Charting differences between tumors and normal tissue is a mainstay of cancer research. However, clonal tumor expansion from complex normal tissue architectures potentially obscures cancer-specific ...events, including divergent epigenetic patterns. Using whole-genome bisulfite sequencing of normal B cell subsets, we observed broad epigenetic programming of selective transcription factor binding sites coincident with the degree of B cell maturation. By comparing normal B cells to malignant B cells from 268 patients with chronic lymphocytic leukemia (CLL), we showed that tumors derive largely from a continuum of maturation states reflected in normal developmental stages. Epigenetic maturation in CLL was associated with an indolent gene expression pattern and increasingly favorable clinical outcomes. We further uncovered that most previously reported tumor-specific methylation events are normally present in non-malignant B cells. Instead, we identified a potential pathogenic role for transcription factor dysregulation in CLL, where excess programming by EGR and NFAT with reduced EBF and AP-1 programming imbalances the normal B cell epigenetic program.
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IJS, NUK, SBMB, UL, UM, UPUK
In chronic lymphocytic leukemia (CLL), a diverse set of genetic mutations is embedded in a deregulated epigenetic landscape that drives cancerogenesis. To elucidate the role of aberrant chromatin ...features, we mapped DNA methylation, seven histone modifications, nucleosome positions, chromatin accessibility, binding of EBF1 and CTCF, as well as the transcriptome of B cells from CLL patients and healthy donors. A globally increased histone deacetylase activity was detected and half of the genome comprised transcriptionally downregulated partially DNA methylated domains demarcated by CTCF. CLL samples displayed a H3K4me3 redistribution and nucleosome gain at promoters as well as changes of enhancer activity and enhancer linkage to target genes. A DNA binding motif analysis identified transcription factors that gained or lost binding in CLL at sites with aberrant chromatin features. These findings were integrated into a gene regulatory enhancer containing network enriched for B‐cell receptor signaling pathway components. Our study predicts novel molecular links to targets of CLL therapies and provides a valuable resource for further studies on the epigenetic contribution to the disease.
Synopsis
Transcriptome profiling and genome‐scale mapping of DNA methylation, seven histone modifications, nucleosome positions, chromatin accessibility, EBF1 and CTCF binding are performed in B cells from CLL patients and healthy donors.
Altered chromatin features were detected at 80% of the differentially regulated genes in CLL and histone deacetylase activity was globally increased.
Half of the CLL genome comprised partially DNA methylated domains that were transcriptionally downregulated, demarcated by CTCF and enriched for H3K9me3 and H3K27me3.
H3K4me3 was redistributed at CLL promoters, including loss of bivalent H3K4me3/H3K27me3 states, and substantial changes of enhancer activity were detected.
A gene regulatory network including enhancers was constructed around the transcription factors targeting 15 central binding motifs that were associated with aberrant CLL chromatin features. Genes involved in BCR signaling were enriched in the network.
Transcriptome profiling and genome‐scale mapping of DNA methylation, seven histone modifications, nucleosome positions, chromatin accessibility, EBF1 and CTCF binding are performed in B cells from CLL patients and healthy donors.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
As a result of the introduction of rapid benchtop sequencers, the time required to subculture a bacterial pathogen to extract sufficient DNA for library preparation can now exceed the time to ...sequence said DNA. We have eliminated this rate-limiting step by developing a protocol to generate DNA libraries for whole-genome sequencing directly from single bacterial colonies grown on primary culture plates.
We developed our protocol using single colonies of 17 bacterial pathogens responsible for severe human infection that were grown using standard diagnostic media and incubation conditions. We then applied this method to four clinical scenarios that currently require time-consuming reference laboratory tests: full identification and genotyping of salmonellae; identification of blaNDM-1, a highly transmissible carbapenemase resistance gene, in Klebsiella pneumoniae; detection of genes encoding staphylococcal toxins associated with specific disease syndromes; and monitoring of vaccine targets to detect vaccine escape in Neisseria meningitidis.
We validated our single-colony whole-genome sequencing protocol for all 40 combinations of pathogen and selective, non-selective or indicator media tested in this study. Moreover, we demonstrated the clinical value of this method compared with current reference laboratory tests.
This advance will facilitate the implementation of whole-genome sequencing into diagnostic and public health microbiology.
Objectives Epidemiological investigations of Legionnaires’ disease outbreaks rely on the rapid identification and typing of clinical and environmental Legionella isolates in order to identify and ...control the source of infection. Rapid bacterial whole-genome sequencing (WGS) is an emerging technology that has the potential to rapidly discriminate outbreak from non-outbreak isolates in a clinically relevant time frame. Methods We performed a pilot study to determine the feasibility of using bacterial WGS to differentiate outbreak from non-outbreak isolates collected during an outbreak of Legionnaires’ disease. Seven Legionella isolates (three clinical and four environmental) were obtained from the reference laboratory and sequenced using the Illumina MiSeq platform at Addenbrooke's Hospital, Cambridge. Bioinformatic analysis was performed blinded to the epidemiological data at the Wellcome Trust Sanger Institute. Results We were able to distinguish outbreak from non-outbreak isolates using bacterial WGS, and to confirm the probable environmental source. Our analysis also highlighted constraints, which were the small number of Legionella pneumophila isolates available for sequencing, and the limited number of published genomes for comparison. Conclusions We have demonstrated the feasibility of using rapid WGS to investigate an outbreak of Legionnaires’ disease. Future work includes building larger genomic databases of L pneumophila from both clinical and environmental sources, developing automated data interpretation software, and conducting a cost–benefit analysis of WGS versus current typing methods.
Antibiotic resistance in bacterial pathogens threatens the future of modern medicine. One such resistant pathogen is methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to nearly ...all β-lactam antibiotics, limiting treatment options. Here, we show that a significant proportion of MRSA isolates from different lineages, including the epidemic USA300 lineage, are susceptible to penicillins when used in combination with β-lactamase inhibitors such as clavulanic acid. Susceptibility is mediated by a combination of two different mutations in the mecA promoter region that lowers mecA-encoded penicillin-binding protein 2a (PBP2a) expression, and in the majority of isolates by either one of two substitutions in PBP2a (E246G or M122I) that increase the affinity of PBP2a for penicillin in the presence of clavulanic acid. Treatment of S. aureus infections in wax moth and mouse models shows that penicillin/β-lactamase inhibitor susceptibility can be exploited as an effective therapeutic choice for 'susceptible' MRSA infection. Finally, we show that isolates with the PBP2a E246G substitution have a growth advantage in the presence of penicillin but the absence of clavulanic acid, which suggests that penicillin/β-lactamase susceptibility is an example of collateral sensitivity (resistance to one antibiotic increases sensitivity to another). Our findings suggest that widely available and currently disregarded antibiotics could be effective in a significant proportion of MRSA infections.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
IMPORTANCE The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more ...effectively contain the spread of multidrug-resistant pathogens. OBJECTIVE To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. DESIGN, SETTING, AND PARTICIPANTS A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. MAIN OUTCOMES AND MEASURES Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. RESULTS We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these. CONCLUSIONS AND RELEVANCE The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance.
Two experiments explored the effects of imagery and text organization on what is learned from reading a passage. In each experiment, all Ss read three different concrete prose passages. Three ...different forms of organization were used for the passage sentences. Instruction to the subjects required half of them to visualize the passage information and half to repeat it to themselves. Comprehension was assessed in experiment one by asking multiple choice questions and in experiment two by asking for written recall of correct text relations. Overall, grouping the substantive sentences pertaining to a particular object and its attributes into a single paragraph produced the best comprehension. Randomized text resulted in the poorest comprehension. Imagery was more successful for learning than repetition. There were also interaction effects between text organization and reading strategy. Regardless of text organization, imagery instructed Ss recalled significantly more correct text relations than repetition subjects. Imagery also resulted in a significantly higher level of inference making and in recall protocol organizations which were consistent with figural representations of text information./// French Deux essais ont analysé les effets de l'organisation de texte et des images sur ce qui s'apprend a partir de la lecture d'un passage. Dans chaque essai, chaque élève a lu trois passages de prose concrète différents. Trois formes d'organisation différentes ont été utilisées pour les phrases de passage. Les instructions données aux sujets étaient les suivantes: la moitié d'entre eux devaient se représenter de façon visuelle l'information du passage et l'autre moitié se la répéter. La compréhension a été évaluée dans l'essai I en posant des questions à choix multiples et dans l'essai 2 en demandant des rappels écrits des relations correctes du texte. De façon globale, le fait de grouper les phrases indépendantes ayant trait à un objet particulier et ses attributs en un seul paragraphe, a produit la meilleure compréhension. Un texte au hasard a produit l'effet contraire. L'usage des images a eu plus de succès que la répétition. On a observé des effets d'interaction entre l'organisation de texte et la stratégie de lecture. Sans se préoccuper de l'organisation de texte, les élèves qui ont appris par l'image se sont mieux souvenus de façon significative des relations de text correctes que les sujets qui ont appris par la répétition. L'image a également produit un niveau considérablement plus élevé de déduction et de rappel des organisations de forme qui étaient en accord avec les représentations à symboles de l'information de texte./// Spanish Dos experimentos exploraron los efectos del conjunto de imágenes y organización de texto en lo que se aprende leyendo un pasaje. En cada experimento, todos los participantes leyeron tres porciones diferentes de prosa. Las oraciones del pasaje estaban organizadas en tres modalidades distintas. La instrucción requería que la mitad de los sujetos visualizaran la información del pasaje leído y la otra mitad se lo repitieran a sí mismos. Comprensión se midió en Experimento 1 haciéndose preguntas de opción alternativa, y en Experimento 2 pidiéndose un sumario escrito indicando la relación de ideas propias del texto. En general, la agrupación de oraciones clave relativas a un tópico concreto y sus detalles en un párrafo único, produjo la mejor comprensión. El pasaje sin orden ni concierto resultó en el índice de comprensión más bajo. La visualización de un conjunto de imágenes fue más efectiva en el processo de aprendizaje que en el de repetición. También se observaron efectos de interacción entre la organización del pasaje y estrategias usadas para la lectura. Prescindiendo de la organización del pasaje, los sujetos instruidos en la visualización de un conjunto de imágenes recordaron con más acierto la relación de ideas propias del texto que los que fueron instruidos con el proceso de repetición. La visualización de un conjunto de imágenes elevó a un nivel considerablemente más alto el proceso de deducción y en la recapitulación protocolaria de organización consistente con las descripciones en el pasaje.
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