5. Therefore, a principled mRNA design algorithm must optimize both structural stability and codon usage. However, owing to synonymous codons, the mRNA design space is prohibitively large-for example, there are around 2.4 × 10632 candidate mRNA sequences for the SARS-CoV-2 spike protein. This poses insurmountable computational challenges. Here we provide a simple and unexpected solution using the classical concept of lattice parsing in computational linguistics, where finding the optimal mRNA sequence is analogous to identifying the most likely sentence among similar-sounding alternatives6. Our algorithm LinearDesign finds an optimal mRNA design for the spike protein in just 11 minutes, and can concurrently optimize stability and codon usage. LinearDesign substantially improves mRNA half-life and protein expression, and profoundly increases antibody titre by up to 128 times in mice compared to the codon-optimization benchmark on mRNA vaccines for COVID-19 and varicella-zoster virus. This result reveals the great potential of principled mRNA design and enables the exploration of previously unreachable but highly stable and efficient designs. Our work is a timely tool for vaccines and other mRNA-based medicines encoding therapeutic proteins such as monoclonal antibodies and anti-cancer drugs7,8.


Asunto(s)
Algoritmos , Vacunas contra la COVID-19 , COVID-19 , Estabilidad del ARN , ARN Mensajero , SARS-CoV-2 , Vacunas de ARNm , Animales , Humanos , Ratones , Codón/genética , COVID-19/genética , COVID-19/inmunología , COVID-19/prevención & control , Vacunas contra la COVID-19/química , Vacunas contra la COVID-19/genética , Vacunas contra la COVID-19/inmunología , Semivida , Herpesvirus Humano 3/genética , Herpesvirus Humano 3/inmunología , Vacunas de ARNm/química , Vacunas de ARNm/genética , Vacunas de ARNm/inmunología , Estabilidad del ARN/genética , Estabilidad del ARN/inmunología , ARN Mensajero/química , ARN Mensajero/genética , ARN Mensajero/inmunología , ARN Mensajero/metabolismo , SARS-CoV-2/genética , SARS-CoV-2/inmunología
11.
Nature ; 590(7846): 468-472, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33505020

RESUMEN

Neutralizing antibody function provides a foundation for the efficacy of vaccines and therapies1-3. Here, using a robust in vitro Ebola virus (EBOV) pseudo-particle infection assay and a well-defined set of solid-phase assays, we describe a wide spectrum of antibody responses in a cohort of healthy survivors of the Sierra Leone EBOV outbreak of 2013-2016. Pseudo-particle virus-neutralizing antibodies correlated with total anti-EBOV reactivity and neutralizing antibodies against live EBOV. Variant EBOV glycoproteins (1995 and 2014 strains) were similarly neutralized. During longitudinal follow-up, antibody responses fluctuated in a 'decay-stimulation-decay' pattern that suggests de novo restimulation by EBOV antigens after recovery. A pharmacodynamic model of antibody reactivity identified a decay half-life of 77-100 days and a doubling time of 46-86 days in a high proportion of survivors. The highest antibody reactivity was observed around 200 days after an individual had recovered. The model suggests that EBOV antibody reactivity declines over 0.5-2 years after recovery. In a high proportion of healthy survivors, antibody responses undergo rapid restimulation. Vigilant follow-up of survivors and possible elective de novo antigenic stimulation by vaccine immunization should be considered in order to prevent EBOV viral recrudescence in recovering individuals and thereby to mitigate the potential risk of reseeding an outbreak.


Asunto(s)
Anticuerpos Antivirales/sangre , Anticuerpos Antivirales/inmunología , Convalecencia , Ebolavirus/inmunología , Fiebre Hemorrágica Ebola/inmunología , Sobrevivientes , Adolescente , Adulto , África Occidental/epidemiología , Anticuerpos Neutralizantes/sangre , Anticuerpos Neutralizantes/inmunología , Estudios de Cohortes , Femenino , Semivida , Fiebre Hemorrágica Ebola/sangre , Fiebre Hemorrágica Ebola/epidemiología , Fiebre Hemorrágica Ebola/prevención & control , Humanos , Masculino , Persona de Mediana Edad , Pruebas de Neutralización , Factores de Tiempo , Viremia/sangre , Viremia/inmunología , Adulto Joven
12.
Nature ; 591(7849): 312-316, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33442060

RESUMEN

Endogenous retroviruses (ERVs) are abundant and heterogenous groups of integrated retroviral sequences that affect genome regulation and cell physiology throughout their RNA-centred life cycle1. Failure to repress ERVs is associated with cancer, infertility, senescence and neurodegenerative diseases2,3. Here, using an unbiased genome-scale CRISPR knockout screen in mouse embryonic stem cells, we identify m6A RNA methylation as a way to restrict ERVs. Methylation of ERV mRNAs is catalysed by the complex of methyltransferase-like METTL3-METTL144 proteins, and we found that depletion of METTL3-METTL14, along with their accessory subunits WTAP and ZC3H13, led to increased mRNA abundance of intracisternal A-particles (IAPs) and related ERVK elements specifically, by targeting their 5' untranslated region. Using controlled auxin-dependent degradation of the METTL3-METTL14 enzymatic complex, we showed that IAP mRNA and protein abundance is dynamically and inversely correlated with m6A catalysis. By monitoring chromatin states and mRNA stability upon METTL3-METTL14 double depletion, we found that m6A methylation mainly acts by reducing the half-life of IAP mRNA, and this occurs by the recruitment of the YTHDF family of m6A reader proteins5. Together, our results indicate that RNA methylation provides a protective effect in maintaining cellular integrity by clearing reactive ERV-derived RNA species, which may be especially important when transcriptional silencing is less stringent.


Asunto(s)
Retrovirus Endógenos/genética , Genes de Partícula A Intracisternal/genética , Metilación , ARN Mensajero/genética , ARN Mensajero/metabolismo , Animales , Sistemas CRISPR-Cas/genética , Proteínas de Ciclo Celular/metabolismo , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , Técnicas de Inactivación de Genes , Semivida , Metiltransferasas/metabolismo , Ratones , Células Madre Embrionarias de Ratones , Proteínas Nucleares/metabolismo , Factores de Empalme de ARN/metabolismo , Estabilidad del ARN , ARN Mensajero/química , Proteínas de Unión al ARN/metabolismo
13.
Nature ; 589(7843): 597-602, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33361818

RESUMEN

Isoprenoids are vital for all organisms, in which they maintain membrane stability and support core functions such as respiration1. IspH, an enzyme in the methyl erythritol phosphate pathway of isoprenoid synthesis, is essential for Gram-negative bacteria, mycobacteria and apicomplexans2,3. Its substrate, (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), is not produced in metazoans, and in humans and other primates it activates cytotoxic Vγ9Vδ2 T cells at extremely low concentrations4-6. Here we describe a class of IspH inhibitors and refine their potency to nanomolar levels through structure-guided analogue design. After modification of these compounds into prodrugs for delivery into bacteria, we show that they kill clinical isolates of several multidrug-resistant bacteria-including those from the genera Acinetobacter, Pseudomonas, Klebsiella, Enterobacter, Vibrio, Shigella, Salmonella, Yersinia, Mycobacterium and Bacillus-yet are relatively non-toxic to mammalian cells. Proteomic analysis reveals that bacteria treated with these prodrugs resemble those after conditional IspH knockdown. Notably, these prodrugs also induce the expansion and activation of human Vγ9Vδ2 T cells in a humanized mouse model of bacterial infection. The prodrugs we describe here synergize the direct killing of bacteria with a simultaneous rapid immune response by cytotoxic γδ T cells, which may limit the increase of antibiotic-resistant bacterial populations.


Asunto(s)
Diseño de Fármacos , Inhibidores Enzimáticos/farmacología , Proteínas de Escherichia coli/antagonistas & inhibidores , Bacterias Gramnegativas/efectos de los fármacos , Bacterias Gramnegativas/inmunología , Activación de Linfocitos/efectos de los fármacos , Viabilidad Microbiana/efectos de los fármacos , Oxidorreductasas/antagonistas & inhibidores , Linfocitos T Citotóxicos/efectos de los fármacos , Animales , Farmacorresistencia Microbiana , Resistencia a Múltiples Medicamentos , Inhibidores Enzimáticos/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Femenino , Semivida , Humanos , Leucocitos Mononucleares/efectos de los fármacos , Leucocitos Mononucleares/inmunología , Leucocitos Mononucleares/microbiología , Masculino , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Pruebas de Sensibilidad Microbiana , Simulación del Acoplamiento Molecular , Oxidorreductasas/deficiencia , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Profármacos/farmacocinética , Profármacos/farmacología , Especificidad por Sustrato , Porcinos/sangre , Linfocitos T Citotóxicos/inmunología
14.
Proc Natl Acad Sci U S A ; 121(14): e2308814121, 2024 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-38527194

RESUMEN

RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in posttranscriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life in Salmonella in early stationary phase is less than 1 min, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with cross-linking and immunoprecipitation followed by RNA sequencing (CLIP-seq) revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3' untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for ProQ in the oxidative stress response. Our findings provide insights into posttranscriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.


Asunto(s)
Perfilación de la Expresión Génica , Rifampin , Teorema de Bayes , Semivida , Transcriptoma , Proteínas de Unión al ARN/metabolismo , ARN/metabolismo , Salmonella/metabolismo , Estabilidad del ARN/genética
15.
N Engl J Med ; 388(8): 694-705, 2023 02 23.
Artículo en Inglés | MEDLINE | ID: mdl-36812433

RESUMEN

BACKGROUND: Valoctocogene roxaparvovec delivers a B-domain-deleted factor VIII coding sequence with an adeno-associated virus vector to prevent bleeding in persons with severe hemophilia A. The findings of a phase 3 study of the efficacy and safety of valoctocogene roxaparvovec therapy evaluated after 52 weeks in men with severe hemophilia A have been published previously. METHODS: We conducted an open-label, single-group, multicenter, phase 3 trial in which 134 men with severe hemophilia A who were receiving factor VIII prophylaxis received a single infusion of 6×1013 vector genomes of valoctocogene roxaparvovec per kilogram of body weight. The primary end point was the change from baseline in the annualized rate of treated bleeding events at week 104 after receipt of the infusion. The pharmacokinetics of valoctocogene roxaparvovec were modeled to estimate the bleeding risk relative to the activity of transgene-derived factor VIII. RESULTS: At week 104, a total of 132 participants, including 112 with data that were prospectively collected at baseline, remained in the study. The mean annualized treated bleeding rate decreased by 84.5% from baseline (P<0.001) among the participants. From week 76 onward, the trajectory of the transgene-derived factor VIII activity showed first-order elimination kinetics; the model-estimated typical half-life of the transgene-derived factor VIII production system was 123 weeks (95% confidence interval, 84 to 232). The risk of joint bleeding was estimated among the trial participants; at a transgene-derived factor VIII level of 5 IU per deciliter measured with chromogenic assay, we expected that participants would have 1.0 episode of joint bleeding per year. At 2 years postinfusion, no new safety signals had emerged and no new serious adverse events related to treatment had occurred. CONCLUSIONS: The study data show the durability of factor VIII activity and bleeding reduction and the safety profile of valoctocogene roxaparvovec at least 2 years after the gene transfer. Models of the risk of joint bleeding suggest that the relationship between transgene-derived factor VIII activity and bleeding episodes is similar to that reported with the use of epidemiologic data for persons with mild-to-moderate hemophilia A. (Funded by BioMarin Pharmaceutical; GENEr8-1 ClinicalTrials.gov number, NCT03370913.).


Asunto(s)
Factor VIII , Hemofilia A , Humanos , Masculino , Factor VIII/uso terapéutico , Técnicas de Transferencia de Gen , Semivida , Hemofilia A/complicaciones , Hemofilia A/tratamiento farmacológico , Hemorragia/etiología , Hemorragia/prevención & control , Proteínas Recombinantes de Fusión/uso terapéutico
16.
N Engl J Med ; 388(4): 310-318, 2023 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-36720133

RESUMEN

BACKGROUND: Efanesoctocog alfa provides high sustained factor VIII activity by overcoming the von Willebrand factor-imposed half-life ceiling. The efficacy, safety, and pharmacokinetics of efanesoctocog alfa for prophylaxis and treatment of bleeding episodes in previously treated patients with severe hemophilia A are unclear. METHODS: We conducted a phase 3 study involving patients 12 years of age or older with severe hemophilia A. In group A, patients received once-weekly prophylaxis with efanesoctocog alfa (50 IU per kilogram of body weight) for 52 weeks. In group B, patients received on-demand treatment with efanesoctocog alfa for 26 weeks, followed by once-weekly prophylaxis with efanesoctocog alfa for 26 weeks. The primary end point was the mean annualized bleeding rate in group A; the key secondary end point was an intrapatient comparison of the annualized bleeding rate during prophylaxis in group A with the rate during prestudy factor VIII prophylaxis. Additional end points included treatment of bleeding episodes, safety, pharmacokinetics, and changes in physical health, pain, and joint health. RESULTS: In group A (133 patients), the median annualized bleeding rate was 0 (interquartile range, 0 to 1.04), and the estimated mean annualized bleeding rate was 0.71 (95% confidence interval [CI], 0.52 to 0.97). The mean annualized bleeding rate decreased from 2.96 (95% CI, 2.00 to 4.37) to 0.69 (95% CI, 0.43 to 1.11), a finding that showed superiority over prestudy factor VIII prophylaxis (P<0.001). A total of 26 patients were enrolled in group B. In the overall population, nearly all bleeding episodes (97%) resolved with one injection of efanesoctocog alfa. Weekly prophylaxis with efanesoctocog alfa provided mean factor VIII activity of more than 40 IU per deciliter for the majority of the week and of 15 IU per deciliter at day 7. Prophylaxis with efanesoctocog alfa for 52 weeks (group A) improved physical health (P<0.001), pain intensity (P = 0.03), and joint health (P = 0.01). In the overall study population, efanesoctocog alfa had an acceptable side-effect profile, and the development of inhibitors to factor VIII was not detected. CONCLUSIONS: In patients with severe hemophilia A, once-weekly efanesoctocog alfa provided superior bleeding prevention to prestudy prophylaxis, normal to near-normal factor VIII activity, and improvements in physical health, pain, and joint health. (Funded by Sanofi and Sobi; XTEND-1 ClinicalTrials.gov number, NCT04161495.).


Asunto(s)
Coagulantes , Factor VIII , Hemofilia A , Hemorragia , Humanos , Esquema de Medicación , Semivida , Hemofilia A/complicaciones , Hemofilia A/tratamiento farmacológico , Hemorragia/tratamiento farmacológico , Hemorragia/etiología , Hemorragia/prevención & control , Factor de von Willebrand/administración & dosificación , Factor de von Willebrand/uso terapéutico , Quimioprevención , Factor VIII/administración & dosificación , Factor VIII/uso terapéutico , Coagulantes/administración & dosificación , Coagulantes/uso terapéutico , Proteínas Recombinantes de Fusión/administración & dosificación , Proteínas Recombinantes de Fusión/uso terapéutico
17.
Hum Mol Genet ; 32(9): 1552-1564, 2023 04 20.
Artículo en Inglés | MEDLINE | ID: mdl-36611016

RESUMEN

Congenital myasthenic syndrome (CMS) is a heterogeneous condition associated with 34 different genes, including SLC5A7, which encodes the high-affinity choline transporter 1 (CHT1). CHT1 is expressed in presynaptic neurons of the neuromuscular junction where it uses the inward sodium gradient to reuptake choline. Biallelic CHT1 mutations often lead to neonatal lethality, and less commonly to non-lethal motor weakness and developmental delays. Here, we report detailed biochemical characterization of two novel mutations in CHT1, p.I294T and p.D349N, which we identified in an 11-year-old patient with a history of neonatal respiratory distress, and subsequent hypotonia and global developmental delay. Heterologous expression of each CHT1 mutant in human embryonic kidney cells showed two different mechanisms of reduced protein function. The p.I294T CHT1 mutant transporter function was detectable, but its abundance and half-life were significantly reduced. In contrast, the p.D349N CHT1 mutant was abundantly expressed at the cell membrane, but transporter function was absent. The residual function of the p.I294T CHT1 mutant may explain the non-lethal form of CMS in this patient, and the divergent mechanisms of reduced CHT1 function that we identified may guide future functional studies of the CHT1 myasthenic syndrome. Based on these in vitro studies that provided a diagnosis, treatment with cholinesterase inhibitor together with physical and occupational therapy significantly improved the patient's strength and quality of life.


Asunto(s)
Proteínas Mutantes , Mutación , Síndromes Miasténicos Congénitos , Simportadores , Síndromes Miasténicos Congénitos/tratamiento farmacológico , Síndromes Miasténicos Congénitos/genética , Síndromes Miasténicos Congénitos/metabolismo , Síndromes Miasténicos Congénitos/rehabilitación , Humanos , Masculino , Niño , Células HEK293 , Proteínas Mutantes/química , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Semivida , Membrana Celular/metabolismo , Transporte de Proteínas , Estaurosporina/farmacología , Bromuro de Piridostigmina/uso terapéutico , Calidad de Vida , Simportadores/química , Simportadores/genética , Simportadores/metabolismo
18.
J Cell Sci ; 136(15)2023 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-37565427

RESUMEN

Human serum albumin (HSA) has a long circulatory half-life owing, in part, to interaction with the neonatal Fc receptor (FcRn or FCGRT) in acidic endosomes and recycling of internalised albumin. Vascular endothelial and innate immune cells are considered the most relevant cells for FcRn-mediated albumin homeostasis in vivo. However, little is known about endocytic trafficking of FcRn-albumin complexes in primary human endothelial cells. To investigate FcRn-albumin trafficking in physiologically relevant endothelial cells, we generated primary human vascular endothelial cell lines from blood endothelial precursors, known as blood outgrowth endothelial cells (BOECs). We mapped the endosomal system in BOECs and showed that BOECs efficiently internalise fluorescently labelled HSA predominantly by fluid-phase macropinocytosis. Pulse-chase studies revealed that intracellular HSA molecules co-localised with FcRn in acidic endosomal structures and that the wildtype HSA, but not the non-FcRn-binding HSAH464Q mutant, was excluded from late endosomes and/or lysosomes. Live imaging revealed that HSA is partitioned into FcRn-positive tubules derived from maturing macropinosomes, which are then transported towards the plasma membrane. These findings identify the FcRn-albumin trafficking pathway in primary vascular endothelial cells, relevant to albumin homeostasis.


Asunto(s)
Albúminas , Células Endoteliales , Humanos , Albúminas/metabolismo , Línea Celular , Endosomas/metabolismo , Células Endoteliales/metabolismo , Semivida , Antígenos de Histocompatibilidad Clase I/metabolismo
19.
RNA ; 29(8): 1243-1254, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37197826

RESUMEN

Following transcription, tRNAs undergo a series of processing and modification events to become functional adaptors in protein synthesis. Eukaryotes have also evolved intracellular transport systems whereby nucleus-encoded tRNAs may travel out and into the nucleus. In trypanosomes, nearly all tRNAs are also imported from the cytoplasm into the mitochondrion, which lacks tRNA genes. Differential subcellular localization of the cytoplasmic splicing machinery and a nuclear enzyme responsible for queuosine modification at the anticodon "wobble" position appear to be important quality control mechanisms for tRNATyr, the only intron-containing tRNA in T. brucei Since tRNA-guanine transglycosylase (TGT), the enzyme responsible for Q formation, cannot act on an intron-containing tRNA, retrograde nuclear transport is an essential step in maturation. Unlike maturation/processing pathways, the general mechanisms of tRNA stabilization and degradation in T. brucei are poorly understood. Using a combination of cellular and molecular approaches, we show that tRNATyr has an unusually short half-life. tRNATyr, and in addition tRNAAsp, also show the presence of slow-migrating bands during electrophoresis; we term these conformers: alt-tRNATyr and alt-tRNAAsp, respectively. Although we do not know the chemical or structural nature of these conformers, alt-tRNATyr has a short half-life resembling that of tRNATyr; the same is not true for alt-tRNAAsp We also show that RRP44, which is usually an exosome subunit in other organisms, is involved in tRNA degradation of the only intron-containing tRNA in T. brucei and is partly responsible for its unusually short half-life.


Asunto(s)
Trypanosoma brucei brucei , Trypanosoma brucei brucei/genética , Trypanosoma brucei brucei/metabolismo , ARN de Transferencia de Tirosina/química , Semivida , ARN de Transferencia de Aspártico/metabolismo , ARN de Transferencia/química
20.
Blood ; 141(16): 1982-1989, 2023 04 20.
Artículo en Inglés | MEDLINE | ID: mdl-36735911

RESUMEN

Inhibitor development remains a major challenge in factor VIII (FVIII) replacement therapy. verITI-8 is the first prospective study of a recombinant FVIII Fc fusion protein (rFVIIIFc; efmoroctocog alfa) for first-time immune tolerance induction (ITI) in males with severe hemophilia A and high-titer inhibitors (historical peak ≥5 Bethesda units [BU]/mL). In this single-arm, open-label, multicenter study, screening was followed by ITI (rFVIIIFc 200 IU/kg per day until tolerization or maximum of 48 weeks). Those who achieved ITI success entered a tapering period, returning to standard prophylaxis, and then entered follow-up. Primary end point was time to tolerization with rFVIIIFc defined by inhibitor titer <0.6 BU/mL, incremental recovery (IR) ≥66% of expected IR (IR ≥1.32 IU/dL per IU/kg), and half-life (t½) ≥7 hours within 48 weeks. Sixteen patients received ≥1 rFVIIIFc dose. Twelve (75%), 11 (69%), and 10 patients (63%), respectively, achieved negative inhibitor titers, an IR ≥66%, and a t½ ≥7 hours (ie, tolerance) within 48 weeks. Median times in weeks to achieve these markers of success were 7.4 (interquartile range [IQR], 2.2-17.8), 6.8 (IQR, 5.4-22.4), and 11.7 (IQR, 9.8-26.2), respectively. All patients experienced ≥1 treatment-emergent adverse event (TEAE), and 1 reported ≥1 related TEAE (injection site pain). Nine patients experienced ≥1 treatment-emergent serious AE. No thrombotic events, discontinuations because of AEs, or deaths were reported during the study. As the first extended half-life rFVIII with prospective data in ITI, rFVIIIFc offered short time to tolerization with durable responses in almost two-thirds of patients and was well tolerated. This trial was registered at www.clinicaltrials.gov as #NCT03093480.


Asunto(s)
Factor VIII , Hemofilia A , Masculino , Humanos , Factor VIII/efectos adversos , Estudios Prospectivos , Semivida , Proteínas Recombinantes de Fusión/efectos adversos , Tolerancia Inmunológica
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