Integration of a multi-omics stem cell differentiation dataset using a dynamical model.

Stem cell differentiation is a highly dynamic process involving pervasive changes in gene expression. The large majority of existing studies has characterized differentiation at the level of individual molecular profiles, such as the transcriptome or the proteome. To obtain a more comprehensive view, we measured protein, mRNA and microRNA abundance during retinoic acid-driven differentiation of mouse embryonic stem cells. We found that mRNA and protein abundance are typically only weakly correlated across time. To understand this finding, we developed a hierarchical dynamical model that allowed us to integrate all data sets. This model was able to explain mRNA-protein discordance for most genes and identified instances of potential microRNA-mediated regulation. Overexpression or depletion of microRNAs identified by the model, followed by RNA sequencing and protein quantification, were used to follow up on the predictions of the model. Overall, our study shows how multi-omics integration by a dynamical model could be used to nominate candidate regulators.

Feasibility of aortic aneurysm sac embolization using a novel shape memory polymer embolic device.

BACKGROUND: We investigated the feasibility of aneurysm sac embolization using a novel self-expanding porous shape memory polymer (SMP) device during endovascular aortic abdominal or thoracic aneurysm repair (EVAR). METHODS: Retrospective analysis of consecutive patients treated at 2 centers in Germany. Patients were treated from January 2019 to July 2021 with follow-up at 7 days and 3, 6, and 12 months. Aneurysm sacs were implanted with SMP devices immediately following endograft placement during the same procedure. Primary endpoint was technically successful SMP-device deployment into the aneurysm sac outside the endograft. Secondary endpoints were changes in aneurysm volume and associated complications (e.g., endoleaks). RESULTS: We included 18 patients (16 males), aged 72 ± 9 years, achieving 100% technical success. Mean preprocedure aortic aneurysm sac volume was 195 ± 117 mL with a perfused aneurysm volume of 97 ± 60 mL. A mean of 24 ± 12 SMP devices per patient were used (range 5-45, corresponding to 6.25-56.25 mL expanded embolic material volume). All evaluable patients exhibited sac regression except 2 patients yet to reach 3-month follow-up. At mean 11 ± 7 months (range 3-24), change in aneurysm volume from baseline was -30 ± 21 mL (p < 0.001). In 8 patients, aneurysm regression was observed despite type 2 endoleaks in 6 and type 1A endoleaks in 2, none of them requiring further intervention to date. No morbidity or mortality related to this treatment occurred. CONCLUSIONS: SMP devices for aortic aneurysm sac embolization during endovascular repair appear feasible and safe in this small case series. Prospective studies are needed. KEY POINTS: • Shape memory polymer is a novel, self-expanding, porous, and radiolucent embolic device material. • Aortic aneurysm sacs were treated with polymer devices immediately following endograft placement. • Aortic aneurysm sac regression was observed in all patients with over 3-month follow-up. • Aortic aneurysm sac regression was observed even in the presence of endoleaks.

Mpox outbreak in the Netherlands, 2022: public health response, characteristics of the first 1,000 cases and protection of the first-generation smallpox vaccine.

In early May 2022, a global outbreak of mpox started among persons without travel history to regions known to be enzootic for monkeypox virus (MPXV). On 8 August 2022, the Netherlands reported its 1,000th mpox case, representing a cumulative incidence of 55 per million population, one of the highest cumulative incidences worldwide. We describe characteristics of the first 1,000 mpox cases in the Netherlands, reported between 20 May and 8 August 2022, within the context of the public health response. These cases were predominantly men who have sex with men aged 31-45 years. The vast majority of infections were acquired through sexual contact with casual partners in private or recreational settings including LGBTQIA+ venues in the Netherlands. This indicates that, although some larger upsurges occurred from point-source and/or travel-related events, the outbreak was mainly characterised by sustained transmission within the Netherlands. In addition, we estimated the protective effect of first-generation smallpox vaccine against moderate/severe mpox and found a vaccine effectiveness of 58% (95% CI: 17-78%), suggesting moderate protection against moderate/severe mpox symptoms on top of any possible protection by this vaccine against MPXV infection and disease. Communication with and supporting the at-risk population in following mitigation measures remains essential.

Management of pediatric appendicitis during the COVID-19 pandemic: A nationwide multicenter cohort study.

BACKGROUND: The COVID-19 pandemic has impacted timely access to care for children, including patients with appendicitis. This study aimed to evaluate the effect of the COVID-19 pandemic on management of appendicitis and patient outcomes. METHODS: A multicenter retrospective study was performed including 19 children's hospitals from April 2019-October 2020 of children (age≤18 years) diagnosed with appendicitis. Groups were defined by each hospital's city/state stay-at-home orders (SAHO), designating patients as Pre-COVID (Pre-SAHO) or COVID (Post-SAHO). Demographic, treatment, and outcome data were obtained, and univariate and multivariable analysis was performed. RESULTS: Of 6,014 patients, 2,413 (40.1%) presented during the COVID-19 pandemic. More patients were managed non-operatively during the COVID-19 pandemic compared to before the pandemic (147 (6.1%) vs 144 (4.0%), p < 0.001). Despite this change, there was no difference in the proportion of complicated appendicitis between groups (1,247 (34.6%) vs 849 (35.2%), p = 0.12). COVID era non-operative patients received fewer additional procedures, including interventional radiology (IR) drain placements, compared to pre-COVID non-operative patients (29 (19.7%) vs 69 (47.9%), p < 0.001). On adjusted analysis, factors associated with increased odds of receiving non-operative management included: increasing duration of symptoms (OR=1.01, 95% CI: 1.01-1.012), African American race (OR=2.4, 95% CI: 1.3-4.6), and testing positive for COVID-19 (OR=10.8, 95% CI: 5.4-21.6). CONCLUSION: Non-operative management of appendicitis increased during the COVID-19 pandemic. Additionally, fewer COVID era cases required IR procedures. These changes in the management of pediatric appendicitis during the COVID pandemic demonstrates the potential for future utilization of non-operative management.

A gastruloid model of the interaction between embryonic and extra-embryonic cell types.

Stem-cell derived in vitro systems, such as organoids or embryoids, hold great potential for modeling in vivo development. Full control over their initial composition, scalability, and easily measurable dynamics make those systems useful for studying specific developmental processes in isolation. Here we report the formation of gastruloids consisting of mouse embryonic stem cells (mESCs) and extraembryonic endoderm (XEN) cells. These XEN-enhanced gastruloids (XEGs) exhibit the formation of neural epithelia, which are absent in gastruloids derived from mESCs only. By single-cell RNA-seq, imaging, and differentiation experiments, we demonstrate the neural characteristics of the epithelial tissue. We further show that the mESCs induce the differentiation of the XEN cells to a visceral endoderm-like state. Finally, we demonstrate that local inhibition of WNT signaling and production of a basement membrane by the XEN cells underlie the formation of the neuroepithelial tissue. In summary, we establish XEGs to explore heterotypic cellular interactions and their developmental consequences in vitro.

EEG-fMRI: Ballistocardiogram Artifact Reduction by Surrogate Method for Improved Source Localization.

For the analysis of simultaneous EEG-fMRI recordings, it is vital to use effective artifact removal tools. This applies in particular to the ballistocardiogram (BCG) artifact which is difficult to remove without distorting signals of interest related to brain activity. Here, we documented the use of surrogate source models to separate the artifact-related signals from brain signals with minimal distortion of the brain activity of interest. The artifact topographies used for surrogate separation were created automatically using principal components analysis (PCA-S) or by manual selection of artifact components utilizing independent components analysis (ICA-S). Using real resting-state data from 55 subjects superimposed with simulated auditory evoked potentials (AEP), both approaches were compared with three established BCG artifact removal methods: Blind Source Separation (BSS), Optimal Basis Set (OBS), and a mixture of both (OBS-ICA). Each method was evaluated for its applicability for ERP and source analysis using the following criteria: the number of events surviving artifact threshold scans, signal-to-noise ratio (SNR), error of source localization, and signal variance explained by the dipolar model. Using these criteria, PCA-S and ICA-S fared best overall, with highly significant differences to the established methods, especially in source localization. The PCA-S approach was also applied to a single subject Berger experiment performed in the MRI scanner. Overall, the removal of BCG artifacts by the surrogate methods provides a substantial improvement for the analysis of simultaneous EEG-fMRI data compared to the established methods.

Pediatric Trauma Arrival Times and the Swing Shift.

BACKGROUND: Trauma center staff and trainees are often assigned to a day and night shift. However, for adult trauma, the swing shift has been found to offer superior clinical exposure compared with a standard day or night shift for trainees. We characterized patterns in pediatric trauma arrival times based on the hour, weekday, and month and studied whether or not the swing shift also maximizes exposure to hands-on experiences in managing pediatric trauma. METHODS: We performed a retrospective review of the trauma database at our urban, level 2 pediatric trauma center. We identified all the pediatric trauma activations in the last 13 years (2006-2018). A retrospective shift log was created, which included day (7:00 am to 7:00 pm), night (7:00 pm to 7:00 am), and swing (noon to midnight) shifts. The shifts were compared using the Wilcoxon match-pairs signed rank test. Weekends data were also compared with weekdays, and comparisons were also made for pediatric patients with Injury Severity Scores (ISS) >15. RESULTS: There were 3532 pediatric patients identified for our study. The swing shift had 1.98 times more activations than the night shift, and 1.33 more than the day shift (P < 0.001). The swing shift was also superior to both the day and night shifts for exposure to patients with Injury Severity Score greater than 15 (P < 0.001). Weekend days had 1.28 times more trauma than the weekdays (P < 0.001). Peak arrival time was between the hours of 3:00 pm and 9:00 pm, and patient age did not have an effect on this trend. CONCLUSIONS: Experience in managing pediatric trauma patients will improve for trainees who utilize the swing shift. In addition, the hours between 3:00 pm and 9:00 pm on weekends may represent a time of particularly high likelihood of pediatric trauma arrivals, which may require extra staff and hospital resources.Level of Evidence: Therapeutic Study, Level IV.

An International, Multicenter Retrospective Observational Study to Assess Technical Success and Clinical Outcomes of Patients Treated with an Endovascular Aneurysm Sealing Device for Type III Endoleak.

INTRODUCTION: Type III endoleaks post-endovascular aortic aneurysm repair (EVAR) warrant treatment because they increase pressure within the aneurysm sac leading to increased rupture risk. The treatment may be difficult with regular endovascular devices. Endovascular aneurysm sealing (EVAS) might provide a treatment option for type III endoleaks, especially if located near the flow divider. This study aims to analyze clinical outcomes of EVAS for type III endoleaks after EVAR. METHODS: This is an international, retrospective, observational cohort study including data from 8 European institutions. RESULTS: A total of 20 patients were identified of which 80% had a type IIIb endoleak and the remainder (20%) a type IIIa endoleak. The median time between EVAR and EVAS was 49.5 months (28.5-89). Mean AAA diameter prior to EVAS revision was 76.6±19.9 mm. Technical success was achieved in 95%, 1 patient had technical failure due to a postoperative myocardial infarction resulting in death. Mean follow-up was 22.8±15.2 months. During follow-up 1 patient had a type Ia endoleak, and 1 patient had a new type IIIa endoleak at an untreated location. There were 5 patients with aneurysm growth. Five patients underwent AAA-related reinterventions indications being: growth with type II endoleak (n=3), type Ia endoleak (n=1), and iliac aneurysm (n=1). At 1-year follow-up, the freedom from clinical failure was 77.5%, freedom from all-cause mortality 94.7%, freedom from aneurysm-related mortality 95%, and freedom from aneurysm-related reinterventions 93.8%. CONCLUSION: The EVAS relining can be safely performed to treat type III endoleaks with an acceptable technical success rate, a low 30-day mortality rate and no secondary ruptures at short-term follow-up. The relatively low clinical success rates, related to reinterventions and AAA enlargement, highlight the need for prolonged follow-up.

Relative Source Power: A novel method for localizing epileptiform EEG discharges.

OBJECTIVE: To validate relative source power (RSP) imaging of extratemporal interictal epileptiform discharges (IEDs). METHODS: The accuracy of RSP was validated in a cohort of patients with extratemporal focal epilepsy and a confined epileptogenic lesion (<19 cm3) using distance to the lesion, concordance with resected area and postoperative outcome. Performance was compared with three conventional methods: voltage maps, equivalent current dipole and a distributed source model. RESULTS: Thirty-three of 41 consecutive patients (80%) had IED averages suitable for analysis. While the peak negativity in voltage maps localized above the epileptogenic lesion only in 18 cases, RSP-maps matched in 29 cases (88%, p < 0.0026). Source localization showed a median distance of 9.8 mm from the lesion. Source-regions with 20 mm radius included 98% of all source-to-lesion distances. In the 21 surgical cases, outcome showed a sensitivity of 82.35% and specificity of 50% without significant differences between the three source imaging methods. CONCLUSIONS: RSP-maps provide a rapid, intuitive and more accurate source estimation than voltage maps. At sublobar level, RSP localizes with an accuracy similar to conventional methods and results of previous studies. SIGNIFICANCE: The definition of a source region with 20 mm radius helps in guiding further exploration in extratemporal focal epilepsy.

Taking the EEG Back Into the Brain: The Power of Multiple Discrete Sources.

Background: In contrast to many neuroimaging modalities, clinical interpretation of EEG does not take advantage of post-processing and digital signal analysis. In most centers, EEG is still interpreted at sensor level, exactly as half a century ago. A major task in clinical EEG interpretation is the identification of interictal epileptiform discharges (IEDs). However, due to the overlap of background activity, IEDs can be hard to detect in the scalp EEG. Since traditional montages, like bipolar and average reference, are linear transformations of the recorded channels, the question is whether we can provide linear transformations of the digital EEG to take it back into the brain, at least on a macroscopic level. The goal is to improve visibility of epileptiform activities and to separate out most of the overlap. Methods: Multiple discrete sources provide a stable linear inverse to transform the EEG into source space with little cross-talk between source regions. The model can be based on a few dipoles or regional sources, adapted to the individual EEG and MRI data, or on selected standard sources evenly distributed throughout the brain, e.g. below the 25 EEG standard electrodes. Results: Auditory and somatosensory evoked potentials serve as teaching examples to show how various source spaces can reveal the underlying source components including their loss or alteration due to lesions. Source spaces were able to reveal the propagation of source activities in frontal IEDs and the sequential activation of the major nodes of the underlying epileptic network in myoclonic epilepsy. The power of multiple discrete sources in separating the activities of different brain regions was also evident in the ongoing EEG of cases with frontal cortical dysplasia and bitemporal lobe epilepsy. The new source space 25 made IEDs more clearly visible over the EEG background signals. The more focal nature of source vs. scalp space was quantitatively confirmed using a new measurement of focality. Conclusion: Multiple discrete sources have the power to transform the EEG back into the brain by defining new EEG traces in source space. Using standard source space 25, these can provide for improved clinical interpretation of EEG.

Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs.

Variable levels of DNA methylation have been reported at tissue-specific differential methylation regions (DMRs) overlapping enhancers, including super-enhancers (SEs) associated with key cell identity genes, but the mechanisms responsible for this intriguing behavior are not well understood. We used allele-specific reporters at the endogenous Sox2 and Mir290 SEs in embryonic stem cells and found that the allelic DNA methylation state is dynamically switching, resulting in cell-to-cell heterogeneity. Dynamic DNA methylation is driven by the balance between DNA methyltransferases and transcription factor binding on one side and co-regulated with the Mediator complex recruitment and H3K27ac level changes at regulatory elements on the other side. DNA methylation at the Sox2 and the Mir290 SEs is independently regulated and has distinct consequences on the cellular differentiation state. Dynamic allele-specific DNA methylation at the two SEs was also seen at different stages in preimplantation embryos, revealing that methylation heterogeneity occurs in vivo.

Preliminary outcome of Nellix-in-Nellix extensions in patients treated with failed endovascular aneurysm sealing.

BACKGROUND: The 1-year results of the use of the Nellix (Endologix Inc, Irvine, Calif) endovascular aneurysm sealing (EVAS) device were initially promising. However, midterm complications including migration and aneurysm growth occurred more frequently than expected, which provided an incentive to refine the instructions for use. Strategies for the management of complications arising after endovascular aneurysm repair are often not applicable for EVAS, given the unique configuration of the Nellix device, and new techniques are needed. This study analyzes the clinical outcomes of both elective and emergency deployment of a new Nellix device within a primarily placed device, for failure of EVAS, which we refer to as a Nellix-in-Nellix application (NINA). METHODS: This is a global, retrospective, observational cohort study focusing on the early outcome of NINA for failed EVAS, including data from 11 European institutions and 1 hospital in New Zealand. RESULTS: A total of 41 patients were identified who underwent a NINA procedure. Of these, 32 (78%) were placed electively and 9 (22%) were placed on an emergency basis. Seven patients were initially treated with chimney EVAS (n = 5 in the elective NINA group and n = 2 in the emergency NINA group). The average time between the primary EVAS procedure and NINA was 573 days (interquartile range, [IQR] 397-1078 days) and 478 days (IQR, 120-806) for the elective and emergency groups, respectively. The indication for elective NINA was endoleak with migration (50%), endoleak without migration (25%), migration without endoleak (16%), and other (9%). Chimney grafts were used in 21 of 32 patients in the elective group and 3 of 9 patients in the emergency group. Technical success was achieved in 94% of patients in the elective group and 100% of patients in the emergency group. At latest follow-up (median, 104 days; IQR, 49-328 days), there were three aneurysm-related deaths (9%), no ruptures, and five device-related reinterventions (16%) within the elective group. In the emergency group (median follow-up, 23 days; IQR, 7-61 days), there were four aneurysm-related deaths and three aneurysm-related reinterventions. CONCLUSIONS: In conclusion, a NINA can be used to treat late failures of EVAS with an acceptable technical success rate and can be used when more established treatment options are unfeasible or contraindicated. The durability of this technique needs to be further reviewed.

Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development.

The current understanding of mammalian kidney development is largely based on mouse models. Recent landmark studies revealed pervasive differences in renal embryogenesis between mouse and human. The scarcity of detailed gene expression data in humans therefore hampers a thorough understanding of human kidney development and the possible developmental origin of kidney diseases. In this paper, we present a single-cell transcriptomics study of the human fetal kidney. We identified 22 cell types and a host of marker genes. Comparison of samples from different developmental ages revealed continuous gene expression changes in podocytes. To demonstrate the usefulness of our data set, we explored the heterogeneity of the nephrogenic niche, localized podocyte precursors, and confirmed disease-associated marker genes. With close to 18,000 renal cells from five different developmental ages, this study provides a rich resource for the elucidation of human kidney development, easily accessible through an interactive web application.

The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression.

Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARγ) are commonly reduced in prostate cancer (PCa). Therefore, we sought to establish the cellular and gene regulatory consequences of reduced RARγ expression, and determine RARγ regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARγ levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RARγ cistrome, which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RARγ to regulate androgen signaling, RARγ knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RARγ downregulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RARγ expression and function. Capture of the miR-96 targetome by biotin-miR-96 identified that RARγ and a number of RARγ interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RARγ target genes (e.g., SOX15) that significantly associated with worse disease-free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p = 0.015). In summary, miR-96 targets a RARγ network to govern AR signaling, PCa progression and disease outcome.

Allele-specific repression of Sox2 through the long non-coding RNA Sox2ot.

The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. This gatekeeper function requires well-regulated Sox2 levels. We postulated that Sox2 regulation is partially controlled by the Sox2 overlapping long non-coding RNA (lncRNA) gene Sox2ot. Here we show that the RNA levels of Sox2ot and Sox2 are inversely correlated during neural differentiation of mouse embryonic stem cells (ESCs). Through allele-specific enhanced transcription of Sox2ot in mouse Sox2eGFP knockin ESCs we demonstrate that increased Sox2ot transcriptional activity reduces Sox2 RNA levels in an allele-specific manner. Enhanced Sox2ot transcription, yielding lower Sox2 RNA levels, correlates with a decreased chromatin interaction of the upstream regulatory sequence of Sox2 and the ESC-specific Sox2 super enhancer. Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development.

Early Experience With Endovascular Aneurysm Sealing in Combination With Parallel Grafts for the Treatment of Complex Abdominal Aneurysms: The ASCEND Registry.

PURPOSE: To report the results of the ASCEND Registry of cases involving endovascular aneurysm sealing (EVAS) in combination with chimney grafts (chEVAS) for the treatment of para- and juxtarenal aortic aneurysms (AAA). METHODS: A retrospective, multicenter registry established in 8 vascular centers between 2013 and 2016 recorded the treatment results and follow-up of chEVAS procedures for nonruptured AAAs; data were analyzed using standardized outcome measures. In the observation period, 154 patients (mean age 72.3±7.7 years; 124 men) underwent elective treatment for de novo juxtarenal and pararenal aneurysms and formed the study group. RESULTS: Sixty-two (40.3%) of the cohort were treated using a single parallel graft, 54 (35.1%) with double chimneys, 27 (17.5%) with triple chimneys, and 11 (7.1%) with 4 chimneys. The 30-day mortality was 2.8%, and there were 4 perioperative strokes (1 fatal). At 1 year, the freedom from all-cause mortality was 89.8% and the freedom from aneurysm-related mortality was 94.3%. There were 3 endoleaks within 90 days of the procedure, one type Ia and 2 type Ib. The freedom from type Ia endoleaks was 95.7% at 1 year. There were no types II or III endoleaks in this series; the freedom from all endoleaks was 94.2% at 1 year. Freedom from reintervention at 1 year was 89.2%. Target vessel patency rates at 1 year were 97.7%, 99.3%, 100%, and 100% for the left renal, right renal, superior mesenteric artery, and celiac axis stents, respectively. CONCLUSION: The ASCEND Registry supports a proof of concept for the use of polymer technology and EVAS with parallel grafts in managing patients with complex aortic disease. The future role of chEVAS will be defined by studies that assess mid- to long-term durability.

A Propensity Score-Matched Analysis of Inflammatory Response With Endovascular Aneurysm Sealing vs Endovascular Aneurysm Repair.

PURPOSE: To evaluate the risk of postimplantation syndrome associated with endovascular aneurysm sealing (EVAS) and endovascular aneurysm repair (EVAR) in patients treated for abdominal aortic aneurysm (AAA). METHODS: From December 2013 to May 2015, 41 AAA patients treated with EVAS (mean age 72±9 years; 38 men) and 63 with EVAR (mean age 74±10 years; 55 men) at a single center were retrospectively reviewed. To control for treatment selection bias, propensity score matching was used to compare outcomes by treatment mode. Main outcomes were postimplantation syndrome (defined as temperature >38°C and leukocyte count >12,000/µL), inflammatory response markers [platelets and high-sensitivity C-reactive protein (hs-CRP)], and clinical complications through 30 days. RESULTS: In 39 matched patients per group, the incidences of postimplantation syndrome (p=0.07), mean body temperature (p=0.05), mean leukocyte count (p=0.003), and mean hs-CRP (p<0.001) were proportionally lower with EVAS vs EVAR. Serious adverse events (0% vs 12.8%, p=0.05) and endoleaks (0% vs 10.3%, p=0.13) through 30 days were less frequent with EVAS, but the group differences were not significantly different. The choice of endovascular graft material influenced postoperative and 30-day clinical outcomes, with greater overall risk observed with polyester stent-grafts. CONCLUSION: Endovascular aneurysm sealing is associated with a blunted systematic inflammatory response compared with EVAR. Polyester stent-grafts induce the greatest periprocedural inflammatory response.

Integration of VDR genome wide binding and GWAS genetic variation data reveals co-occurrence of VDR and NF-κB binding that is linked to immune phenotypes.

BACKGROUND: The nuclear hormone receptor superfamily acts as a genomic sensor of diverse signals. Their actions are often intertwined with other transcription factors. Nuclear hormone receptors are targets for many therapeutic drugs, and include the vitamin D receptor (VDR). VDR signaling is pleotropic, being implicated in calcaemic function, antibacterial actions, growth control, immunomodulation and anti-cancer actions. Specifically, we hypothesized that the biologically significant relationships between the VDR transcriptome and phenotype-associated biology could be discovered by integrating the known VDR transcription factor binding sites and all published trait- and disease-associated SNPs. By integrating VDR genome-wide binding data (ChIP-seq) with the National Human Genome Research Institute (NHGRI) GWAS catalog of SNPs we would see where and which target gene interactions and pathways are impacted by inherited genetic variation in VDR binding sites, indicating which of VDR's multiple functions are most biologically significant. RESULTS: To examine how genetic variation impacts VDR function we overlapped 23,409 VDR genomic binding peaks from six VDR ChIP-seq datasets with 191,482 SNPs, derived from GWAS-significant SNPs (Lead SNPs) and their correlated variants (r 2 > 0.8) from HapMap3 and the 1000 genomes project. In total, 574 SNPs (71 Lead and 503 SNPs in linkage disequilibrium with Lead SNPs) were present at VDR binding loci and associated with 211 phenotypes. For each phenotype a hypergeometric test was used to determine if SNPs were enriched at VDR binding sites. Bonferroni correction for multiple testing across the 211 phenotypes yielded 42 SNPs that were either disease- or phenotype-associated with seven predominately immune related including self-reported allergy; esophageal cancer was the only cancer phenotype. Motif analyses revealed that only two of these 42 SNPs reside within a canonical VDR binding site (DR3 motif), and that 1/3 of the 42 SNPs significantly impacted binding and gene regulation by other transcription factors, including NF-κB. This suggests a plausible link for the potential cross-talk between VDR and NF-κB. CONCLUSIONS: These analyses showed that VDR peaks are enriched for SNPs associated with immune phenotypes suggesting that VDR immunomodulatory functions are amongst its most important actions. The enrichment of genetic variation in non-DR3 motifs suggests a significant role for the VDR to bind in multimeric complexes containing other transcription factors that are the primary DNA binding component. Our work provides a framework for the combination of ChIP-seq and GWAS findings to provide insight into the underlying phenotype-associated biology of a given transcription factor.

Dumping Syndrome: A Review of the Current Concepts of Pathophysiology, Diagnosis, and Treatment.

Gastric surgery has long been known to be a cause of dumping syndrome (DS). However, the increasing incidence of gastric bypass surgery, as well as reports of DS unrelated to previous gastric surgeries, has increased the importance of understanding DS in recent years. DS is due to the gastrointestinal response to voluminous and hyperosmolar chyme that is rapidly expelled from the stomach into the small intestine. This response involves neural and hormonal mechanisms. This review encompasses the symptoms, diagnosis, and treatment approaches of DS and also focuses on the current research status of the pathophysiology of DS.

Integrative genomic analysis in K562 chronic myelogenous leukemia cells reveals that proximal NCOR1 binding positively regulates genes that govern erythroid differentiation and Imatinib sensitivity.

To define the functions of NCOR1 we developed an integrative analysis that combined ENCODE and NCI-60 data, followed by in vitro validation. NCOR1 and H3K9me3 ChIP-Seq, FAIRE-seq and DNA CpG methylation interactions were related to gene expression using bootstrapping approaches. Most NCOR1 combinations (24/44) were associated with significantly elevated level expression of protein coding genes and only very few combinations related to gene repression. DAVID's biological process annotation revealed that elevated gene expression was uniquely associated with acetylation and ETS binding. A matrix of gene and drug interactions built on NCI-60 data identified that Imatinib significantly targeted the NCOR1 governed transcriptome. Stable knockdown of NCOR1 in K562 cells slowed growth and significantly repressed genes associated with NCOR1 cistrome, again, with the GO terms acetylation and ETS binding, and significantly dampened sensitivity to Imatinib-induced erythroid differentiation. Mining public microarray data revealed that NCOR1-targeted genes were significantly enriched in Imatinib response gene signatures in cell lines and chronic myelogenous leukemia (CML) patients. These approaches integrated cistrome, transcriptome and drug sensitivity relationships to reveal that NCOR1 function is surprisingly most associated with elevated gene expression, and that these targets, both in CML cell lines and patients, associate with sensitivity to Imatinib.