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1.
Neuro Oncol ; 24(11): 1857-1868, 2022 11 02.
Artículo en Inglés | MEDLINE | ID: mdl-35305088

RESUMEN

BACKGROUND: Neddylation inhibition, affecting posttranslational protein function and turnover, is a promising therapeutic approach to cancer. We report vulnerability to MLN4924 or pevonedistat (a neddylation inhibitor) in a subset of glioblastoma (GBM) preclinical models and identify biomarkers, mechanisms, and signatures of differential response. METHODS: GBM sequencing data were queried for genes associated with MLN4924 response status; candidates were validated by molecular techniques. Time-course transcriptomics and proteomics revealed processes implicated in MLN4924 response. RESULTS: Vulnerability to MLN4924 is associated with elevated S-phase populations, re-replication, and DNA damage. Transcriptomics and shotgun proteomics depict PTEN signaling, DNA replication, and chromatin instability pathways as significant differentiators between sensitive and resistant models. Loss of PTEN and its nuclear functions is associated with resistance to MLN4924. Time-course proteomics identified elevated TOP2A in resistant models through treatment. TOP2A inhibitors combined with MLN4924 prove synergistic. CONCLUSIONS: We show that PTEN status serves as both a novel biomarker for MLN4924 response in GBM and reveals a vulnerability to TOP2A inhibitors in combination with MLN4924.


Asunto(s)
Glioblastoma , Fosfohidrolasa PTEN , Inhibidores de Topoisomerasa II , Humanos , Apoptosis , Línea Celular Tumoral , Ciclopentanos/farmacología , Ciclopentanos/uso terapéutico , Glioblastoma/tratamiento farmacológico , Proteína NEDD8/metabolismo , Fosfohidrolasa PTEN/genética , Pirimidinas/farmacología , Inhibidores de Topoisomerasa II/farmacología , Inhibidores de Topoisomerasa II/uso terapéutico , Resistencia a Antineoplásicos
2.
Life Sci ; 284: 119879, 2021 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-34390723

RESUMEN

AIMS: Doxorubicin (DOX) is an important drug for the treatment of various tumor entities. However, the occurrence of heart failure limits its application. This study investigated differential gene expression profiles in the left and right ventricles of DOX treated mice with either preserved or impaired myocardial function. We provide new mechanistic insights into the pathophysiology of DOX-induced heart failure and have discovered pathways that counteract DOX-induced cardiotoxicity. MAIN METHODS: We used in total 48 male mice and applied a chronic low dose DOX administration (5 mg/kg per injection, in total 20 mg/kg over 4 weeks) to induce heart failure. Echocardiographic parameters were evaluated one week after the final dose and mice were separated according to functional parameters into doxorubicin responding and non-responding animals. Post mortem, measurements of reactive oxygen species (ROS) and gene expression profiling was performed in separated right and left hearts. KEY FINDINGS: We detected significant ROS production in the left heart of the mice in response to DOX treatment, although interestingly, not in the right heart. We found that transcriptional changes differ between right and left heart correlating with the occurrence of myocardial dysfunction. SIGNIFICANCE: Doxorubicin induces changes in gene expression in the entire heart of animals without necessarily impairing cardiac function. We identified a set of transcripts that are associated with DOX cardiotoxicity. These might represent promising targets to ameliorate DOX-induced heart failure. Moreover, our results emphasize that parameters of left and right heart function should be evaluated during standardized echocardiography in patients undergoing DOX therapy.


Asunto(s)
Doxorrubicina/efectos adversos , Pruebas de Función Cardíaca , Miocardio/patología , Transcripción Genética , Animales , Análisis por Conglomerados , Electrocardiografía , Perfilación de la Expresión Génica , Pruebas de Función Cardíaca/efectos de los fármacos , Ratones Endogámicos C57BL , Estrés Oxidativo/efectos de los fármacos , Transcripción Genética/efectos de los fármacos
3.
J R Coll Physicians Edinb ; 51(1): 13-18, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33877128

RESUMEN

BACKGROUND: Primary percutaneous coronary intervention (PPCI) is the first-line treatment for acute ST-elevation myocardial infarction (STEMI). Evidence of benefit from PPCI in the elderly is sparse. Our aim was to evaluate survival outcomes in patients aged ≥85 years who undergo PPCI for STEMI. METHODS: Clinical data were collected retrospectively on all patients aged ≥85 years who were referred and accepted for PPCI to our centre between 2013 and 2018. RESULTS: One hundred and forty-three patients received PPCI. Median hospital stay was seven days. One hundred and thirty-one patients survived admission. One-year mortality was 33.5%. Age and baseline renal function were independent predictors of one-year mortality. Median survival was 2.55 years. CONCLUSION: Advanced age alone should not be used as an exclusion criterion for PPCI; rather, a personalised approach that takes into account all clinically relevant patient factors should guide PCI decision-making. Our findings suggest that PPCI as first-line treatment for STEMI in the very old should be considered routinely.


Asunto(s)
Infarto del Miocardio , Intervención Coronaria Percutánea , Infarto del Miocardio con Elevación del ST , Anciano , Humanos , Infarto del Miocardio/terapia , Estudios Retrospectivos , Infarto del Miocardio con Elevación del ST/cirugía , Terapia Trombolítica , Resultado del Tratamiento
4.
J Comp Neurol ; 529(5): 1029-1051, 2021 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-32779183

RESUMEN

The cetacean hippocampal formation has been noted to be one of the smallest relative to brain size of all mammals studied. This region, comprised of the dentate gyrus, hippocampus proper, subiculum, presubiculum, parasubiculum and the entorhinal cortex, is important in learning, memory, and navigation. There have been a number of studies detailing the distribution of acetylcholinesterase (AChE) in the hippocampal formation of terrestrial mammals with the goal of gaining a greater understanding of some aspects of the cholinergic innervation to this region, as well as its parcellation. The present study was undertaken to describe the organization, cytoarchitecture, and distribution of AChE in the hippocampal formation of the Atlantic white-sided dolphin (AWSD) with the view to understand similarities and differences between this aquatic mammal and terrestrial mammals. Nissl-staining demonstrated cytoarchitecture of the hippocampal formation in the AWSD comparable to that reported in other cetaceans. In addition, the AWSD had a rich pattern of AChE staining that distinctly varied between regions and laminae. A number of differences in the distribution of AChE staining in areas comparable to those of terrestrial species reported suggested possible alterations in connectivity of this region. Overall, however, AChE-staining suggested that cholinergic innervation, neural pathways and function of the hippocampal formation of the AWSD is conserved, similar to other mammals.


Asunto(s)
Acetilcolinesterasa/análisis , Delfines/fisiología , Hipocampo/enzimología , Proteínas del Tejido Nervioso/análisis , Animales , Giro Dentado/enzimología , Corteza Entorrinal/enzimología , Femenino , Hipocampo/ultraestructura , Masculino
5.
Emerg Infect Dis ; 26(3): 606-609, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-31922952

RESUMEN

The full geographic range of coccidioidomycosis is unknown, although it is most likely expanding with environmental change. We report an apparently autochthonous coccidioidomycosis patient from Spokane, Washington, USA, a location to which Coccidioides spp. are not known to be endemic.


Asunto(s)
Coccidioides/aislamiento & purificación , Coccidioidomicosis/diagnóstico , Neumonía/diagnóstico , Anciano de 80 o más Años , Antifúngicos/uso terapéutico , Coccidioidomicosis/diagnóstico por imagen , Coccidioidomicosis/tratamiento farmacológico , Tos/etiología , Diagnóstico Diferencial , Femenino , Fluconazol/uso terapéutico , Humanos , Neumonía/diagnóstico por imagen , Neumonía/tratamiento farmacológico , Washingtón
6.
Blood ; 133(21): 2305-2319, 2019 05 23.
Artículo en Inglés | MEDLINE | ID: mdl-30814062

RESUMEN

Neural cell adhesion molecule 1 (NCAM1; CD56) is expressed in up to 20% of acute myeloid leukemia (AML) patients. NCAM1 is widely used as a marker of minimal residual disease; however, the biological function of NCAM1 in AML remains elusive. In this study, we investigated the impact of NCAM1 expression on leukemogenesis, drug resistance, and its role as a biomarker to guide therapy. Beside t(8;21) leukemia, NCAM1 expression was found in most molecular AML subgroups at highly heterogeneous expression levels. Using complementary genetic strategies, we demonstrated an essential role of NCAM1 in the regulation of cell survival and stress resistance. Perturbation of NCAM1 induced cell death or differentiation and sensitized leukemic blasts toward genotoxic agents in vitro and in vivo. Furthermore, Ncam1 was highly expressed in leukemic progenitor cells in a murine leukemia model, and genetic depletion of Ncam1 prolonged disease latency and significantly reduced leukemia-initiating cells upon serial transplantation. To further analyze the mechanism of the NCAM1-associated phenotype, we performed phosphoproteomics and transcriptomics in different AML cell lines. NCAM1 expression strongly associated with constitutive activation of the MAPK-signaling pathway, regulation of apoptosis, or glycolysis. Pharmacological inhibition of MEK1/2 specifically inhibited proliferation and sensitized NCAM1+ AML cells to chemotherapy. In summary, our data demonstrate that aberrant expression of NCAM1 is involved in the maintenance of leukemic stem cells and confers stress resistance, likely due to activation of the MAPK pathway. Targeting MEK1/2 sensitizes AML blasts to genotoxic agents, indicating a role for NCAM1 as a biomarker to guide AML treatment.


Asunto(s)
Biomarcadores de Tumor/metabolismo , Crisis Blástica/metabolismo , Antígeno CD56/metabolismo , Resistencia a Antineoplásicos , Leucemia Mieloide Aguda/metabolismo , Proteínas de Neoplasias/metabolismo , Animales , Apoptosis/genética , Biomarcadores de Tumor/genética , Crisis Blástica/genética , Crisis Blástica/patología , Crisis Blástica/terapia , Antígeno CD56/genética , Femenino , Glucólisis/genética , Células HL-60 , Humanos , Células K562 , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/patología , Leucemia Mieloide Aguda/terapia , Sistema de Señalización de MAP Quinasas/genética , Masculino , Ratones , Ratones Endogámicos NOD , Ratones Noqueados , Proteínas de Neoplasias/genética
7.
J Comp Neurol ; 526(12): 1910-1926, 2018 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-29700823

RESUMEN

The basal forebrain (BFB) cholinergic neurotransmitter system is important in a number of brain functions including attention, memory, and the sleep-wake cycle. The size of this region has been linked to the increase in encephalization of the brain in a number of species. Cetaceans, particularly those belonging to the family Delphinidae, have a relatively large brain compared to its body size and it is expected that the cholinergic BFB in the dolphin would be a prominent feature. However, this has not yet been explored in detail. This study examines and maps the neuroanatomy and cholinergic chemoarchitecture of the BFB in the Atlantic white-sided dolphin (Lagenorhynchus acutus). As in some other mammals, the BFB in this species is a prominent structure along the medioventral surface of the brain. The parcellation and distribution of cholinergic neural elements of the dolphin BFB was comparable to that observed in other mammals in that it has a medial septal nucleus, a nucleus of the vertical limb of the diagonal band of Broca, a nucleus of the horizontal limb of the diagonal band of Broca, and a nucleus basalis of Meynert. The observed BFB cholinergic system of this dolphin is consistent with evolutionarily conserved and important functions for survival.


Asunto(s)
Prosencéfalo Basal/anatomía & histología , Neuronas Colinérgicas/citología , Delfines/anatomía & histología , Animales , Colina O-Acetiltransferasa/análisis
8.
Mol Syst Biol ; 14(2): e7678, 2018 02 23.
Artículo en Inglés | MEDLINE | ID: mdl-29476006

RESUMEN

Cellular decision-making and environmental adaptation are dependent upon a heterogeneous response of gene expression to external cues. Heterogeneity arises in transcription from random switching between transcriptionally active and inactive states, resulting in bursts of RNA synthesis. Furthermore, the cellular state influences the competency of transcription, thereby globally affecting gene expression in a cell-specific manner. We determined how external stimuli interplay with cellular state to modulate the kinetics of bursting. To this end, single-cell dynamics of nascent transcripts were monitored at the endogenous estrogen-responsive GREB1 locus. Stochastic modeling of gene expression implicated a two-state promoter model in which the estrogen stimulus modulates the frequency of transcriptional bursting. The cellular state affects transcriptional dynamics by altering initiation and elongation kinetics and acts globally, as GREB1 alleles in the same cell correlate in their transcriptional output. Our results suggest that cellular state strongly affects the first step of the central dogma of gene expression, to promote heterogeneity in the transcriptional output of isogenic cells.


Asunto(s)
Estrógenos/farmacología , Proteínas de Neoplasias/genética , Análisis de la Célula Individual/métodos , Transcripción Genética/efectos de los fármacos , Perfilación de la Expresión Génica , Humanos , Células MCF-7 , Modelos Genéticos , Regiones Promotoras Genéticas , Procesos Estocásticos
9.
J Intensive Care Soc ; 19(1): 15-18, 2018 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-29456596

RESUMEN

Point-of-care ultrasound is increasingly recognised as a valuable adjunct to patient care. Trainees in intensive care medicine are expected to accredit in focused intensive care echocardiography, but the availability of trained mentors and logistical/geographical factors make this difficult within the time constraints required. As a result, many trainees who are enthusiastic about point-of-care ultrasound find it difficult to achieve accreditation. We present a secure, web-based, multi-user system which mitigates many of these difficulties and allows for clinical mentorship to take place without geographical barriers, and at a time convenient for the participants.

10.
PeerJ ; 5: e3742, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28970965

RESUMEN

We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone.

11.
Alzheimers Dement (N Y) ; 3(2): 166-176, 2017 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-29067326

RESUMEN

INTRODUCTION: Diagnosis of Alzheimer's disease (AD) in vivo, by molecular imaging of amyloid or tau, is constrained because similar changes can be found in brains of cognitively normal individuals. Butyrylcholinesterase (BChE), which becomes associated with these structures in AD, could elevate the accuracy of AD diagnosis by focusing on BChE pathology in the cerebral cortex, a region of scant BChE activity in healthy brain. METHODS: N-methylpiperidin-4-yl 4-[123I]iodobenzoate, a BChE radiotracer, was injected intravenously into B6SJL-Tg(APPSwFlLon, PSEN1∗M146 L∗L286 V) 6799Vas/Mmjax (5XFAD) mice and their wild-type (WT) counterparts for comparative single photon emission computed tomography (SPECT) studies. SPECT, computed tomography (CT), and magnetic resonance imaging (MRI) enabled comparison of whole brain and regional retention of the BChE radiotracer in both mouse strains. RESULTS: Retention of the BChE radiotracer was consistently higher in the 5XFAD mouse than in WT, and differences were particularly evident in the cerebral cortex. DISCUSSION: Cerebral cortical BChE imaging with SPECT can distinguish 5XFAD mouse model from the WT counterpart.

12.
Brain Res ; 1671: 102-110, 2017 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-28729192

RESUMEN

Alzheimer's disease (AD) is the most common neurodegenerative disorder causing dementia. One hallmark of the AD brain is the deposition of ß-amyloid (Aß) plaques. AD is also a state of cholinergic dysfunction and butyrylcholinesterase (BChE) associates with Aß pathology. A transgenic mouse (5XFAD) is an aggressive amyloidosis model, producing Aß plaques with which BChE also associates. A derived strain (5XFAD/BChE-KO), with the BChE gene knocked out, has significantly lower fibrillar Aß than 5XFAD mice at the same age. Therefore, BChE may have a role in Aß pathogenesis. Furthermore, in AD, diminished glucose metabolism in the brain can be detected in vivo with positron emission tomography (PET) imaging following 2-deoxy-2-(18F)fluoro-D-glucose (18FDG) administration. To determine whether hypometabolism is related to BChE-induced changes in fibrillar Aß burden, whole brain and regional uptake of 18FDG in 5XFAD and 5XFAD/BChE-KO mice was compared to corresponding wild-type (WT5XFAD and WTBChE-KO) strains at 5months. Diminished fibrillar Aß burden was confirmed in 5XFAD/BChE-KO mice relative to 5XFAD. 5XFAD and 5XFAD/BChE-KO mice demonstrated reduction in whole brain 18FDG retention compared to respective wild-types. Regional analysis of relevant AD structures revealed reduction in 18FDG retention in 5XFAD mice in all brain regions analyzed (save cerebellum) compared to WT5XFAD. Alternatively, 5XFAD/BChE-KO mice demonstrated a more selective pattern of reduced retention in the cerebral cortex and thalamus compared to WTBChE-KO, while retention in hippocampal formation, amygdala and basal ganglia remained unchanged. This suggests that in knocking out BChE and reducing fibrillar Aß, a possible protective effect on brain function may be conferred in a number of structures in 5XFAD/BChE-KO mice.


Asunto(s)
Enfermedad de Alzheimer/metabolismo , Péptidos beta-Amiloides/metabolismo , Amiloide/metabolismo , Butirilcolinesterasa/deficiencia , Fluorodesoxiglucosa F18/farmacología , Enfermedad de Alzheimer/diagnóstico por imagen , Enfermedad de Alzheimer/genética , Amiloide/genética , Péptidos beta-Amiloides/genética , Precursor de Proteína beta-Amiloide/genética , Precursor de Proteína beta-Amiloide/metabolismo , Animales , Ganglios Basales/metabolismo , Encéfalo/metabolismo , Butirilcolinesterasa/genética , Butirilcolinesterasa/metabolismo , Modelos Animales de Enfermedad , Femenino , Técnicas de Inactivación de Genes , Glucosa/metabolismo , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Ratones Transgénicos , Placa Amiloide/metabolismo , Tomografía de Emisión de Positrones/métodos , Radiofármacos/farmacocinética
13.
J Alzheimers Dis ; 58(2): 491-505, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28453492

RESUMEN

Amyloid-ß (Aß) plaques are a neuropathological hallmark of Alzheimer's disease (AD); however, a significant number of cognitively normal older adults can also have Aß plaques. Thus, distinguishing AD from cognitively normal individuals with Aß plaques (NwAß) based on Aß plaque detection is challenging. It has been observed that butyrylcholinesterase (BChE) accumulates in plaques preferentially in AD. Thus, detecting BChE-associated plaques has the potential as an improved AD biomarker. We present Aß, thioflavin-S, and BChE quantification of 26 postmortem brain tissues; AD (n = 8), NwAß (n = 6), cognitively normal without plaques (n = 8), and other common dementias including corticobasal degeneration, frontotemporal dementia with tau, dementia with Lewy bodies, and vascular dementia. Pathology burden in the orbitofrontal cortex, entorhinal cortex, amygdala, and hippocampal formation was determined and compared. The predictive value of Aß and BChE quantification was determined, via receiver-operating characteristic plots, to evaluate their AD diagnostic performance using sensitivity, specificity, and area under curve (AUC) metrics. In general, Aß and BChE-associated pathology were greater in AD, particularly in the orbitofrontal cortex. In this region, the largest increase (9.3-fold) was in BChE-associated pathology, observed between NwAß and AD, due to the virtual absence of BChE-associated plaques in NwAß brains. Furthermore, BChE did not associate with pathology of the other dementias. In this sample, BChE-associated pathology provided better diagnostic performance (AUC = 1.0, sensitivity/specificity = 100% /100%) when compared to Aß (AUC = 0.98, 100% /85.7%). These findings highlight the predictive value of BChE as a biomarker for AD that could facilitate timely disease diagnosis and management.


Asunto(s)
Enfermedad de Alzheimer/patología , Encéfalo/metabolismo , Butirilcolinesterasa/metabolismo , Placa Amiloide/patología , Anciano , Anciano de 80 o más Años , Péptidos beta-Amiloides/metabolismo , Encéfalo/patología , Diagnóstico , Femenino , Humanos , Masculino , Persona de Mediana Edad , Placa Amiloide/metabolismo , Escalas de Valoración Psiquiátrica , Curva ROC
14.
Genome Biol ; 16: 246, 2015 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-26541514

RESUMEN

BACKGROUND: Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. RESULTS: Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40-700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. CONCLUSIONS: These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells.


Asunto(s)
Cromatina/genética , Proteínas de Unión al ADN/genética , ADN/genética , Isquemia/genética , Hipoxia de la Célula/genética , Línea Celular , Cromatina/ultraestructura , Proteínas de Unión al ADN/metabolismo , Desoxirribonucleasa I/genética , Recuperación de Fluorescencia tras Fotoblanqueo , Heterocromatina/genética , Heterocromatina/ultraestructura , Histonas/genética , Histonas/metabolismo , Humanos , Isquemia/patología , Miocitos Cardíacos/metabolismo , Miocitos Cardíacos/patología , Unión Proteica , Procesamiento Proteico-Postraduccional/genética
15.
Proc Natl Acad Sci U S A ; 112(42): 13115-20, 2015 Oct 20.
Artículo en Inglés | MEDLINE | ID: mdl-26438844

RESUMEN

Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles because of differences in transcription time, degradation rate, and RNA-processing kinetics. Recent studies have shown that a splicing-associated RNA production delay can be significant. To investigate this issue more generally, it is useful to develop methods applicable to genome-wide datasets. We introduce a joint model of transcriptional activation and mRNA accumulation that can be used for inference of transcription rate, RNA production delay, and degradation rate given data from high-throughput sequencing time course experiments. We combine a mechanistic differential equation model with a nonparametric statistical modeling approach allowing us to capture a broad range of activation kinetics, and we use Bayesian parameter estimation to quantify the uncertainty in estimates of the kinetic parameters. We apply the model to data from estrogen receptor α activation in the MCF-7 breast cancer cell line. We use RNA polymerase II ChIP-Seq time course data to characterize transcriptional activation and mRNA-Seq time course data to quantify mature transcripts. We find that 11% of genes with a good signal in the data display a delay of more than 20 min between completing transcription and mature mRNA production. The genes displaying these long delays are significantly more likely to be short. We also find a statistical association between high delay and late intron retention in pre-mRNA data, indicating significant splicing-associated production delays in many genes.


Asunto(s)
Genoma Humano , Modelos Genéticos , ARN/biosíntesis , Transcripción Genética , Receptor alfa de Estrógeno/metabolismo , Humanos , Cinética , Células MCF-7 , ARN/genética , Transducción de Señal
16.
Clin Epigenetics ; 7: 19, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25763115

RESUMEN

BACKGROUND: Primary cells enter replicative senescence after a limited number of cell divisions. This process needs to be considered in cell culture experiments, and it is particularly important for regenerative medicine. Replicative senescence is associated with reproducible changes in DNA methylation (DNAm) at specific sites in the genome. The mechanism that drives senescence-associated DNAm changes remains unknown - it may involve stochastic DNAm drift due to imperfect maintenance of epigenetic marks or it is directly regulated at specific sites in the genome. RESULTS: In this study, we analyzed the reorganization of nuclear architecture and DNAm changes during long-term culture of human fibroblasts and mesenchymal stromal cells (MSCs). We demonstrate that telomeres shorten and shift towards the nuclear center at later passages. In addition, DNAm profiles, either analyzed by MethylCap-seq or by 450k IlluminaBeadChip technology, revealed consistent senescence-associated hypermethylation in regions associated with H3K27me3, H3K4me3, and H3K4me1 histone marks, whereas hypomethylation was associated with chromatin containing H3K9me3 and lamina-associated domains (LADs). DNA hypermethylation was significantly enriched in the vicinity of genes that are either up- or downregulated at later passages. Furthermore, specific transcription factor binding motifs (e.g. EGR1, TFAP2A, and ETS1) were significantly enriched in differentially methylated regions and in the promoters of differentially expressed genes. CONCLUSIONS: Senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence. These results indicate that tightly regulated epigenetic modifications during long-term culture contribute to changes in nuclear organization and gene expression.

17.
PLoS Comput Biol ; 10(5): e1003598, 2014 May.
Artículo en Inglés | MEDLINE | ID: mdl-24830797

RESUMEN

Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2). The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ERα) and FOXA1 binding in their proximal promoter regions.


Asunto(s)
Inmunoprecipitación de Cromatina/métodos , ARN Polimerasas Dirigidas por ADN/genética , Modelos Genéticos , Modelos Estadísticos , Regiones Promotoras Genéticas/genética , Transcripción Genética/genética , Activación Transcripcional/genética , Animales , Simulación por Computador , Humanos , Unión Proteica
18.
Anal Chem ; 85(19): 8928-32, 2013 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-24003862

RESUMEN

Detector response is not always equivalent between detectors or instrument types. Factors that impact detector response include molecular structure and detection wavelength. In liquid chromatography (LC), ultraviolet (UV) is often the primary detector; however, without determination of UV response factors for each analyte, chromatographic results are reported on an area percent rather than a weight percent. In extreme cases, response factors can differ by several orders of magnitude for structurally dissimilar compounds, making the uncalibrated data useless for quantitative applications. While impurity reference standards are normally used to calculate UV relative response factors (RRFs), reference standards of reaction mixture components are typically not available during route scouting or in the early stages of process development. Here, we describe an approach to establish RRFs from a single experiment using both online nuclear magnetic resonance (NMR) and LC. NMR is used as a mass detector from which a UV response factor can be determined to correct the high performance liquid chromatography (HPLC) data. Online reaction monitoring using simultaneous NMR and HPLC provides a platform to expedite the development and understanding of pharmaceutical reaction processes. Ultimately, the knowledge provided by a structurally information rich technique such as NMR can be correlated with more prevalent and mobile instrumentation [e.g., LC, mid-infrared spectrometers (MIR)] for additional routine process understanding and optimization.


Asunto(s)
Cromatografía Líquida de Alta Presión/instrumentación , Espectroscopía de Resonancia Magnética/instrumentación , Sistemas en Línea/instrumentación , Preparaciones Farmacéuticas/química , Tecnología Farmacéutica/instrumentación , Estructura Molecular
19.
PLoS Comput Biol ; 9(6): e1003100, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23818839

RESUMEN

Identification of responsive genes to an extra-cellular cue enables characterization of pathophysiologically crucial biological processes. Deep sequencing technologies provide a powerful means to identify responsive genes, which creates a need for computational methods able to analyze dynamic and multi-level deep sequencing data. To answer this need we introduce here a data-driven algorithm, SPINLONG, which is designed to search for genes that match the user-defined hypotheses or models. SPINLONG is applicable to various experimental setups measuring several molecular markers in parallel. To demonstrate the SPINLONG approach, we analyzed ChIP-seq data reporting PolII, estrogen receptor α (ERα), H3K4me3 and H2A.Z occupancy at five time points in the MCF-7 breast cancer cell line after estradiol stimulus. We obtained 777 ERa early responsive genes and compared the biological functions of the genes having ERα binding within 20 kb of the transcription start site (TSS) to genes without such binding site. Our results show that the non-genomic action of ERα via the MAPK pathway, instead of direct ERa binding, may be responsible for early cell responses to ERα activation. Our results also indicate that the ERα responsive genes triggered by the genomic pathway are transcribed faster than those without ERα binding sites. The survival analysis of the 777 ERα responsive genes with 150 primary breast cancer tumors and in two independent validation cohorts indicated the ATAD3B gene, which does not have ERα binding site within 20 kb of its TSS, to be significantly associated with poor patient survival.


Asunto(s)
Adenosina Trifosfatasas/genética , Neoplasias de la Mama/genética , Receptor alfa de Estrógeno/genética , Proteínas de la Membrana/genética , Proteínas Mitocondriales/genética , ATPasas Asociadas con Actividades Celulares Diversas , Neoplasias de la Mama/patología , Femenino , Humanos , Células MCF-7 , Análisis de Supervivencia , Transcripción Genética
20.
J Neuropathol Exp Neurol ; 71(1): 2-14, 2012 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-22157615

RESUMEN

Histochemical analysis of Alzheimer disease (AD) brain tissues indicates that butyrylcholinesterase (BuChE) is present in ß-amyloid (Aß) plaques. The role of BuChE in AD pathology is unknown, but an animal model developing similar BuChE-associated Aß plaques could provide insights. The APPSWE/PSEN1dE9 transgenic mouse (ADTg), which develops Aß plaques, was examined to determine if BuChE associates with these plaques, as in AD. We found that in mature ADTg mice, BuChE activity associated with Aß plaques. The Aß-, thioflavin-S- and BuChE-positive plaques mainly accumulated in the olfactory structures, cerebral cortex, hippocampal formation, amygdala, and cerebellum. No plaques were stained for acetylcholinesterase activity. The distribution and abundance of plaque staining in ADTg closely resembled many aspects of plaque staining in AD. Butyrylcholinesterase staining consistently showed fewer plaques than were detected with Aß immunostaining but a greater number of plaques than were visualized with thioflavin-S. Double-labeling experiments demonstrated that all BuChE-positive plaques were Aß positive, whereas only some BuChE-positive plaques were thioflavin-S positive. These observations suggest that BuChE is associated with a subpopulation of Aß plaques and may play a role in AD plaque maturation. A further study of this animal model could clarify the role of BuChE in AD pathology.


Asunto(s)
Enfermedad de Alzheimer/enzimología , Enfermedad de Alzheimer/patología , Precursor de Proteína beta-Amiloide , Butirilcolinesterasa/biosíntesis , Modelos Animales de Enfermedad , Placa Amiloide/enzimología , Placa Amiloide/patología , Presenilina-1 , Precursor de Proteína beta-Amiloide/genética , Animales , Encéfalo/enzimología , Encéfalo/patología , Masculino , Ratones , Ratones Endogámicos C3H , Ratones Endogámicos C57BL , Ratones Transgénicos , Presenilina-1/genética
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