Notch1 Induces Defective Epithelial Surfactant Processing and Pulmonary Fibrosis.

Rationale: Although type II alveolar epithelial cells (AEC2s) are chronically injured in idiopathic pulmonary fibrosis (IPF), they contribute to epithelial regeneration in IPF. Objectives: We hypothesized that Notch signaling may contribute to AEC2 proliferation, dedifferentiation characterized by loss of surfactant processing machinery, and lung fibrosis in IPF. Methods: We applied microarray analysis, kinome profiling, flow cytometry, immunofluorescence analysis, western blotting, quantitative PCR, and proliferation and surface activity analysis to study epithelial differentiation, proliferation, and matrix deposition in vitro (AEC2 lines, primary murine/human AEC2s), ex vivo (human IPF-derived precision-cut lung slices), and in vivo (bleomycin and pepstatin application, Notch1 [Notch receptor 1] intracellular domain overexpression). Measurements and Main Results: We document here extensive SP-B and -C (surfactant protein-B and -C) processing defects in IPF AEC2s, due to loss of Napsin A, resulting in increased intra-alveolar surface tension and alveolar collapse and induction of endoplasmic reticulum stress in AEC2s. In vivo pharmacological inhibition of Napsin A results in the development of AEC2 injury and overt lung fibrosis. We also demonstrate that Notch1 signaling is already activated early in IPF and determines AEC2 fate by inhibiting differentiation (reduced lamellar body compartment, reduced capacity to process hydrophobic SP) and by causing increased epithelial proliferation and development of lung fibrosis, putatively via altered JAK (Janus kinase)/Stat (signal transducer and activator of transcription) signaling in AEC2s. Conversely, inhibition of Notch signaling in IPF-derived precision-cut lung slices improved the surfactant processing capacity of AEC2s and reversed fibrosis. Conclusions: Notch1 is a central regulator of AEC2 fate in IPF. It induces alveolar epithelial proliferation and loss of Napsin A and of surfactant proprotein processing, and it contributes to fibroproliferation.

Epigenetic inheritance of DNA methylation changes in fish living in hydrogen sulfide-rich springs.

Environmental factors can promote phenotypic variation through alterations in the epigenome and facilitate adaptation of an organism to the environment. Although hydrogen sulfide is toxic to most organisms, the fish Poecilia mexicana has adapted to survive in environments with high levels that exceed toxicity thresholds by orders of magnitude. Epigenetic changes in response to this environmental stressor were examined by assessing DNA methylation alterations in red blood cells, which are nucleated in fish. Males and females were sampled from sulfidic and nonsulfidic natural environments; individuals were also propagated for two generations in a nonsulfidic laboratory environment. We compared epimutations between the sexes as well as field and laboratory populations. For both the wild-caught (F0) and the laboratory-reared (F2) fish, comparing the sulfidic and nonsulfidic populations revealed evidence for significant differential DNA methylation regions (DMRs). More importantly, there was over 80% overlap in DMRs across generations, suggesting that the DMRs have stable generational inheritance in the absence of the sulfidic environment. This is an example of epigenetic generational stability after the removal of an environmental stressor. The DMR-associated genes were related to sulfur toxicity and metabolic processes. These findings suggest that adaptation of P. mexicana to sulfidic environments in southern Mexico may, in part, be promoted through epigenetic DNA methylation alterations that become stable and are inherited by subsequent generations independent of the environment.

Disease progression modelling of Alzheimer's disease using probabilistic principal components analysis.

The recent biological redefinition of Alzheimer's Disease (AD) has spurred the development of statistical models that relate changes in biomarkers with neurodegeneration and worsening condition linked to AD. The ability to measure such changes may facilitate earlier diagnoses for affected individuals and help in monitoring the evolution of their condition. Amongst such statistical tools, disease progression models (DPMs) are quantitative, data-driven methods that specifically attempt to describe the temporal dynamics of biomarkers relevant to AD. Due to the heterogeneous nature of this disease, with patients of similar age experiencing different AD-related changes, a challenge facing longitudinal mixed-effects-based DPMs is the estimation of patient-realigning time-shifts. These time-shifts are indispensable for meaningful biomarker modelling, but may impact fitting time or vary with missing data in jointly estimated models. In this work, we estimate an individual's progression through Alzheimer's disease by combining multiple biomarkers into a single value using a probabilistic formulation of principal components analysis. Our results show that this variable, which summarises AD through observable biomarkers, is remarkably similar to jointly estimated time-shifts when we compute our scores for the baseline visit, on cross-sectional data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Reproducing the expected properties of clinical datasets, we confirm that estimated scores are robust to missing data or unavailable biomarkers. In addition to cross-sectional insights, we can model the latent variable as an individual progression score by repeating estimations at follow-up examinations and refining long-term estimates as more data is gathered, which would be ideal in a clinical setting. Finally, we verify that our score can be used as a pseudo-temporal scale instead of age to ignore some patient heterogeneity in cohort data and highlight the general trend in expected biomarker evolution in affected individuals.

Graph embedding-based link prediction for literature-based discovery in Alzheimer's Disease.

OBJECTIVE: We explore the framing of literature-based discovery (LBD) as link prediction and graph embedding learning, with Alzheimer's Disease (AD) as our focus disease context. The key link prediction setting of prediction window length is specifically examined in the context of a time-sliced evaluation methodology. METHODS: We propose a four-stage approach to explore literature-based discovery for Alzheimer's Disease, creating and analyzing a knowledge graph tailored to the AD context, and predicting and evaluating new knowledge based on time-sliced link prediction. The first stage is to collect an AD-specific corpus. The second stage involves constructing an AD knowledge graph with identified AD-specific concepts and relations from the corpus. In the third stage, 20 pairs of training and testing datasets are constructed with the time-slicing methodology. Finally, we infer new knowledge with graph embedding-based link prediction methods. We compare different link prediction methods in this context. The impact of limiting prediction evaluation of LBD models in the context of short-term and longer-term knowledge evolution for Alzheimer's Disease is assessed. RESULTS: We constructed an AD corpus of over 16 k papers published in 1977-2021, and automatically annotated it with concepts and relations covering 11 AD-specific semantic entity types. The knowledge graph of Alzheimer's Disease derived from this resource consisted of ∼11 k nodes and ∼394 k edges, among which 34% were genotype-phenotype relationships, 57% were genotype-genotype relationships, and 9% were phenotype-phenotype relationships. A Structural Deep Network Embedding (SDNE) model consistently showed the best performance in terms of returning the most confident set of link predictions as time progresses over 20 years. A huge improvement in model performance was observed when changing the link prediction evaluation setting to consider a more distant future, reflecting the time required for knowledge accumulation. CONCLUSION: Neural network graph-embedding link prediction methods show promise for the literature-based discovery context, although the prediction setting is extremely challenging, with graph densities of less than 1%. Varying prediction window length on the time-sliced evaluation methodology leads to hugely different results and interpretations of LBD studies. Our approach can be generalized to enable knowledge discovery for other diseases. AVAILABILITY: Code, AD ontology, and data are available at https://github.com/READ-BioMed/readbiomed-lbd.

Interstitial Lung Disease: Seasonality of Hospitalizations and In-Hospital Mortality 2005-2015.

BACKGROUND: The overall incidence of interstitial lung disease and disease-associated mortality have been found on the rise. Hospitalizations for interstitial lung disease are typically caused by airway infection or the acute exacerbation of the underlying disease. Seasonal variance in ambient air pollution has recently been linked to exacerbation and mortality. We sought to examine the seasonal pattern of hospitalizations in Germany, use of mechanical ventilation, and in-hospital mortality on a year-by-year basis to identify their overall trend and to characterize seasonal patterns. METHODS: The national in-patient database of the federal statistical office of Germany was searched for cases of interstitial lung disease. RESULTS: A total of 130,366 hospitalizations for ILD occurred from 2005 to 2015. Time series data were examined for seasonality using X-11 statistics. The incidence of hospitalizations, mechanical ventilation, and in-hospital mortality show clear seasonal peaks in the cold season. The observed seasonality cannot be attributed to the variance of selected comorbidities. Also, there is a significant overall upward trend regarding hospitalization counts, especially in the use of non-invasive ventilation. CONCLUSION: Time series analysis of in-hospital data shows an ILD-related rise of hospitalizations, in-hospital mortality, and non-invasive ventilation. This emphasizes a growing importance of interstitial lung diseases for health-care systems. Strong seasonality is seen in these variables. Data therefore support previous studies of ILD exacerbation. More research on infectious causes and environmental factors is warranted.

Investigating the short and long-term effects of "nutritional-score" pricing on food pantry selections.

Approximately one out of ten households in the U.S. experienced food insecurity in 2019 (U. S. Department of Agriculture, 2020). Food pantries have taken on an important role in helping those with both short term and persistent food insecurity. As pantries are increasingly being arranged to allow clients to choose their own food, the question of how to encourage healthy choices is becoming an important topic for discussion. The Des Moines Area Religious Council (DMARC) implemented a "Nutritional-Score" program on September 1, 2017 as an experiment aimed at answering the above question. This program essentially changes the budgets of food pantry clients to make healthier choices cheaper and less healthy choices more expensive. We perform a Bayesian analysis using a zero-inflated Poisson (ZIP) model to help describe the effects of this program on the frequency with which clients choose less healthy items. We find evidence that the Nutritional-score program had a positive effect on the probability of rejecting less healthy items in the short and long term.

Pas de Deux of an NO Couple: Synchronous Photoswitching from a Double-Linear to a Double-Bent Ru(NO)2 Core under Nitrosyl Charge Conservation.

The {Ru(NO)2 }10 dinitrosylruthenium complex [Ru(NO)2 (PPh3 )2 ] (1) shows photo-induced linkage isomerism (PLI) of a special kind: the two NO ligands switch, on photo-excitation, synchronously from the ground state (GS) with two almost linear RuNO functions to a metastable state (MS) which persists up to 230 K and can be populated to ≈50 %. The MS was experimentally characterised by photo-crystallography, IR spectroscopy and DS-calorimetry as a double-bent variant of the double-linear GS. The experimental results are confirmed by computation which unravels the GS/MS transition as a disrotatory synchronous 50° turn of the two nitrosyl ligands. Although 1 shows the usual redshift of the N-O stretch on bending the MNO unit, there is no increased charge transfer from Ru to NO along the GS-to-MS path. In terms of the effective-oxidation-state (EOS) method, both isomers of 1 and the transition state are Ru-II (NO+ )2 species.

Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach.

BACKGROUND: Deep learning is an active bioinformatics artificial intelligence field that is useful in solving many biological problems, including predicting altered epigenetics such as DNA methylation regions. Deep learning (DL) can learn an informative representation that addresses the need for defining relevant features. However, deep learning models are computationally expensive, and they require large training datasets to achieve good classification performance. RESULTS: One approach to addressing these challenges is to use a less complex deep learning network for feature selection and Machine Learning (ML) for classification. In the current study, we introduce a hybrid DL-ML approach that uses a deep neural network for extracting molecular features and a non-DL classifier to predict environmentally responsive transgenerational differential DNA methylated regions (DMRs), termed epimutations, based on the extracted DL-based features. Various environmental toxicant induced epigenetic transgenerational inheritance sperm epimutations were used to train the model on the rat genome DNA sequence and use the model to predict transgenerational DMRs (epimutations) across the entire genome. CONCLUSION: The approach was also used to predict potential DMRs in the human genome. Experimental results show that the hybrid DL-ML approach outperforms deep learning and traditional machine learning methods.

Developmental origins of transgenerational sperm histone retention following ancestral exposures.

Numerous environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. Alterations in the germline epigenome are necessary to transmit transgenerational phenotypes. In previous studies, the pesticide DDT (dichlorodiphenyltrichloroethane) and the agricultural fungicide vinclozolin were shown to promote the transgenerational inheritance of sperm differential DNA methylation regions, non-coding RNAs and histone retention, which are termed epimutations. These epimutations are able to mediate this epigenetic inheritance of disease and phenotypic variation. The current study was designed to investigate the developmental origins of the transgenerational differential histone retention sites (called DHRs) during gametogenesis of the sperm. Vinclozolin and DDT were independently used to promote the epigenetic transgenerational inheritance of these DHRs. Male control lineage, DDT lineage and vinclozolin lineage F3 generation rats were used to isolate round spermatids, caput epididymal spermatozoa, and caudal sperm. The DHRs distinguishing the control versus DDT lineage or vinclozolin lineage samples were determined at these three developmental stages. DHRs and a reproducible core of histone H3 retention sites were observed using an H3 chromatin immunoprecipitation-sequencing (ChIP-Seq) analysis in each of the germ cell populations. The chromosomal locations and genomic features of the DHRs were analyzed. A cascade of epigenetic histone retention site alterations was found to be initiated in the round spermatids and then further modified during epididymal sperm maturation. Observations show that in addition to alterations in sperm DNA methylation and ncRNA expression previously identified, the induction of differential histone retention sites (DHRs) in the later stages of spermatogenesis also occurs. This novel component of epigenetic programming during spermatogenesis can be environmentally altered and transmitted to subsequent generations through epigenetic transgenerational inheritance.

Epigenetic transgenerational inheritance of parent-of-origin allelic transmission of outcross pathology and sperm epimutations.

Epigenetic transgenerational inheritance potentially impacts disease etiology, phenotypic variation, and evolution. An increasing number of environmental factors from nutrition to toxicants have been shown to promote the epigenetic transgenerational inheritance of disease. Previous observations have demonstrated that the agricultural fungicide vinclozolin and pesticide DDT (dichlorodiphenyltrichloroethane) induce transgenerational sperm epimutations involving DNA methylation, ncRNA, and histone modifications or retention. These two environmental toxicants were used to investigate the impacts of parent-of-origin outcross on the epigenetic transgenerational inheritance of disease. Male and female rats were collected from a paternal outcross (POC) or a maternal outcross (MOC) F4 generation control and exposure lineages for pathology and epigenetic analysis. This model allows the parental allelic transmission of disease and epimutations to be investigated. There was increased pathology incidence in the MOC F4 generation male prostate, kidney, obesity, and multiple diseases through a maternal allelic transmission. The POC F4 generation female offspring had increased pathology incidence for kidney, obesity and multiple types of diseases through the paternal allelic transmission. Some disease such as testis or ovarian pathology appear to be transmitted through the combined actions of both male and female alleles. Analysis of the F4 generation sperm epigenomes identified differential DNA methylated regions (DMRs) in a genome-wide analysis. Observations demonstrate that DDT and vinclozolin have the potential to promote the epigenetic transgenerational inheritance of disease and sperm epimutations to the outcross F4 generation in a sex specific and exposure specific manner. The parent-of-origin allelic transmission observed appears similar to the process involved with imprinted-like genes.

Transgenerational disease specific epigenetic sperm biomarkers after ancestral exposure to dioxin.

Dioxin was historically one of the most common industrial contaminants with several major industry accidents, as well as governmental actions involving military service, having exposed large numbers of the worldwide population over the past century. Previous rat studies have demonstrated the ability of dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)) exposure to promote the epigenetic transgenerational inheritance of disease susceptibility in subsequent generations. The types of disease previously observed include puberty abnormalities, testis, ovary, kidney, prostate and obesity pathologies. The current study was designed to use an epigenome-wide association study (EWAS) to identify potential sperm DNA methylation biomarkers for specific transgenerational diseases. Therefore, the transgenerational F3 generation dioxin lineage male rats with and without a specific disease were compared to identify differential DNA methylation regions (DMRs) as biomarkers for disease. The genomic features of the disease-specific DMRs were characterized. Observations demonstrate that disease-specific epimutation DMRs exist for the transgenerational dioxin lineage rats that can potentially be used as epigenetic biomarkers for testis, kidney, prostate and obesity diseases. These disease-specific DMRs were associated with genes that have previously been shown to be linked with the specific diseases. This EWAS for transgenerational disease identified potential epigenetic biomarkers and provides the proof of concept of the potential to develop similar biomarkers for humans to diagnose disease susceptibilities and facilitate preventative medicine.

Developmental origins of transgenerational sperm DNA methylation epimutations following ancestral DDT exposure.

Epigenetic alterations in the germline can be triggered by a number of different environmental factors from diet to toxicants. These environmentally induced germline changes can promote the epigenetic transgenerational inheritance of disease and phenotypic variation. In previous studies, the pesticide DDT was shown to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs), also called epimutations, which can in part mediate this epigenetic inheritance. In the current study, the developmental origins of the transgenerational DMRs during gametogenesis have been investigated. Male control and DDT lineage F3 generation rats were used to isolate embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, adult pachytene spermatocytes, round spermatids, caput epididymal spermatozoa, and caudal sperm. The DMRs between the control versus DDT lineage samples were determined at each developmental stage. The top 100 statistically significant DMRs at each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed. The chromosomal locations and genomic features of the different stage DMRs were analyzed. Although previous studies have demonstrated alterations in the DMRs of primordial germ cells (PGCs), the majority of the DMRs identified in the caudal sperm originated during the spermatogonia stages in the testis. Interestingly, a cascade of epigenetic alterations initiated in the PGCs is required to alter the epigenetic programming during spermatogenesis to obtain the sperm epigenetics involved in the epigenetic transgenerational inheritance phenomenon.

Epigenome-wide association study for pesticide (Permethrin and DEET) induced DNA methylation epimutation biomarkers for specific transgenerational disease.

BACKGROUND: Permethrin and N,N-diethyl-meta-toluamide (DEET) are the pesticides and insect repellent most commonly used by humans. These pesticides have been shown to promote the epigenetic transgenerational inheritance of disease in rats. The current study was designed as an epigenome-wide association study (EWAS) to identify potential sperm DNA methylation epimutation biomarkers for specific transgenerational disease. METHODS: Outbred Sprague Dawley gestating female rats (F0) were transiently exposed during fetal gonadal sex determination to the pesticide combination including Permethrin and DEET. The F3 generation great-grand offspring within the pesticide lineage were aged to 1 year. The transgenerational adult male rat sperm were collected from individuals with single and multiple diseases and compared to non-diseased animals to identify differential DNA methylation regions (DMRs) as biomarkers for specific transgenerational disease. RESULTS: The exposure of gestating female rats to a permethrin and DEET pesticide combination promoted transgenerational testis disease, prostate disease, kidney disease, and the presence of multiple disease in the subsequent F3 generation great-grand offspring. The disease DMRs were found to be disease specific with negligible overlap between different diseases. The genomic features of CpG density, DMR length, and chromosomal locations of the disease specific DMRs were investigated. Interestingly, the majority of the disease specific sperm DMR associated genes have been previously found to be linked to relevant disease specific genes. CONCLUSIONS: Observations demonstrate the EWAS approach identified disease specific biomarkers that can be potentially used to assess transgenerational disease susceptibility and facilitate the clinical management of environmentally induced pathology.

Paediatric glaucoma in Scotland.

BACKGROUND: The primary aim was to estimate the incidence of primary and secondary childhood glaucoma in Scotland over a 2-year period. The secondary aim was to gauge the confidence and experience of ophthalmologists in Scotland in managing these patients. METHODS: A 7 question electronic survey was distributed to all consultant members of the Scottish Paediatric Club and Scottish Glaucoma Club. Respondents were asked to report the number of cases and types of childhood glaucoma they had managed in the last 2 years. Respondents were also asked about experience and confidence in a range of glaucoma procedures, number of patients requiring referral to specialist centres and interest in the development of a centre of excellence in Scotland. RESULTS: The survey returned a 56% response rate, reporting 85 new cases of paediatric glaucoma in Scotland over the preceding 2 years. 11 (12.9%) had primary glaucoma and 74 (87.1%) had secondary glaucoma. The most common subtype of secondary glaucoma was uveitic glaucoma (n = 29). None of the respondents declared confidence or experience in trabeculotomy or goniotomy procedures. Eleven children required referral to a specialist unit outside Scotland. 85.7% of respondents felt Scotland would benefit from a specialist unit for paediatric glaucoma. CONCLUSIONS: This survey reflects an appetite for a specialist service for paediatric glaucoma in Scotland. However, further consideration is needed to determine if there is sufficient patient load to maintain such a service.

Clinical characteristics of patients with familial idiopathic pulmonary fibrosis (f-IPF).

BACKGROUND: The aim of this study was to analyze the relative frequency, clinical characteristics, disease onset and progression in f-IPF vs. sporadic IPF (s-IPF). METHODS: Familial IPF index patients and their family members were recruited into the European IPF registry/biobank (eurIPFreg) at the Universities of Giessen and Marburg (UGMLC). Initially, we employed wide range criteria of f-IPF (e.g. relatives who presumably died of some kind of parenchymal lung disease). After narrowing down the search to occurrence of idiopathic interstitial pneumonia (IIP) in at least one first grade relative, 28 index patients were finally identified, prospectively interviewed and examined. Their family members were phenotyped with establishment of pedigree charts. RESULTS: Within the 28 IPF families, overall 79 patients with f-IPF were identified. In the same observation period, 286 f-IIP and s-IIP patients were recruited into the eurIPFreg at our UGMLC sites, corresponding to a familial versus s-IPF of 9.8%. The both groups showed no difference in demographics (61 vs. 79% males), smoking history, and exposure to any environmental triggers known to cause lung fibrosis. The f-IPF group differed by an earlier age at the onset of the disease (55.4 vs. 63.2 years; p < 0.001). On average, the f-IPF patients presented a significantly milder extent of functional impairment at the time point of inclusion vs. the s-IPF group (FVC 75% pred. vs. FVC 62% pred., p = 0.011). In contrast, the decline in FVC was found to be faster in the f-IPF vs. the s-IPF group (4.94% decline in 6 months in f-IPF vs. 2.48% in s-IPF, p = 0.12). The average age of death in f-IPF group was 67 years vs. 71.8 years in s-IPF group (p = 0.059). The f-IIP group displayed diverse inheritance patterns, mostly autosomal-dominant with variable penetrance. In the f-IPF, the younger generations showed a tendency for earlier manifestation of IPF vs. the older generation (58 vs. 66 years, p = 0.013). CONCLUSIONS: The 28 f-IPF index patients presented an earlier onset and more aggressive natural course of the disease. The disease seems to affect consecutive generations at a younger age. TRIAL REGISTRATION: Nr. NCT02951416 http://www.www.clinicaltrials.gov.

HN2 O2 - as a Ligand in Mononuclear Hydrogenhyponitrite-κ2 -N,O Ruthenium Complexes with Bisphosphane Co-Ligands.

The hyponitrite anion is a tentative intermediate in the reduction of nitric oxide (NO) to nitrous oxide (N2 O) catalyzed by nitric-oxide reductase (NOR) in the process of bacterial denitrification. Owing to the considerable number of known coordination modes for the hyponitrito ligand, its actual bonding form in the enzymatic cycle is a point of current discussion. Here, we contribute to the hardly known ligand properties of a key intermediate, the monoprotonated hyponitrite anion. Three air- and water-stable ruthenium complexes with hydrogenhyponitrite as the ligand were synthesized by using commercially available bisphosphane co-ligands (1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)ethene (dppv)). The starting compounds [Ru(dppe)2 (tos)]BF4 (1) and [Ru(dppp)2 (tos)]BF4 (2) contained the bidentate coordinating tosylate anion (tos) as a particularly well-suited leaving group. To confirm the protonated and deprotonated species, X-ray diffraction, IR, UV/Vis spectroscopy (solution and solid state), solid-state NMR spectroscopy, and high-resolution mass spectroscopy were used. DFT calculations give insight into the bonding situation. We report on [Ru(dppe)2 (HN2 O2 )]BF4 (5), [Ru(dppp)2 (HN2 O2 )]BF4 (6), [Ru(dppv)2 (HN2 O2 )]BF4 (7), [Ru(dppp)2 (HN2 O2 )]BF4 ⋅Imi (9; Imi=imidazole) as the first mononuclear trans-hydrogenhyponitrite complexes. Isolated deprotonated analogs are [Ru(dppe)2 (N2 O2 )]⋅HImi(BF4 ) (8) and [Ru(dppv)2 (N2 O2 )] ⋅HImi(BF4 )⋅Imi (10).

Synthetic Lethal Screen Demonstrates That a JAK2 Inhibitor Suppresses a BCL6-dependent IL10RA/JAK2/STAT3 Pathway in High Grade B-cell Lymphoma.

We demonstrate the usefulness of synthetic lethal screening of a conditionally BCL6-deficient Burkitt lymphoma cell line, DG75-AB7, with a library of small molecules to determine survival pathways suppressed by BCL6 and suggest mechanism-based treatments for lymphoma. Lestaurtinib, a JAK2 inhibitor and one of the hits from the screen, repressed survival of BCL6-deficient cells in vitro and reduced growth and proliferation of xenografts in vivo BCL6 deficiency in DG75-AB7 induced JAK2 mRNA and protein expression and STAT3 phosphorylation. Surface IL10RA was elevated by BCL6 deficiency, and blockade of IL10RA repressed STAT3 phosphorylation. Therefore, we define an IL10RA/JAK2/STAT3 pathway each component of which is repressed by BCL6. We also show for the first time that JAK2 is a direct BCL6 target gene; BCL6 bound to the JAK2 promoter in vitro and was enriched by ChIP-seq. The place of JAK2 inhibitors in the treatment of diffuse large B-cell lymphoma has not been defined; we suggest that JAK2 inhibitors might be most effective in poor prognosis ABC-DLBCL, which shows higher levels of IL10RA, JAK2, and STAT3 but lower levels of BCL6 than GC-DLBCL and might be usefully combined with novel approaches such as inhibition of IL10RA.

Epigenetic variation between urban and rural populations of Darwin's finches.

BACKGROUND: The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in rapid adaptation to new environments. An important first step in evaluating this hypothesis is to test for the presence of epigenetic variation between natural populations living under different environmental conditions. RESULTS: In the current study we explored variation between populations of Darwin's finches, which comprise one of the best-studied examples of adaptive radiation. We tested for morphological, genetic, and epigenetic differences between adjacent "urban" and "rural" populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa, on Santa Cruz Island in the Galápagos. Using data collected from more than 1000 birds, we found significant morphological differences between populations of G. fortis, but not G. fuliginosa. We did not find large size copy number variation (CNV) genetic differences between populations of either species. However, other genetic variants were not investigated. In contrast, we did find dramatic epigenetic differences between the urban and rural populations of both species, based on DNA methylation analysis. We explored genomic features and gene associations of the differentially DNA methylated regions (DMR), as well as their possible functional significance. CONCLUSIONS: In summary, our study documents local population epigenetic variation within each of two species of Darwin's finches.

Right Ventricular Longitudinal Strain In Left Ventricular Assist Device Surgery-A Retrospective Cohort Study.

OBJECTIVES: Right ventricular (RV) failure is common after left ventricular assist device (LVAD) surgery and is associated with higher mortality. Measurement of longitudinal RV strain using speckle-tracking technology is a novel approach to quantify RV function. The authors hypothesized that depressed peak longitudinal RV strain measured by intraoperative transesophageal echocardiography (TEE) examinations would be associated with adverse outcomes after LVAD surgery. DESIGN: Retrospective cohort study. SETTING: Tertiary academic medical center. PARTICIPANTS: Following Institutional Review Board approval, the authors retrospectively identified adult patients who underwent implantation of non-pulsatile LVAD. Exclusion criteria included inadequate TEE images and device explantation within 6 months for heart transplantation. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The postoperative adverse event outcome was defined as a composite of one or more of death within 6 months, ≥14 days of inotropes, mechanical RV support, or device thrombosis. Intraoperative TEE images were analyzed for peak RV free wall longitudinal strain by two blinded investigators. Simple logistic regression was used to assess the relationship between adverse outcome and the mean of the strain measurements of the two raters. Agreement between the raters was assessed by intra-class correlation (0.62) and Pearson correlation coefficient (0.63). Of the 57 subjects, 21 (37%) had an adverse outcome. The logistic regression indicated no significant association between RV peak longitudinal strain and adverse events. CONCLUSIONS: In this retrospective study of patients undergoing non-pulsatile LVAD implantation, peak longitudinal strain of the RV free wall was not associated with adverse outcomes within 6 months after surgery. Additional quantitative echocardiographic measures for intraoperative RV assessment should be explored.

Seed: a user-friendly tool for exploring and visualizing microbial community data.

SUMMARY: In this article we present Simple Exploration of Ecological Data (Seed), a data exploration tool for microbial communities. Seed is written in R using the Shiny library. This provides access to powerful R-based functions and libraries through a simple user interface. Seed allows users to explore ecological datasets using principal coordinate analyses, scatter plots, bar plots, hierarchal clustering and heatmaps. AVAILABILITY AND IMPLEMENTATION: Seed is open source and available at https://github.com/danlbek/Seed. CONTACT: danlbek@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.