RNA polymerase II promotes the organization of chromatin following DNA replication

Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.

Functional Contribution and Clinical Implication of Cancer-Associated Fibroblasts in Glioblastoma

PURPOSE

The abundance and biological contribution of cancer-associated fibroblasts (CAF) in glioblastoma (GBM) are poorly understood. Here, we aim to uncover its molecular signature, cellular roles, and potential tumorigenesis implications.

EXPERIMENTAL DESIGN

We first applied single-cell RNA sequencing (RNA-seq) and bioinformatics analysis to identify and characterize stromal cells with CAF transcriptomic features in human GBM tumors. Then, we performed functional enrichment analysis and in vitro assays to investigate their interactions with malignant GBM cells.

RESULTS

We found that CAF abundance was low but significantly correlated with tumor grade, poor clinical outcome, and activation of extracellular matrix remodeling using three large cohorts containing bulk RNA-seq data and clinical information. Proteomic analysis of a GBM-derived CAF line and its secretome revealed fibronectin (FN1) as a critical candidate factor mediating CAF functions. This was validated using in vitro cellular models, which demonstrated that CAF-conditioned media and recombinant FN1 could facilitate the migration and invasion of GBM cells. In addition, we showed that CAFs were more abundant in the mesenchymal-like state (or subtype) than in other states of GBMs. Interestingly, cell lines resembling the proneural state responded to the CAF signaling better for the migratory and invasive phenotypes.

CONCLUSIONS

Overall, this study characterized the molecular features and functional impacts of CAFs in GBM, alluding to novel cell interactions mediated by CAFs in the GBM microenvironment.

αKG-mediated carnitine synthesis promotes homologous recombination via histone acetylation

Homologous recombination (HR) deficiency enhances sensitivity to DNA damaging agents commonly used to treat cancer. In HR-proficient cancers, metabolic mechanisms driving response or resistance to DNA damaging agents remain unclear. Here we identified that depletion of alpha-ketoglutarate (αKG) sensitizes HR-proficient cells to DNA damaging agents by metabolic regulation of histone acetylation. αKG is required for the activity of αKG-dependent dioxygenases (αKGDDs), and prior work has shown that changes in αKGDD affect demethylases. Using a targeted CRISPR knockout library consisting of 64 αKGDDs, we discovered that Trimethyllysine Hydroxylase Epsilon (TMLHE), the first and rate-limiting enzyme in de novo carnitine synthesis, is necessary for proliferation of HR-proficient cells in the presence of DNA damaging agents. Unexpectedly, αKG-mediated TMLHE-dependent carnitine synthesis was required for histone acetylation, while histone methylation was affected but dispensable. The increase in histone acetylation via αKG-dependent carnitine synthesis promoted HR-mediated DNA repair through site- and substrate-specific histone acetylation. These data demonstrate for the first time that HR-proficiency is mediated through αKG directly influencing histone acetylation via carnitine synthesis and provide a metabolic avenue to induce HR-deficiency and sensitivity to DNA damaging agents.

TMEM106B Puncta Is Increased in Multiple Sclerosis Plaques, and Reduced Protein in Mice Results in Delayed Lipid Clearance Following CNS Injury

During inflammatory, demyelinating diseases such as multiple sclerosis (MS), inflammation and axonal damage are prevalent early in the course. Axonal damage includes swelling, defects in transport, and failure to clear damaged intracellular proteins, all of which affect recovery and compromise neuronal integrity. The clearance of damaged cell components is important to maintain normal turnover and restore homeostasis. In this study, we used mass spectrometry to identify insoluble proteins within high-speed/mercaptoethanol/sarcosyl-insoluble pellets from purified white matter plaques isolated from the brains of individuals with relapsing-remitting MS (RRMS). We determined that the transmembrane protein 106B (TMEM106B), normally lysosome-associated, is insoluble in RRMS plaques relative to normal-appearing white matter from individuals with Alzheimer's disease and non-neurologic controls. Relative to wild-type mice, hypomorphic mice with a reduction in TMEM106B have increased axonal damage and lipid droplet accumulation in the spinal cord following myelin-oligodendrocyte-glycoprotein-induced experimental autoimmune encephalomyelitis. Additionally, the corpora callosa from cuprizone-challenged hypomorphic mice fail to clear lipid droplets efficiently during remyelination, suggesting that when TMEM106B is compromised, protein and lipid clearance by the lysosome is delayed. As TMEM106B contains putative lipid- and LC3-binding sites, further exploration of these sites is warranted.

Parallel genome-scale CRISPR screens distinguish pluripotency and self-renewal

Pluripotent stem cells are defined by both the ability to unlimitedly self-renew and differentiate to any somatic cell lineage, but understanding the mechanisms that control stem cell fitness versus the pluripotent cell identity is challenging. We performed four parallel genome-scale CRISPR-Cas9 screens to investigate the interplay between these two aspects of pluripotency. Our comparative analyses led to the discovery of genes with distinct roles in pluripotency regulation, including many mitochondrial and metabolism regulators crucial for stem cell fitness, and chromatin regulators that control stem cell identity. We further discovered a core set of factors that control both stem cell fitness and pluripotency identity, including an interconnected network of chromatin factors that safeguard pluripotency. Our unbiased and systematic screening and comparative analyses disentangle two interconnected aspects of pluripotency, provide rich datasets for exploring pluripotent cell identity versus self-renewal, and offer a valuable model for categorizing gene function in broad biological contexts.

MODELING REACTIVATED HETEROCHROMATIN USING AN AGING 3D CELL MODEL

Chromatin state and dynamics is modulated by chromatin interacting proteins, in particular histones and their post-translational modifications. We investigate the chromatin-bound proteome in aging to understand how DNA readout is misregulated in senescent cells. We focus on domains of reactivated heterochromatin, i.e. chromatin domains undergoing anomalous decondensation and decorated by histones co-modified with markers of condensed heterochromatin and active transcription. We optimize our mass spectrometry methods 3D cell models, and then apply them on B-cells retrieved from Ashkenazi Jews donors. In this cohort, we particularly focus on offsprings of exceptional longevity, i.e. individuals in their 70s with projected longer lifespan due to their centenarians ancestors. Preliminary data on 60 individuals revealed the enrichment of unusual histone modifications in the OPEL group, the group we utilize as indicator of projected longer lifespan. We have then applied biochemistry techniques to identify the role of these unusual modifications on chromatin readout.

Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue

Flat cultures of mammalian cells are a widely used in vitro approach for understanding cell physiology, but this system is limited in modeling solid tissues due to unnaturally rapid cell replication. This is particularly challenging when modeling mature chromatin, as fast replicating cells are frequently involved in DNA replication and have a heterogeneous polyploid population. Presented below is a workflow for modeling, treating, and analyzing quiescent chromatin modifications using a three-dimensional (3D) cell culture system. Using this protocol, hepatocellular carcinoma cell lines are grown as reproducible 3D spheroids in an incubator providing active nutrient diffusion and low shearing forces. Treatment with sodium butyrate and sodium succinate induced an increase in histone acetylation and succinylation, respectively. Increases in levels of histone acetylation and succinylation are associated with a more open chromatin state. Spheroids are then collected for isolation of cell nuclei, from which histone proteins are extracted for the analysis of their post-translational modifications. Histone analysis is performed via liquid chromatography coupled online with tandem mass spectrometry, followed by an in-house computational pipeline. Finally, examples of data representation to investigate the frequency and occurrence of combinatorial histone marks are shown.

[Asthma in clinical practice: from inflammatory phenotypes to personalized treatment]

Asthma is a chronic inflammatory disease of the airways. Classification of asthma in different phenotypes has therapeutic implications and may lead to personalized medicine. Induced sputum is the gold standard for asthma phenotyping but is complex, time-consuming and not widely available. The combination of different biomarkers such as exhaled nitric oxide, blood eosinophils and total serum IgE levels allows the prediction of inflammatory phenotype in 58% of asthmatic patients when sputum is not available. We recently demonstrated the interest of measuring volatile organic compounds in exhaled breath to phenotype asthma. These compounds could play an important role in the future to predict the response to expensive biologicals available in severe asthma to reduce exacerbations and the use of systemic corticosteroids.

[Probiotics in asthma treatment]

Asthma is the most prevalent chronic inflammatory airway disease worldwide. The gut microbiota possesses an important link with the development of the immunity in youth and a dysregulation of the gut flora was implicated in the asthmatic disease emergence. Moreover, a dysregulation of the intestinal microbiota exists in asthmatic individual. Probiotics are micro-organisms that can regulate our microbiome conferring potential beneficial effects on health. Thereby, their use in asthma prevention and treatment is attractive and could lead to new therapeutic perspectives. Indeed, they are well tolerated and safe and possess anti-inflammatory and immunoregulatory properties. This article is intended to update the current state of knowledge regarding the use of probiotics in the context of asthma.

Circular versus linear RNA topology: different modes of RNA-RNA interactions in vitro and in human cells

Circular RNA is progressively reported to occur in various species including mammals where it is thought to be involved in the post-transcriptional regulation of gene expression, partly via interactions with microRNA. Here, we asked whether the circular topology causes functional differences to linear forms when interacting with short RNA strands in vitro and in human cells. Kinetic studies with human bladder cancer-derived synthetic circular RNA versus linear transcripts, respectively, with short oligoribonucleotides showed similar association rates for both topologies. Conversely, a substantial topology-related difference was measured for the activation entropy and the activation enthalpy of RNA–RNA annealing. This finding strongly indicates a significant difference of the mechanism of RNA–RNA interactions. To investigate whether these characteristics of circular RNA are biologically meaningful we performed transient transfection experiments with a microRNA-regulated expression system for luciferase in bladder cancer-derived cells. We co-transfected linear or circular RNA containing one microRNA binding site for the target-suppressing microRNA mlet7a. Here, the circular isoform showed a strongly increased competition with microRNA function versus linear versions. In summary, this study suggests novel topology-related characteristics of RNA–RNA interactions involving circRNA in vitro and in living cells.

Asthma in elderly is characterized by increased sputum neutrophils, lower airway caliber variability and air trapping

BACKGROUND

Elderly asthmatics represent an important group that is often excluded from clinical studies. In this study we wanted to present characteristics of asthmatics older than 70 years old as compared to younger patients.

METHODS

We conducted a retrospective analysis on a series of 758 asthmatics subdivided in three groups: lower than 40, between 40 and 70 and older than 70. All the patients who had a successful sputum induction were included in the study.

RESULTS

Older patients had a higher Body Mass Index, had less active smokers and were more often treated with Long Acting anti-Muscarinic Agents. We found a significant increase in sputum neutrophil counts with ageing. There was no significant difference in blood inflammatory cell counts whatever the age group. Forced expiratory volume in one second (FEV₁) and FEV₁/FVC values were significantly lower in elderly who had lower bronchial hyperresponsiveness and signs of air trapping. We found a lower occurrence of the allergic component in advanced ages. Asthmatics older than 70 years old had later onset of the disease and a significant longer disease duration.

CONCLUSION

Our study highlights that asthmatics older than 70 years old have higher bronchial neutrophilic inflammation, a poorer lung function, signs of air trapping and lower airway variability. The role of immunosenescence inducing chronic low-grade inflammation in this asthma subtype remains to be elucidated.

Chronic oral corticosteroids use and persistent eosinophilia in severe asthmatics from the Belgian severe asthma registry

BACKGROUND

Severe asthma (SA) may require frequent courses or chronic use of oral corticosteroids (OCS), inducing many known side effects and complications. Therefore, it is important to identify risk factors of chronic use of OCS in SA, considering the heterogeneity of clinical and inflammatory asthma phenotypes. Another aim of the present analysis is to characterize a subpopulation of severe asthmatics, in whom blood eosinophil counts (BEC) remain elevated despite chronic OCS treatment.

METHODS

In a cross-sectional analysis of 982 SA patients enrolled in the Belgian Severe Asthma Registry (BSAR) between March 2009 and February 2019, we investigated the characteristics of the OCS treated patients with special attention to their inflammatory profile.

RESULTS

At enrollment, 211 (21%) SA patients were taking maintenance OCS (median dose: 8 [IQR: 5-10]) mg prednisone equivalent). BEC was high (> 400/mm3) in 44% of the OCS treated population. Multivariable logistic regression analysis showed that risk factors for chronic use of OCS in SA were late-onset asthma (i.e. age of onset > 40 yr), frequent exacerbations (i.e. ≥2 exacerbations in the previous year) and non-atopic asthma. Late-onset asthma was also a predictor for persistently high BEC in OCS treated SA patients.

CONCLUSION

These data showed a significant association between a persistently high BEC and late-onset asthma in OCS treated SA patients. Whether it is poor compliance to treatment or corticosteroid insensitivity the reasons for this association warrants further investigation.

Predictors of a good response to inhaled corticosteroids in obesity-associated asthma

INTRODUCTION

Asthma in obese subjects is poorly understood. According to GINA guidelines, pulmonologists increase ICS in case of poor asthma control but lung volume restriction may also worsen respiratory symptoms in obese asthmatics leading to overtreatment in this subpopulation.

METHODS

We conducted a retrospective study on 1217 asthmatics recruited from University Hospital of Liege. 92 patients with a BMI ≥30 came at least two times at the asthma clinic (mean interval: 335 days). In this obese population, we identified predictors of good (decrease in ACQ ≥0.5) versus poor response (rise in ACQ ≥0.5) to ICS step-up therapy.

RESULTS

Obese asthmatics had a poorer asthma control and quality of life as compared to non-obese and exhibited reduced FVC, higher levels of blood leucocytes and markers of systemic inflammation. The proportion of asthma inflammatory phenotypes was similar to that observed in a general population of asthmatics. Among uncontrolled obese asthmatics receiving ICS step-up therapy, 53% improved their asthma control while 31% had a worsening of their asthma. Uncontrolled obese asthmatics showing a good response to increase in ICS had higher ACQ, lower CRP levels, higher sputum eosinophil counts and higher FeNO levels at visit 1. Uncontrolled obese asthmatics that worsened after increasing the dose of ICS had lower FVC, lower sputum eosinophil counts and higher sputum neutrophil counts.

CONCLUSION

We observed poorer asthma control in obese asthmatics despite similar bronchial inflammation. Managing obese asthmatics according to ACQ alone seems to underestimate asthma control and the contribution of restriction to dyspnea. Increasing the dose of ICS in the absence of sputum eosinophilic inflammation or in the presence of restriction or bronchial neutrophilia led to poorer asthma control. In those patients, management of obesity should be the first choice.

Risk of stroke after bereavement-a systematic literature review

Several studies have suggested that psychological stress may increase the risk of stroke. However, this link remains a controversial issue because of conflicting findings. Bereavement, the loss of a close relative, is considered a severely stressful life event. Increased risk of stroke could thus be expected after bereavement if stress plays a causal role. We aimed to evaluate the association between bereavement and stroke by performing a systematic review of the existing literature. The literature search was conducted according to the PRISMA guidelines for systematic reviews. A search in Medline and Embase identified eligible studies, which were reviewed by two researchers independently according to specific inclusion criteria. We included six studies: five cohort studies and one case-crossover study. Five studies found that loss of a first-degree relative was associated with a 1.1- to 2.4-fold higher risk of stroke. However, one study found a statistically significant overall risk only for women. Five studies evaluated the risk of stroke according to time since the loss; one study found no association, two studies indicated short-term effect, one study indicated long-term effect, and one study indicated both short-term and long-term effect. Three studies stratified their analysis by sex; two found higher association in bereaved women than men. Our systematic review suggests that bereavement-related stress is associated with a higher risk of stroke. As relatively few studies were identified, new studies are needed to verify this association. These should aim to quantify the risk, describe the effect of time since bereavement, and identify risk-modifying factors.

Changing places: policies to make a healthy choice the easy choice

The environments where people live, learn, work and play have a profound influence on health. Policies affecting physical activity, access to healthy foods, and the prevalence of tobacco products in our neighbourhoods can either promote or discourage behaviour associated with cancer and other chronic diseases. Given the regulatory landscape in the USA, where federal law controls venues with the widest possible scope (such as television and the Internet), states and cities have tremendous latitude in regulating the physical environments that residents experience every day. This paper explores innovative and meaningful ways to improve public health through policy initiatives targeted specifically at places such as homes and neighbourhoods, schools, shops, restaurants, bars and recreational areas.

Development of a Standardized Susceptibility Test forCampylobacterwith Quality-Control Ranges for Ciprofloxacin, Doxycycline, Erythromycin, Gentamicin, and Meropenem

A standardized agar dilution susceptibility testing method was developed for Campylobacter that consisted of testing on Mueller-Hinton medium supplemented with 5% defibrinated sheep blood in an atmosphere of 10% CO2, 5% O2, and 85% N2. Campylobacter jejuni ATCC 33560 was identified as a quality-control (QC) strain. Minimal inhibitory concentration (MIC) QC ranges were determined for two incubation time/temperature combinations: 36 degrees C for 48 hr and 42 degrees C for 24 hr. Quality-control ranges were determined for ciprofloxacin, doxycycline, erythromycin, gentamicin, and meropenem. For all antimicrobial agents tested at both temperatures, 95-100% of the QC MIC results fell within recommended QC ranges. Twenty-one Campylobacter clinical isolates, encompassing five species of Campylobacter (C. jejuni, C. coli, C. jejuni, subsp. doylei, C. fetus, and C. lari) were tested in conjunction with the C. jejuni QC strain. While C. jejuni and C. coli could be reliably tested under both test conditions, growth of C. jejuni subsp. doylei, C. fetus, and C. lari isolates was inconsistent when incubated at 42 degrees C. Therefore, it is recommended that these species only be tested at 36 degrees C.

BOD5 estimation for pulp and paper mill effluent using UV absorbance

A novel method based on UV absorbance, is presented for estimating the BOD5 in pulp and paper mill effluent. This method could eventually be incorporated into an on-line sensor for BOD5 that is suitable for process control applications. Two streams, the reactor entrance and the final effluent, from two different mills were studied. One mill employed the Kraft pulping process, while the second mill was a thermo-mechanical one. The absorbance over the range 200-350 nm showed significant differences between the two mills. Because the two mills use very distinct processes, separate correlations were used to relate the absorbance to the BOD5 for both the mills. Results indicate that prediction of reactor entrance BOD5 was reasonable, whereas prediction of final effluent BOD5 was inaccurate, for both mills. Also studied was the effect of aeration on BOD5 results obtained at low BOD5 values for the Kraft mill.

High-risk population health management--achieving improved patient outcomes and near-term financial results

OBJECTIVE

A managed care organization sought to achieve efficiencies in care delivery and cost savings by anticipating and better caring for its frail and least stable members.

STUDY DESIGN

Time sequence case study of program intervention across an entire managed care population in its first year compared with the prior baseline year.

PATIENTS AND METHODS

Key attributes of the intervention included predictive registries of at-risk members based on existing data, relentless focus on the high-risk group, an integrated clinical and psychosocial approach to assessments and are planning, a reengineered care management process, secured Internet applications enabling rapid implementation and broad connectivity, and population-based outcomes metrics derived from widely used measures of resource utilization and functional status.

RESULTS

Concentrating on the highest-risk group, which averaged just 1.1% prevalence in the total membership, yielded bottom line results. When the year before program implementation (July 1997 through June 1998) was compared with the subsequent year, the total population's annualized commercial admission rate was reduced 5.3%, and seniors' was reduced 3.0%. A claims-paid analysis exclusively of the highest-risk group revealed that their efficiencies and savings overwhelmingly contributed to the membershipwide effect. This subgroup's costs dropped 35.7% from preprogram levels of $2590 per member per month (excluding pharmaceuticals). During the same time, patient-derived cross-sectional functional status rose 12.5%.

CONCLUSIONS

A sharply focused, Internet-deployed case management strategy achieved economic and functional status results on a population basis and produced systemwide savings in its first year of implementation.

Fracture of the distal radius: classification of treatment and indications for external fixation

A number of classifications have been created for fractures of the distal radius. We describe those of Older et al., Frykman, Thomas, Melone, McMurtry, Fernandez, the Mayo and the AO/ASIF. These classifications help to identify unstable fractures and offer insight into the indications for external skeletal fixation.

Major congenital anomalies in infants and glycosylated hemoglobin levels in insulin-requiring diabetic mothers

Glycosylated hemoglobin levels were obtained in 133 diabetic pregnancies. Nongestational diabetic mothers delivered of infants with major congenital anomalies had significantly higher glycosylated hemoglobin levels than the remaining nongestational diabetic mothers (P less than .001). The higher a mother's glycosylated hemoglobin level, the higher her risk of having a severely affected infant was. The positive predictive value for a nongestational diabetic mother having an infant with severe congenital anomalies was 26% if the glycosylated hemoglobin level was greater than or equal to 11%, 40% if the level was greater than or equal to 12%, and 56% if the level greater than or equal to 13%. However, high glycosylated hemoglobin levels in insulin-requiring gestational diabetic mothers were not predictive of major congenital anomalies.