EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma.

Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or a highly related FET/ETS chimera. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma cells using a well-validated 'knock-down/rescue' model of EWS/FLI function in combination with next generation sequencing assays to evaluate how the chromatin landscape changes with loss, and recovery, of EWS/FLI expression. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. This EWS/FLI binding signature is associated with establishment of topologically-associated domain (TAD) boundaries, compartment activation, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. In addition, EWS/FLI co-localizes with the loop-extrusion factor cohesin to promote chromatin loops and TAD boundaries. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators of three-dimensional reprogramming of chromatin.

Identifying patients at risk for hereditary myeloid malignancy syndromes incorporating a novel, self-administered questionnaire to an initial screening platform.

INTRODUCTION: Four to 10% of cases of myeloid malignancies are inherited. We report our experience on hereditary myeloid malignancy syndromes (HMMS) incorporating a novel questionnaire in the screening platform for patients with myeloid malignancies and aplastic anemia. METHODS: The questionnaire was sent via electronic patient portal prior to clinic visits. Patients screened positive based on responses to questionnaire items, presence of suspicion disease characteristics (young age, family history, monosomy 7 etc.) and/or presence of signs of HMMS. Those deemed at-risk based on questionnaire responses, clinical features and/or somatic mutation profile were offered germline testing. RESULTS: A total of 408 patients were screened, 141 (35%) were deemed at-risk. Fifty-four (38%) of at-risk patients were seen in the genetics clinic. Forty-one (76%) of the patients seen agreed to germline testing and 13 declined due to cost or personal decision. Twenty pathogenic (P)/likely-pathogenic (LP) germline mutations were identified in 16 (39%) of the tested patients. Five patients also had a variant of uncertain significance (VUS) and an additional 13 had at least 1 VUS without P/LP mutations (total 29 VUS's were found in 18 (44%) of tested patients). The median age of diagnosis for patients with P/LP mutations was 56 years versus 66 years in the entire cohort. CONCLUSION: Incorporating an electronic questionnaire is an effective screening method for HMMS. Many patients declined testing due to cost. These results highlight the importance of germline testing in patients with myeloid malignancies, further research in HMMS, and coverage by healthcare plans.

Civatte Bodies in Pediatric Esophageal Biopsies: Does Lichen Esophagitis Pattern Occur in Children?

PURPOSE AND CONTEXT: Civatte bodies (CB) are associated with cutaneous and mucosal lichen planus in adults. They are a distinct feature of Lichen Esophagitis Pattern, which is not well described in children. We characterized clinicopathologic associations of archival esophageal CB at our Children's Hospital to determine whether lichen planus or Lichen Esophagitis Pattern occurs in children. METHOD: Pathology records were queried for pediatric esophageal biopsy diagnoses containing "CB," "apoptosis, "necrosis," or "dyskeratosis." Cases with concurrent eosinophilic/acute esophagitis were excluded. H&E slides and clinical reports were reviewed. KEY RESULTS: Biopsies with CB or similar were identified from 19 patients and had been termed "dyskeratotic cells" in 8 reports. Patients had variable age and presenting symptoms, male predominance (74%), and frequent clinical history of polypharmacy (47%), Crohn disease (42%), and/or celiac disease (21%). Civatte bodies were prominent in the distal esophagus (95%), as few isolated cells (63%), and with variable chronic inflammation (absent, pauci-inflammatory, and lichen planus-like in approximately one-third of cases each). CONCLUSIONS: We show that esophageal CB from pediatric patients are under-recognized and may have different features and implications compared to Lichen Esophagitis Pattern in adults. Recognition and documentation of pediatric esophageal CB is needed to understand their clinical significance.

Eosinophilic esophagitis: comorbidities and atopic disease in Nevada.

Eosinophilic esophagitis (EoE) is a rare, immune-mediated illness. We aimed to examine the comorbidities and sensitization patterns associated with an EoE diagnosis in Nevada. The study goal was two-fold: to determine the most common EoE comorbidities and sequela in the state of Nevada using healthcare utilization records across all settings and to determine the most common food and aeroallergens in histologically positive EoE pediatric patients using clinical sensitization data. Esophageal obstruction/stricture was the most frequently reported diagnosis in adults with EoE (29.5%). Among pediatrics, the highest ranking comorbidities included asthma (13.4%); diseases of the stomach, duodenum, and intestine (7.26%); allergies (7.01%); and gastroesophageal reflux disease (GERD) (3.69%). Additionally, the top sensitizations reported in histologically positive EoE patients were largely pollen related (82.9%). Atopic disease and specifically food allergens are commonly reported as comorbid conditions with EoE in the literature. However, our clinical pediatric data set from this study revealed that aeroallergen sensitizations far exceeded that of food allergens (82.9% aero-positive vs. 17.1% dood positive). The high presence of esophageal stricture/obstruction in adults could be indicative of late diagnosis; in addition, the aeroallergen sensitization in children could suggest different clinical management techniques necessary may be needed for this disease. Education among healthcare providers regarding the presence of aeroallergen sensitization in this population may result in earlier diagnoses and help reduce morbidity and the cost from this disease.

Shell deformity as a marker for retrospective detection of a pathogenic unicellular alga, Coccomyxa sp., in mytilid mussels: A first case study and research agenda.

An L-shaped shell deformity (LSSD) on the posterior shell edge is known exclusively in wild mytilid mussels infected with photosynthetic Coccomyxa-like algae. LSSD forms due to the appearance of extra shell material; it only occurs if the mussel is heavily infected with the alga. Traditionally, observation of high amount of the green spots (algal colonies) on a large area of host soft tissues (most of the mantle and in adductor muscle) has been used to indicate a high infection rate. We examined 300 Mytilus spp. (100 small, 20-30 mm; 200 large, 40-60 mm) with a high degree of LSSD (parameter "d" > 5 mm) from the Lower St. Lawrence Estuary (Québec, Canada). Green spots were absent in two large mussels, and were only present along the mantle posterior edge in 14 large mussels; other individuals had high infection levels. Our observations suggest that some individuals could be in a state of remission, or, even more optimistically - mussels may be able to resist the pathogen. LSSD is the stable through-time marker for detection of mytilid mussels that are or were infected with Coccomyxa algae, and, thus, may provide information for the study of mussel immunity and control of alga distribution/migration in coastal waters worldwide.

A Framework for a European Economic Recovery After COVID-19.

The success of support measures as COVID-19 lockdowns are relaxed depends on the type of recovery the EU wants to achieve.

Factors Associated with Rapid Readmission Among Nevada State Psychiatric Hospital Patients.

Rapid readmission (RR) of psychiatric patients within 30 days of discharge places a costly burden on state psychiatric facilities and may indicate suboptimal service provisions. Information regarding variables associated with RR of psychiatric patients is limited, particularly in Nevada. This study attempts to identify factors associated with RR at a Nevada state psychiatric hospital. Participants included 7177 patients admitted between May 2012 and April 2014. Using logistic regression, all admissions were reviewed and rapid readmits compared to counterparts who were not readmitted within 30 days. Nevada suffers from budget cuts in mental health care spending because of recent economic crisis and severe lack of bed space. This study demonstrates that it may be possible to reduce rates of costly RR by focusing on those with a history of RR and modifiable factors including social and financial support, as well as reliable and stable housing.

How I treat patients with a history of heparin-induced thrombocytopenia.

Heparin-induced thrombocytopenia (HIT) is a relatively common prothrombotic adverse drug reaction of unusual pathogenesis that features platelet-activating immunoglobulin G antibodies. The HIT immune response is remarkably transient, with heparin-dependent antibodies no longer detectable 40 to 100 days (median) after an episode of HIT, depending on the assay performed. Moreover, the minimum interval from an immunizing heparin exposure to the development of HIT is 5 days irrespective of the patient's previous heparin exposure status or history of HIT. This means that short-term heparin reexposure can be safely performed if platelet-activating antibodies are no longer detectable at reexposure baseline and is recommended when heparin is the clear anticoagulant of choice, such as for cardiac or vascular surgery. The risk of recurrent HIT 1 to 2 weeks after heparin reexposure is ∼2% to 5% and is attributable to formation of delayed-onset (or autoimmune-like) HIT antibodies that activate platelets even in the absence of pharmacologic heparin. Some studies suggest that longer-term heparin reexposure (eg, for chronic hemodialysis) may also be reasonable. However, for other antithrombotic indications that involve patients with a history of HIT (eg, treatment of venous thromboembolism or acute coronary syndrome), preference should be given to non-heparin agents such as fondaparinux, danaparoid, argatroban, bivalirudin, or one of the new direct-acting oral anticoagulants as appropriate.

Mytilus trossulus and hybrid (M. edulis-M. trossulus) - New hosts organisms for pathogenic microalgae Coccomyxa sp. from the Estuary and northwestern Gulf of St. Lawrence, Canada.

During summer 2014-2017, wild mytilid mussels, highly infested with the pathogenic Coccomyxa-like microalgae, were collected along the Estuary and northwestern part of Gulf of St. Lawrence (Québec, Canada). Molecular identification showed that algae can be assigned to a single taxon, Coccomyxa sp. (KJ372210), whereas hosts are represented by Mytilus edulis, M. trossulus and hybrid between these two species. This is the first record of M. trossulus and hybrid among hosts of this pathogenic alga. Our results are indicative of a possible widespread distribution of Coccomyxa sp. in the Lower St. Lawrence Estuary and along coastal waters of Canadian Maritime provinces.

Interleukin 1 Receptor-Like 1 Protein (ST2) is a Potential Biomarker for Cardiomyopathy in Duchenne Muscular Dystrophy.

Duchenne muscular dystrophy (DMD) is a rare, fatal X-linked disorder characterized by the lack of dystrophin, a key sarcolemma muscle protein. Cardiac failure is a significant cause of death in DMD subjects. The purpose of our research was to identify potential cardiac serum biomarkers associated with DMD cardiomyopathy. This is an observational, case-controlled study using subjects from the CINRG DMD natural history study with cardiomyopathy (ejection fraction (EF) <55%; shortening fraction (SF) <28%), subjects without cardiomyopathy (EF ≥ 55%; SF ≥ 28%) compared to normal healthy volunteer subjects. The DMD with cardiomyopathy group had significantly lower average EF and SF (EF = 45 ± 10/SF = 25 ± 2%) than the DMD without cardiomyopathy group (EF = 58 ± 5% and SF = 32 ± 3%; p < 0.01). Among a selected set of potential biomarkers for cardiomyopathy (MMP9, BNP, GAL3, CRP, LEP, TNC, TLR4 and ST2) we validated ST2 as significantly elevated in the serum of DMD cardiomyopathy group (35,798 ± 4884 pg/mL) compared to normal controls (9940 ± 2680 pg/mL; p < 0.01; n = 6). Matrix metallopeptidase 9 (MMP9) levels were found significantly increased in both DMD groups compared to controls (p < 0.01). No significant differences were seen in BNP, GAL3, CRP, LEP, TNC or TLR4 levels. Increased ST2 levels were found in serum of DMD subjects compared to healthy volunteers and further elevated in DMD subjects with cardiomyopathy. Future studies correlating cardiomyopathy with ST2 levels may allow for improved non-invasive monitoring of cardiac disease in DMD subjects.

Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study.

Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool.

Lactose-Free Milk or Soy-Based Formulas Do Not Improve Caregivers' Distress or Perceptions of Difficult Infant Behavior.

OBJECTIVES: The aim of the study was to test the hypothesis that caregiver-reported difficulties in infant behavior and caregivers' distress will significantly improve on lactose-free (LF) milk-based or LF soy-based formulas compared with a milk-based, lactose-containing formula. METHODS: In this double-blind randomized controlled trial, infants (mean age: 4.97 weeks) with caregiver-reported feeding problems on a milk-based lactose-containing formula were randomized to receive either LF milk-based (n = 96), LF soy-based (n = 97), or milk-based, lactose-containing (n = 103) formula. Study formula was infants' sole item of diet for 14 days. Infants' caregivers completed measures of infant behavior and caregivers' distress for the week preceding baseline and again for the week preceding the 14-day follow-up. RESULTS: Infants who received LF milk or LF soy-based formulas did not significantly differ from those who received milk-based, lactose-containing formula on follow-up caregiver-reported measures of infant difficultness from the Infant Characteristics Questionnaire, F(2, 277) = 0.83, nor on measures of caregivers' distress, assessed with measures of caregivers' mental health and parenting efficacy, F(2, 285) = 0.73-1.07. Across the 3 formula groups, scores on outcome measures significantly improved from baseline to follow-up (P < 0.001). CONCLUSIONS: Our study does not support LF milk or LF soy-based formulas to alleviate common infant behaviors such as fussiness, crying, or need for attention. Moreover, the data suggest that some difficulties in infant behaviors, as well as caregivers' distress and perceived efficacy in parenting difficult infants, may improve within a couple weeks of reporting difficulties to the pediatrician.

Mitotic asynchrony induces transforming growth factor-ß1 secretion from airway epithelium.

We recently proposed that mitotic asynchrony in repairing tissue may underlie chronic inflammation and fibrosis, where immune cell infiltration is secondary to proinflammatory cross-talk among asynchronously repairing adjacent tissues. Building on our previous finding that mitotic asynchrony is associated with proinflammatory/fibrotic cytokine secretion (e.g., transforming growth factor [TGF]-ß1), here we provide evidence supporting cause-and-effect. Under normal conditions, primary airway epithelial basal cell populations undergo mitosis synchronously and do not secrete proinflammatory or profibrotic cytokines. However, when pairs of nonasthmatic cultures were mitotically synchronized at 12 hours off-set and then combined, the mixed cell populations secreted elevated levels of TGF-ß1. This shows that mitotic asynchrony is not only associated with but is also causative of TGF-ß1 secretion. The secreted cytokines and other mediators from asthmatic cells were not the cause of asynchronous regeneration; synchronously mitotic nonasthmatic epithelia exposed to conditioned media from asthmatic cells did not show changes in mitotic synchrony. We also tested if resynchronization of regenerating asthmatic airway epithelia reduces TGF-ß1 secretion and found that pulse-dosed dexamethasone, simvastatin, and aphidicolin were all effective. We therefore propose a new model for chronic inflammatory and fibrotic conditions where an underlying factor is mitotic asynchrony.

Predicting persistence of functional abdominal pain from childhood into young adulthood.

BACKGROUND & AIMS: Pediatric functional abdominal pain has been linked to functional gastrointestinal disorders (FGIDs) in adulthood, but little is known about patient characteristics in childhood that increase the risk for FGID in young adulthood. We investigated the contribution of gastrointestinal symptoms, extraintestinal somatic symptoms, and depressive symptoms in pediatric patients with functional abdominal pain and whether these predicted FGIDs later in life. METHODS: In a longitudinal study, consecutive new pediatric patients, diagnosed with functional abdominal pain in a subspecialty clinic, completed a comprehensive baseline evaluation of the severity of their physical and emotional symptoms. They were contacted 5 to 15 years later and evaluated, based on Rome III symptom criteria, for abdominal pain-related FGIDs, including irritable bowel syndrome, functional dyspepsia, functional abdominal pain syndrome, and abdominal migraine. Controlling for age, sex, baseline severity of abdominal pain, and time to follow-up evaluation, multivariable logistic regression was used to evaluate the association of baseline gastrointestinal, extraintestinal somatic, and depressive symptoms in childhood with FGID in adolescence and young adulthood. RESULTS: Of 392 patients interviewed an average of 9.2 years after their initial evaluation, 41% (n = 162) met symptom criteria for FGID; most met the criteria for irritable bowel syndrome. Extraintestinal somatic and depressive symptoms at the initial pediatric evaluation were significant predictors of FGID later in life, after controlling for initial levels of GI symptoms. Age, sex, and abdominal pain severity at initial presentation were not significant predictors of FGID later in life. CONCLUSIONS: In pediatric patients with functional abdominal pain, assessment of extraintestinal and depressive symptoms may be useful in identifying those at risk for FGID in adolescence and young adulthood.