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1.
Cell ; 184(19): 4874-4885.e16, 2021 09 16.
Artículo en Inglés | MEDLINE | ID: mdl-34433011

RESUMEN

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.


Asunto(s)
Evolución Molecular , Genoma , Perisodáctilos/genética , Animales , Demografía , Flujo Génico , Variación Genética , Geografía , Heterocigoto , Homocigoto , Especificidad del Huésped , Cadenas de Markov , Mutación/genética , Filogenia , Especificidad de la Especie , Factores de Tiempo
2.
Nat Immunol ; 23(6): 947-959, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35552540

RESUMEN

Inflammation is an important component of fibrosis but immune processes that orchestrate kidney fibrosis are not well understood. Here we apply single-cell sequencing to a mouse model of kidney fibrosis. We identify a subset of kidney tubule cells with a profibrotic-inflammatory phenotype characterized by the expression of cytokines and chemokines associated with immune cell recruitment. Receptor-ligand interaction analysis and experimental validation indicate that CXCL1 secreted by profibrotic tubules recruits CXCR2+ basophils. In mice, these basophils are an important source of interleukin-6 and recruitment of the TH17 subset of helper T cells. Genetic deletion or antibody-based depletion of basophils results in reduced renal fibrosis. Human kidney single-cell, bulk gene expression and immunostaining validate a function for basophils in patients with kidney fibrosis. Collectively, these studies identify basophils as contributors to the development of renal fibrosis and suggest that targeting these cells might be a useful clinical strategy to manage chronic kidney disease.


Asunto(s)
Basófilos , Insuficiencia Renal Crónica , Animales , Fibrosis , Humanos , Riñón/metabolismo , Túbulos Renales , Ratones , Insuficiencia Renal Crónica/metabolismo , Análisis de la Célula Individual
3.
Cell ; 178(3): 653-671.e19, 2019 07 25.
Artículo en Inglés | MEDLINE | ID: mdl-31348890

RESUMEN

Nociceptin and its receptor are widely distributed throughout the brain in regions associated with reward behavior, yet how and when they act is unknown. Here, we dissected the role of a nociceptin peptide circuit in reward seeking. We generated a prepronociceptin (Pnoc)-Cre mouse line that revealed a unique subpopulation of paranigral ventral tegmental area (pnVTA) neurons enriched in prepronociceptin. Fiber photometry recordings during progressive ratio operant behavior revealed pnVTAPnoc neurons become most active when mice stop seeking natural rewards. Selective pnVTAPnoc neuron ablation, inhibition, and conditional VTA nociceptin receptor (NOPR) deletion increased operant responding, revealing that the pnVTAPnoc nucleus and VTA NOPR signaling are necessary for regulating reward motivation. Additionally, optogenetic and chemogenetic activation of this pnVTAPnoc nucleus caused avoidance and decreased motivation for rewards. These findings provide insight into neuromodulatory circuits that regulate motivated behaviors through identification of a previously unknown neuropeptide-containing pnVTA nucleus that limits motivation for rewards.


Asunto(s)
Motivación/efectos de los fármacos , Péptidos Opioides/farmacología , Recompensa , Área Tegmental Ventral/metabolismo , Potenciales de Acción , Animales , Conducta Animal/efectos de los fármacos , Femenino , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Neuronas/fisiología , Técnicas de Placa-Clamp , Precursores de Proteínas/genética , Receptores Opioides/agonistas , Receptores Opioides/deficiencia , Receptores Opioides/genética , Receptor de Nociceptina , Nociceptina
4.
Nat Immunol ; 20(2): 129-140, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30664762

RESUMEN

Basophils are evolutionarily conserved in vertebrates, despite their small numbers and short life span, suggesting that they have beneficial roles in maintaining health. However, these roles are not fully defined. Here we demonstrate that basophil-deficient mice exhibit reduced bacterial clearance and increased morbidity and mortality in the cecal ligation and puncture (CLP) model of sepsis. Among the several proinflammatory mediators that we measured, tumor necrosis factor (TNF) was the only cytokine that was significantly reduced in basophil-deficient mice after CLP. In accordance with that observation, we found that mice with genetic ablation of Tnf in basophils exhibited reduced systemic concentrations of TNF during endotoxemia. Moreover, after CLP, mice whose basophils could not produce TNF, exhibited reduced neutrophil and macrophage TNF production and effector functions, reduced bacterial clearance, and increased mortality. Taken together, our results show that basophils can enhance the innate immune response to bacterial infection and help prevent sepsis.


Asunto(s)
Basófilos/inmunología , Endotoxemia/inmunología , Inmunidad Innata , Factor de Necrosis Tumoral alfa/inmunología , Traslado Adoptivo , Animales , Basófilos/metabolismo , Ciego/microbiología , Modelos Animales de Enfermedad , Endotoxemia/microbiología , Endotoxemia/terapia , Microbioma Gastrointestinal , Humanos , Lipopolisacáridos/inmunología , Macrófagos/inmunología , Macrófagos/metabolismo , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Neutrófilos/inmunología , Neutrófilos/metabolismo , Tasa de Supervivencia , Factor de Necrosis Tumoral alfa/genética
5.
Nature ; 624(7991): 263-266, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37931645

RESUMEN

Brown dwarfs serve as ideal laboratories for studying the atmospheres of giant exoplanets on wide orbits, as the governing physical and chemical processes within them are nearly identical1,2. Understanding the formation of gas-giant planets is challenging, often involving the endeavour to link atmospheric abundance ratios, such as the carbon-to-oxygen (C/O) ratio, to formation scenarios3. However, the complexity of planet formation requires further tracers, as the unambiguous interpretation of the measured C/O ratio is fraught with complexity4. Isotope ratios, such as deuterium to hydrogen and 14N/15N, offer a promising avenue to gain further insight into this formation process, mirroring their use within the Solar System5-7. For exoplanets, only a handful of constraints on 12C/13C exist, pointing to the accretion of 13C-rich ice from beyond the CO iceline of the disks8,9. Here we report on the mid-infrared detection of the 14NH3 and 15NH3 isotopologues in the atmosphere of a cool brown dwarf with an effective temperature of 380 K in a spectrum taken with the Mid-Infrared Instrument (MIRI) of JWST. As expected, our results reveal a 14N/15N value consistent with star-like formation by gravitational collapse, demonstrating that this ratio can be accurately constrained. Because young stars and their planets should be more strongly enriched in the 15N isotope10, we expect that 15NH3 will be detectable in several cold, wide-separation exoplanets.

6.
N Engl J Med ; 391(7): 598-608, 2024 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-39141852

RESUMEN

BACKGROUND: Patients with brain injury who are unresponsive to commands may perform cognitive tasks that are detected on functional magnetic resonance imaging (fMRI) and electroencephalography (EEG). This phenomenon, known as cognitive motor dissociation, has not been systematically studied in a large cohort of persons with disorders of consciousness. METHODS: In this prospective cohort study conducted at six international centers, we collected clinical, behavioral, and task-based fMRI and EEG data from a convenience sample of 353 adults with disorders of consciousness. We assessed the response to commands on task-based fMRI or EEG in participants without an observable response to verbal commands (i.e., those with a behavioral diagnosis of coma, vegetative state, or minimally conscious state-minus) and in participants with an observable response to verbal commands. The presence or absence of an observable response to commands was assessed with the use of the Coma Recovery Scale-Revised (CRS-R). RESULTS: Data from fMRI only or EEG only were available for 65% of the participants, and data from both fMRI and EEG were available for 35%. The median age of the participants was 37.9 years, the median time between brain injury and assessment with the CRS-R was 7.9 months (25% of the participants were assessed with the CRS-R within 28 days after injury), and brain trauma was an etiologic factor in 50%. We detected cognitive motor dissociation in 60 of the 241 participants (25%) without an observable response to commands, of whom 11 had been assessed with the use of fMRI only, 13 with the use of EEG only, and 36 with the use of both techniques. Cognitive motor dissociation was associated with younger age, longer time since injury, and brain trauma as an etiologic factor. In contrast, responses on task-based fMRI or EEG occurred in 43 of 112 participants (38%) with an observable response to verbal commands. CONCLUSIONS: Approximately one in four participants without an observable response to commands performed a cognitive task on fMRI or EEG as compared with one in three participants with an observable response to commands. (Funded by the James S. McDonnell Foundation and others.).


Asunto(s)
Lesiones Encefálicas , Trastornos de la Conciencia , Trastornos Disociativos , Estado Vegetativo Persistente , Adulto , Femenino , Humanos , Masculino , Persona de Mediana Edad , Adulto Joven , Encéfalo/diagnóstico por imagen , Encéfalo/fisiopatología , Lesiones Encefálicas/fisiopatología , Lesiones Encefálicas/complicaciones , Lesiones Encefálicas/diagnóstico por imagen , Cognición/fisiología , Trastornos de la Conciencia/diagnóstico por imagen , Trastornos de la Conciencia/etiología , Trastornos de la Conciencia/fisiopatología , Electroencefalografía , Imagen por Resonancia Magnética , Estado Vegetativo Persistente/diagnóstico por imagen , Estado Vegetativo Persistente/etiología , Estado Vegetativo Persistente/fisiopatología , Estudios Prospectivos , Trastornos Disociativos/diagnóstico por imagen , Trastornos Disociativos/etiología , Trastornos Disociativos/fisiopatología
7.
Cell ; 148(1-2): 59-71, 2012 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-22265402

RESUMEN

Genomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in a one-step catastrophic event termed chromothripsis. We report the whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome), uncovering massive, complex chromosome rearrangements. Integrating TP53 status with microarray and deep sequencing-based DNA rearrangement data in additional patients reveals a striking association between TP53 mutation and chromothripsis in SHH-MBs. Analysis of additional tumor entities substantiates a link between TP53 mutation and chromothripsis, and indicates a context-specific role for p53 in catastrophic DNA rearrangements. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings connect p53 status and chromothripsis in specific tumor types, providing a genetic basis for understanding particularly aggressive subtypes of cancer.


Asunto(s)
Neoplasias Encefálicas/genética , Reordenamiento Génico , Meduloblastoma/genética , Proteína p53 Supresora de Tumor/genética , Animales , Niño , Aberraciones Cromosómicas , Variaciones en el Número de Copia de ADN , Análisis Mutacional de ADN , Modelos Animales de Enfermedad , Humanos , Leucemia Mieloide Aguda/genética , Síndrome de Li-Fraumeni/fisiopatología , Ratones , Persona de Mediana Edad
8.
Nature ; 591(7849): 265-269, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33597750

RESUMEN

Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.


Asunto(s)
ADN Antiguo/análisis , Evolución Molecular , Genoma Mitocondrial/genética , Genómica , Mamuts/genética , Filogenia , Aclimatación/genética , Alelos , Animales , Teorema de Bayes , ADN Antiguo/aislamiento & purificación , Elefantes/genética , Europa (Continente) , Femenino , Fósiles , Variación Genética/genética , Cadenas de Markov , Diente Molar , América del Norte , Datación Radiométrica , Siberia , Factores de Tiempo
9.
Proc Natl Acad Sci U S A ; 121(36): e2402723121, 2024 Sep 03.
Artículo en Inglés | MEDLINE | ID: mdl-39186658

RESUMEN

Recent advancements in functional neuroimaging have demonstrated that some unresponsive patients in the intensive care unit retain a level of consciousness that is inconsistent with their behavioral diagnosis of awareness. Functional near-infrared spectroscopy (fNIRS) is a portable optical neuroimaging method that can be used to measure neural activity with good temporal and spatial resolution. However, the reliability of fNIRS for detecting the neural correlates of consciousness remains to be established. In a series of studies, we evaluated whether fNIRS can record sensory, perceptual, and command-driven neural processing in healthy participants and in behaviorally nonresponsive patients. At the individual healthy subject level, we demonstrate that fNIRS can detect commonly studied resting state networks, sensorimotor processing, speech-specific auditory processing, and volitional command-driven brain activity to a motor imagery task. We then tested fNIRS with three acutely brain injured patients and found that one could willfully modulate their brain activity when instructed to imagine playing a game of tennis-providing evidence of preserved consciousness despite no observable behavioral signs of awareness. The successful application of fNIRS for detecting preserved awareness among behaviorally nonresponsive patients highlights its potential as a valuable tool for uncovering hidden cognitive states in critical care settings.


Asunto(s)
Lesiones Encefálicas , Estado de Conciencia , Espectroscopía Infrarroja Corta , Humanos , Espectroscopía Infrarroja Corta/métodos , Estado de Conciencia/fisiología , Masculino , Adulto , Femenino , Lesiones Encefálicas/fisiopatología , Lesiones Encefálicas/diagnóstico por imagen , Encéfalo/fisiopatología , Encéfalo/diagnóstico por imagen , Persona de Mediana Edad , Neuroimagen Funcional/métodos , Adulto Joven
10.
Annu Rev Genomics Hum Genet ; 24: 333-346, 2023 08 25.
Artículo en Inglés | MEDLINE | ID: mdl-36630592

RESUMEN

This article reviews evolving legal implications for clinicians and researchers as genomics is used more widely in both the clinic and in translational research, reflecting rapid changes in scientific knowledge as well as the surrounding cultural and political environment. Professionals will face new and changing duties to make or act upon a genetic diagnosis, address direct-to-consumer genetic testing in patient care, consider the health implications of results for patients' family members, and recontact patients when test results change over time. Professional duties in reproductive genetic testing will need to be recalibrated in response to disruptive changes to reproductive rights in the United States. We also review the debate over who controls the flow of genetic information and who is responsible for its protection, considering the globally influential European Union General Data Protection Regulation and the rapidly evolving data privacy law landscape of the United States.


Asunto(s)
Instituciones de Atención Ambulatoria , Pruebas Dirigidas al Consumidor , Humanos , Unión Europea , Familia , Genómica
11.
EMBO J ; 41(1): e105026, 2022 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-34791698

RESUMEN

Intronic GGGGCC (G4C2) hexanucleotide repeat expansion within the human C9orf72 gene represents the most common cause of familial forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9ALS/FTD). Repeat-associated non-AUG (RAN) translation of repeat-containing C9orf72 RNA results in the production of neurotoxic dipeptide-repeat proteins (DPRs). Here, we developed a high-throughput drug screen for the identification of positive and negative modulators of DPR levels. We found that HSP90 inhibitor geldanamycin and aldosterone antagonist spironolactone reduced DPR levels by promoting protein degradation via the proteasome and autophagy pathways respectively. Surprisingly, cAMP-elevating compounds boosting protein kinase A (PKA) activity increased DPR levels. Inhibition of PKA activity, by both pharmacological and genetic approaches, reduced DPR levels in cells and rescued pathological phenotypes in a Drosophila model of C9ALS/FTD. Moreover, knockdown of PKA-catalytic subunits correlated with reduced translation efficiency of DPRs, while the PKA inhibitor H89 reduced endogenous DPR levels in C9ALS/FTD patient-derived iPSC motor neurons. Together, our results suggest new and druggable pathways modulating DPR levels in C9ALS/FTD.


Asunto(s)
Proteína C9orf72/metabolismo , Proteínas Quinasas Dependientes de AMP Cíclico/antagonistas & inhibidores , Dipéptidos/metabolismo , Proteolisis , Bibliotecas de Moléculas Pequeñas/farmacología , Animales , Línea Celular , Codón Iniciador/genética , Proteínas Quinasas Dependientes de AMP Cíclico/metabolismo , Expansión de las Repeticiones de ADN/genética , Modelos Animales de Enfermedad , Drosophila/efectos de los fármacos , Demencia Frontotemporal/patología , Células HEK293 , Ensayos Analíticos de Alto Rendimiento , Humanos , Células Madre Pluripotentes Inducidas/patología , Isoquinolinas/farmacología , Longevidad/efectos de los fármacos , Neuronas Motoras/efectos de los fármacos , Neuronas Motoras/patología , Biosíntesis de Proteínas/efectos de los fármacos , Proteolisis/efectos de los fármacos , Interferencia de ARN , Sulfonamidas/farmacología
12.
Nucleic Acids Res ; 52(2): 906-920, 2024 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-38033317

RESUMEN

Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. It utilizes a CRISPR RNA (crRNA) to target RNA sequences and trigger a composite active site formed by two 'Higher Eukaryotes and Prokaryotes Nucleotide' (HEPN) domains, cleaving any solvent-exposed RNA. In this system, an intriguing form of allosteric communication controls the RNA cleavage activity, yet its molecular details are unknown. Here, multiple-microsecond molecular dynamics simulations are combined with graph theory to decipher this intricate activation mechanism. We show that the binding of a target RNA acts as an allosteric effector, by amplifying the communication signals over the dynamical noise through interactions of the crRNA at the buried HEPN1-2 interface. By introducing a novel Signal-to-Noise Ratio (SNR) of communication efficiency, we reveal critical allosteric residues-R377, N378, and R973-that rearrange their interactions upon target RNA binding. Alanine mutation of these residues is shown to select target RNA over an extended complementary sequence beyond guide-target duplex for RNA cleavage, establishing the functional significance of these hotspots. Collectively our findings offer a fundamental understanding of the Cas13a mechanism of action and pave new avenues for the development of highly selective RNA-based cleavage and detection tools.


Asunto(s)
Proteínas Asociadas a CRISPR , ARN Guía de Sistemas CRISPR-Cas , Regulación Alostérica , Sistemas CRISPR-Cas , Mutación , ARN/genética , Proteínas Asociadas a CRISPR/química , Proteínas Asociadas a CRISPR/genética , Proteínas Asociadas a CRISPR/metabolismo
13.
Nucleic Acids Res ; 52(2): 921-939, 2024 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-38033324

RESUMEN

An increasingly pressing need for clinical diagnostics has required the development of novel nucleic acid-based detection technologies that are sensitive, fast, and inexpensive, and that can be deployed at point-of-care. Recently, the RNA-guided ribonuclease CRISPR-Cas13 has been successfully harnessed for such purposes. However, developing assays for detection of genetic variability, for example single-nucleotide polymorphisms, is still challenging and previously described design strategies are not always generalizable. Here, we expanded our characterization of LbuCas13a RNA-detection specificity by performing a combination of experimental RNA mismatch tolerance profiling, molecular dynamics simulations, protein, and crRNA engineering. We found certain positions in the crRNA-target-RNA duplex that are particularly sensitive to mismatches and establish the effect of RNA concentration in mismatch tolerance. Additionally, we determined that shortening the crRNA spacer or modifying the direct repeat of the crRNA leads to stricter specificities. Furthermore, we harnessed our understanding of LbuCas13a allosteric activation pathways through molecular dynamics and structure-guided engineering to develop novel Cas13a variants that display increased sensitivities to single-nucleotide mismatches. We deployed these Cas13a variants and crRNA design strategies to achieve superior discrimination of SARS-CoV-2 strains compared to wild-type LbuCas13a. Together, our work provides new design criteria and Cas13a variants to use in future easier-to-implement Cas13-based RNA detection applications.


Asunto(s)
ARN Guía de Sistemas CRISPR-Cas , ARN , ARN/genética , Sistemas CRISPR-Cas
14.
Nucleic Acids Res ; 52(D1): D513-D521, 2024 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-37962356

RESUMEN

In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.


Asunto(s)
Bases de Datos Genéticas , Ecosistema , Genoma , Proteoma , Genoma/genética , Filogenia , Sintenía , Internet , Orden Génico/genética
15.
PLoS Genet ; 19(9): e1010893, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37733679

RESUMEN

Brains are highly metabolically active organs, consuming 20% of a person's energy at resting state. A decline in glucose metabolism is a common feature across a number of neurodegenerative diseases. Another common feature is the progressive accumulation of insoluble protein deposits, it's unclear if the two are linked. Glucose metabolism in the brain is highly coupled between neurons and glia, with glucose taken up by glia and metabolised to lactate, which is then shuttled via transporters to neurons, where it is converted back to pyruvate and fed into the TCA cycle for ATP production. Monocarboxylates are also involved in signalling, and play broad ranging roles in brain homeostasis and metabolic reprogramming. However, the role of monocarboxylates in dementia has not been tested. Here, we find that increasing pyruvate import in Drosophila neurons by over-expression of the transporter bumpel, leads to a rescue of lifespan and behavioural phenotypes in fly models of both frontotemporal dementia and Alzheimer's disease. The rescue is linked to a clearance of late stage autolysosomes, leading to degradation of toxic peptides associated with disease. We propose upregulation of pyruvate import into neurons as potentially a broad-scope therapeutic approach to increase neuronal autophagy, which could be beneficial for multiple dementias.


Asunto(s)
Enfermedad de Alzheimer , Demencia Frontotemporal , Humanos , Animales , Demencia Frontotemporal/genética , Enfermedad de Alzheimer/genética , Neuroglía , Ácido Pirúvico , Drosophila , Glucosa
16.
Genome Res ; 32(4): 643-655, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35177558

RESUMEN

The occurrence and formation of genomic structural variants (SVs) is known to be influenced by the 3D chromatin architecture, but the extent and magnitude have been challenging to study. Here, we apply Hi-C to study chromatin organization before and after induction of chromothripsis in human cells. We use Hi-C to manually assemble the derivative chromosomes following the occurrence of massive complex rearrangements, which allows us to study the sources of SV formation and their consequences on gene regulation. We observe an action-reaction interplay whereby the 3D chromatin architecture directly impacts the location and formation of SVs. In turn, the SVs reshape the chromatin organization to alter the local topologies, replication timing, and gene regulation in cis We show that SVs have a strong tendency to occur between similar chromatin compartments and replication timing regions. Moreover, we find that SVs frequently occur at 3D loop anchors, that SVs can cause a switch in chromatin compartments and replication timing, and that this is a major source of SV-mediated effects on nearby gene expression changes. Finally, we provide evidence for a general mechanistic bias of the 3D chromatin on SV occurrence using data from more than 2700 patient-derived cancer genomes.


Asunto(s)
Cromotripsis , Genoma , Cromatina/genética , Cromosomas , Genoma Humano , Variación Estructural del Genoma , Humanos
17.
J Immunol ; 211(4): 648-657, 2023 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-37405700

RESUMEN

Drugs are needed to protect against the neutrophil-derived histones responsible for endothelial injury in acute inflammatory conditions such as trauma and sepsis. Heparin and other polyanions can neutralize histones but challenges with dosing or side effects such as bleeding limit clinical application. In this study, we demonstrate that suramin, a widely available polyanionic drug, completely neutralizes the toxic effects of individual histones, but not citrullinated histones from neutrophil extracellular traps. The sulfate groups on suramin form stable electrostatic interactions with hydrogen bonds in the histone octamer with a dissociation constant of 250 nM. In cultured endothelial cells (Ea.Hy926), histone-induced thrombin generation was significantly decreased by suramin. In isolated murine blood vessels, suramin abolished aberrant endothelial cell calcium signals and rescued impaired endothelial-dependent vasodilation caused by histones. Suramin significantly decreased pulmonary endothelial cell ICAM-1 expression and neutrophil recruitment caused by infusion of sublethal doses of histones in vivo. Suramin also prevented histone-induced lung endothelial cell cytotoxicity in vitro and lung edema, intra-alveolar hemorrhage, and mortality in mice receiving a lethal dose of histones. Protection of vascular endothelial function from histone-induced damage is a novel mechanism of action for suramin with therapeutic implications for conditions characterized by elevated histone levels.


Asunto(s)
Histonas , Suramina , Ratones , Animales , Histonas/metabolismo , Suramina/farmacología , Células Endoteliales/metabolismo , Endotelio/metabolismo , Hemorragia
18.
Am J Respir Crit Care Med ; 209(10): 1246-1254, 2024 05 15.
Artículo en Inglés | MEDLINE | ID: mdl-38190702

RESUMEN

Rationale: Mycobacterium avium complex (MAC) is the most common cause of nontuberculous mycobacterial (NTM) pulmonary disease (PD), which exhibits increasing global incidence. Current microbiologic methods routinely used in clinical practice lack sensitivity and have long latencies, leading to delays in diagnosis and treatment initiation and evaluation. A clustered regularly interspaced short palindromic repeats (CRISPR)-based assay that measures MAC cell-free DNA (cfDNA) concentrations in serum could provide a rapid means to detect MAC infection and monitor response to antimicrobial treatment. Objectives: To develop and optimize a CRISPR MAC assay for MAC infection detection and to evaluate its diagnostic and prognostic performance in two MAC disease cohorts. Methods: MAC cfDNA serum concentrations were measured in individuals with diagnoses of MAC disease or who had bronchiectasis or chronic obstructive pulmonary disease diagnoses without histories of NTM PD or NTM-positive sputum cultures. Diagnostic performance was analyzed using pretreatment serum from two cohorts. Serum MAC cfDNA changes during MAC PD treatment were evaluated in a subset of patients with MAC PD who received macrolide-based multidrug regimens. Measurements and Main Results: The CRISPR MAC assay detected MAC cfDNA in MAC PD with 97.6% (91.6-99.7%) sensitivity and 97.6% (91.5-99.7%) specificity overall. Serum MAC cfDNA concentrations markedly decreased after MAC-directed treatment initiation in patients with MAC PD who demonstrated MAC culture conversion. Conclusions: This study provides preliminary evidence for the utility of a serum-based CRISPR MAC assay to rapidly detect MAC infection and monitor the response to treatment.


Asunto(s)
Ácidos Nucleicos Libres de Células , Complejo Mycobacterium avium , Infección por Mycobacterium avium-intracellulare , Humanos , Infección por Mycobacterium avium-intracellulare/diagnóstico , Infección por Mycobacterium avium-intracellulare/sangre , Infección por Mycobacterium avium-intracellulare/tratamiento farmacológico , Femenino , Masculino , Ácidos Nucleicos Libres de Células/sangre , Complejo Mycobacterium avium/genética , Complejo Mycobacterium avium/aislamiento & purificación , Anciano , Persona de Mediana Edad , ADN Bacteriano/sangre , ADN Bacteriano/análisis , Sensibilidad y Especificidad , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Estudios de Cohortes , Antibacterianos/uso terapéutico
19.
J Neurosci ; 43(49): 8536-8546, 2023 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-37932104

RESUMEN

Humor comprehension (i.e., getting a joke) and humor appreciation (i.e., enjoying a joke) are distinct, cognitively complex processes. Functional magnetic resonance imaging (fMRI) investigations have identified several key cortical regions but have overlooked subcortical structures that have theoretical importance in humor processing. The dorsal striatum (DS) contributes to working memory, ambiguity processing, and cognitive flexibility, cognitive functions that are required to accurately recognize humorous stimuli. The ventral striatum (VS) is critical in reward processing and enjoyment. We hypothesized that the DS and VS play important roles in humor comprehension and appreciation, respectively. We investigated the engagement of these regions in these distinct processes using fMRI. Twenty-six healthy young male and female human adults completed two humor-elicitation tasks during a 3 tesla fMRI scan consisting of a traditional behavior-based joke task and a naturalistic audiovisual sitcom paradigm (i.e., Seinfeld viewing task). Across both humor-elicitation methods, whole-brain analyses revealed cortical activation in the inferior frontal gyrus, the middle frontal gyrus, and the middle temporal gyrus for humor comprehension, and the temporal cortex for humor appreciation. Additionally, with region of interest analyses, we specifically examined whether DS and VS activation correlated with these processes. Across both tasks, we demonstrated that humor comprehension implicates both the DS and the VS, whereas humor appreciation only engages the VS. These results establish the role of the DS in humor comprehension, which has been previously overlooked, and emphasize the role of the VS in humor processing more generally.SIGNIFICANCE STATEMENT Humorous stimuli are processed by the brain in at least two distinct stages. First, humor comprehension involves understanding humorous intent through cognitive and problem-solving mechanisms. Second, humor appreciation involves enjoyment, mirth, and laughter in response to a joke. The roles of smaller subcortical brain regions in humor processing, such as the DS and VS, have been overlooked in previous investigations. However, these regions are involved in functions that support humor comprehension (e.g., working memory ambiguity resolution, and cognitive flexibility) and humor appreciation (e.g., reward processing, pleasure, and enjoyment). In this study, we used neuroimaging to demonstrate that the DS and VS play important roles in humor comprehension and appreciation, respectively, across two different humor-elicitation tasks.


Asunto(s)
Comprensión , Imagen por Resonancia Magnética , Adulto , Humanos , Masculino , Femenino , Comprensión/fisiología , Imagen por Resonancia Magnética/métodos , Encéfalo/fisiología , Lóbulo Temporal/fisiología , Lóbulo Frontal/fisiología , Mapeo Encefálico
20.
Biochemistry ; 63(17): 2141-2152, 2024 Sep 03.
Artículo en Inglés | MEDLINE | ID: mdl-39146246

RESUMEN

Dipeptide repeat proteins (DPRs) are aberrant protein species found in C9orf72-linked amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two neurodegenerative diseases characterized by the cytoplasmic mislocalization and aggregation of RNA-binding proteins (RBPs). In particular, arginine (R)-rich DPRs (poly-GR and poly-PR) have been suggested to promiscuously interact with multiple cellular proteins and thereby exert high cytotoxicity. Components of the protein arginine methylation machinery have been identified as modulators of DPR toxicity and/or potential cellular interactors of R-rich DPRs; however, the molecular details and consequences of such an interaction are currently not well understood. Here, we demonstrate that several members of the family of protein arginine methyltransferases (PRMTs) can directly interact with R-rich DPRs in vitro and in the cytosol. In vitro, R-rich DPRs reduce solubility and promote phase separation of PRMT1, the main enzyme responsible for asymmetric arginine-dimethylation (ADMA) in mammalian cells, in a concentration- and length-dependent manner. Moreover, we demonstrate that poly-GR interferes more efficiently than poly-PR with PRMT1-mediated arginine methylation of RBPs such as hnRNPA3. We additionally show by two alternative approaches that poly-GR itself is a substrate for PRMT1-mediated arginine dimethylation. We propose that poly-GR may act as a direct competitor for arginine methylation of cellular PRMT1 targets, such as disease-linked RBPs.


Asunto(s)
Arginina , Proteína-Arginina N-Metiltransferasas , Proteínas de Unión al ARN , Proteínas Represoras , Proteína-Arginina N-Metiltransferasas/metabolismo , Proteína-Arginina N-Metiltransferasas/genética , Humanos , Arginina/metabolismo , Metilación , Proteínas Represoras/metabolismo , Proteínas Represoras/genética , Proteínas de Unión al ARN/metabolismo , Proteínas de Unión al ARN/genética , Esclerosis Amiotrófica Lateral/metabolismo , Esclerosis Amiotrófica Lateral/genética , Demencia Frontotemporal/metabolismo , Demencia Frontotemporal/genética , Proteína C9orf72/metabolismo , Proteína C9orf72/genética , Células HEK293
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