CytoCellDB: a comprehensive resource for exploring extrachromosomal DNA in cancer cell lines.

Recently, the cancer community has gained a heightened awareness of the roles of extrachromosomal DNA (ecDNA) in cancer proliferation, drug resistance and epigenetic remodeling. However, a hindrance to studying ecDNA is the lack of available cancer model systems that express ecDNA. Increasing our awareness of which model systems express ecDNA will advance our understanding of fundamental ecDNA biology and unlock a wealth of potential targeting strategies for ecDNA-driven cancers. To bridge this gap, we created CytoCellDB, a resource that provides karyotype annotations for cell lines within the Cancer Dependency Map (DepMap) and the Cancer Cell Line Encyclopedia (CCLE). We identify 139 cell lines that express ecDNA, a 200% increase from what is currently known. We expanded the total number of cancer cell lines with ecDNA annotations to 577, which is a 400% increase, covering 31% of cell lines in CCLE/DepMap. We experimentally validate several cell lines that we predict express ecDNA or homogeneous staining regions (HSRs). We demonstrate that CytoCellDB can be used to characterize aneuploidy alongside other molecular phenotypes, (gene essentialities, drug sensitivities, gene expression). We anticipate that CytoCellDB will advance cytogenomics research as well as provide insights into strategies for developing therapeutics that overcome ecDNA-driven drug resistance.

Comorbidity between mood and substance-related disorders: A systematic review and meta-analysis.

BACKGROUND AND OBJECTIVES: Evidence indicates that mood disorders often co-occur with substance-related disorders. However, pooling comorbidity estimates can be challenging due to heterogeneity in diagnostic criteria and in the overall study design. The aim of this study was to systematically review and, where appropriate, meta-analyse estimates related to the pairwise comorbidity between mood disorders and substance-related disorders, after sorting these estimates by various study designs. METHODS: We searched PubMed (MEDLINE), Embase, CINAHL and Web of Science for publications between 1980 and 2017 regardless of geographical location and language. We meta-analysed estimates from original articles in 4 broadly defined mood and 35 substance-related disorders. RESULTS: After multiple eligibility steps, we included 120 studies for quantitative analysis. In general, regardless of variations in diagnosis type, temporal order or use of adjustments, there was substantial comorbidity between mood and substance-related disorders. We found a sixfold elevated risk between broadly defined mood disorder and drug dependence (odds ratio = 5.7) and fivefold risk between depression and cannabis dependence (odds ratio = 4.9) while the highest pooled estimate, based on period prevalence risk, was found between broadly defined dysthymic disorder and drug dependence (odds ratio = 11.3). Based on 56 separate meta-analyses, all pooled odds ratios were above 1, and 46 were significantly greater than 1 (i.e. the 95% confidence intervals did not include 1). CONCLUSION: This review found robust and consistent evidence of an increased risk of comorbidity between many combinations of mood and substance-related disorders. We also identified a number of under-researched mood and substance-related disorders, suitable for future scrutiny. This review reinforces the need for clinicians to remain vigilant in order to promptly identify and treat these common types of comorbidity.

An adaptable and non-invasive method for tracking Bifidobacterium animalis subspecies lactis 420 in the mouse gut.

Probiotic strains from the Bifidobacterium or Lactobacillus genera improve health outcomes in models of metabolic and cardiovascular disease. Yet, underlying mechanisms governing these improved health outcomes are rooted in the interaction of gut microbiota, intestinal interface, and probiotic strain. Central to defining the underlying mechanisms governing these improved health outcomes is the development of adaptable and non-invasive tools to study probiotic localization and colonization within the host gut microbiome. The objective of this study was to test labeling and tracking efficacy of Bifidobacterium animalis subspecies lactis 420 (B420) using a common clinical imaging agent, indocyanine green (ICG). ICG was an effective in situ labeling agent visualized in either intact mouse or excised gastrointestinal (GI) tract at different time intervals. Quantitative PCR was used to validate ICG visualization of B420, which also demonstrated that B420 transit time matched normal murine GI motility (~8 hours). Contrary to previous thoughts, B420 did not colonize any region of the GI tract whether following a single bolus or daily administration for up to 10 days. We conclude that ICG may provide a useful tool to visualize and track probiotic species such as B420 without implementing complex molecular and genetic tools. Proof-of-concept studies indicate that B420 did not colonize and establish residency align the murine GI tract.

Co-morbidity between mood and anxiety disorders: A systematic review and meta-analysis.

There is consistent evidence that mood disorders often co-occur with anxiety disorders, however, the strength of the association of these two broad groups of disorders has been challenging to summarize across different studies. The aim was to conduct a meta-analysis of publications reporting on the pairwise comorbidity between mood and anxiety disorders after sorting into comparable study types. We searched MEDLINE, Embase, CINAHL, Web of Science, and the grey literature for publications between 1980 and 2017 regardless of geographical locations and languages. We meta-analyzed estimates from original articles after sorting by: (a) broad or narrow diagnostic criteria, (b) study time-frame, and (c) estimates with or without covariate adjustments. Over 43 000 unique studies were identified through electronic searches, of which 391 were selected for full-text review. Finally, 171 studies were eligible for inclusion, including 53 articles from additional snowball searching. In general, regardless of variations in diagnosis type, study time-frame, temporal order, or use of adjustments, there was substantial comorbidity between mood and anxiety disorders. Based on the entire 90 separate meta-analyses, the median OR was 6.1 (range 1.5-18.7). Of these estimates, all 90 were above 1, and 87 were significantly greater than 1 (i.e., the 95% confidence intervals did not include 1). Fourteen of the 90 pooled estimates had ORs that were greater than 10. This systematic review found robust and consistent evidence of comorbidity between broadly defined mood and anxiety disorders. Clinicians should be vigilant for the prompt identification and treatment of this common type of comorbidity.

Using 4-vinylcyclohexene diepoxide as a model of menopause for cardiovascular disease.

There is a sharp rise in cardiovascular disease (CVD) risk and progression with the onset of menopause. The 4-vinylcyclohexene diepoxide (VCD) model of menopause recapitulates the natural, physiological transition through perimenopause to menopause. We hypothesized that menopausal female mice were more susceptible to CVD than pre- or perimenopausal females. Female mice were treated with VCD or vehicle for 20 consecutive days. Premenopausal, perimenopausal, and menopausal mice were administered angiotensin II (ANG II) or subjected to ischemia-reperfusion (I/R). Menopausal females were more susceptible to pathological ANG II-induced cardiac remodeling and cardiac injury from a myocardial infarction (MI), while perimenopausal, like premenopausal, females remained protected. Specifically, ANG II significantly elevated diastolic (130.9 ± 6.0 vs. 114.7 ± 6.2 mmHg) and systolic (156.9 ± 4.8 vs. 141.7 ± 5.0 mmHg) blood pressure and normalized cardiac mass (15.9 ± 1.0 vs. 7.7 ± 1.5%) to a greater extent in menopausal females compared with controls, whereas perimenopausal females demonstrated a similar elevation of diastolic (93.7 ± 2.9 vs. 100.5 ± 4.1 mmHg) and systolic (155.9 ± 7.3 vs. 152.3 ± 6.5 mmHg) blood pressure and normalized cardiac mass (8.3 ± 2.1 vs. 7.5 ± 1.4%) compared with controls. Similarly, menopausal females demonstrated a threefold increase in fibrosis measured by Picrosirus red staining. Finally, hearts of menopausal females (41 ± 5%) showed larger infarct sizes following I/R injury than perimenopausal (18.0 ± 5.6%) and premenopausal (16.2 ± 3.3, 20.1 ± 4.8%) groups. Using the VCD model of menopause, we provide evidence that menopausal females were more susceptible to pathological cardiac remodeling. We suggest that the VCD model of menopause may be critical to better elucidate cellular and molecular mechanisms underlying the transition to CVD susceptibility in menopausal women.NEW & NOTEWORTHY Before menopause, women are protected against cardiovascular disease (CVD) compared with age-matched men; this protection is gradually lost after menopause. We present the first evidence that demonstrates menopausal females are more susceptible to pathological cardiac remodeling while perimenopausal and cycling females are not. The VCD model permits appropriate examination of how increased susceptibility to the pathological process of cardiac remodeling accelerates from pre- to perimenopause to menopause.

Resilience Factors Important in Health-Related Quality of Life of Subjects With COPD.

BACKGROUND: Common among patients with COPD is declining health-related quality of life (HRQOL). Although results of research identified some factors associated with HRQOL, resilience factors are yet to be fully investigated. METHODS: This study examined resilience and demographic factors associated with HRQOL. Participants >40 y old were recruited from community health programs and hospitals in South East Queensland. Self-administered questionnaires were used to query subjects' HRQOL and levels of resilience. A decision tree examined the factors important to HRQOL in 159 subjects with COPD. RESULTS: Factors of importance in the HRQOL of subjects with COPD were found in 3 domains of the St George Respiratory Questionnaire. Of importance on the breathlessness domain was marital status, defensive coping, coping, number of comorbidities, relationships, decision-making, self-esteem, self-efficacy, and professional support of health and well-being. Of the symptoms domain, self-efficacy, recruitment location, anxiety/depression, decision-making, self-esteem, coping, relationships, professional support of health and well-being, and risks were important. The cough domain found recruitment location, anxiety/depression, professional support of health and well-being, coping, and defensive coping to be important for subjects' HRQOL. CONCLUSIONS: Resilience and confounding factors were of importance in the HRQOL of subjects with COPD. Thus, consultation with a medical professional, especially at discharge, who identifies, encourages, and approves of the patient's disease management abilities will enhance both resilience and HRQOL.

The effects of chronic obstructive pulmonary disease self-management interventions on improvement of quality of life in COPD patients: A meta-analysis.

This article aimed to analyse the outcome of self-management randomised control trials and their impact upon chronic obstructive pulmonary disease patients' health outcomes using meta-analysis approach. PubMed, Scopus, CINAHL, Web of Science databases and Cochrane Library, were searched for articles between 1990 and December 2015 by two researchers. Self-management programs significantly improved patients' quality of life across all domains of the St George Respiratory Questionnaire (SGRQ) (activity -2.21 (95% CI: -3.61 to -0.80), p = 0.002; impact -3.30 (95% CI: -5.28 to -1.32), p = 0.001; symptoms -3.12 (95% CI: -4.94 to -1.03), p = 0.001; total -3.32 (95% CI: -4.60 to -2.04), p < 0.001), the six-minute walk test (-30.50 (95% CI: 3.32 to 57.68), p = 0.028), and across three domains of the chronic obstructive pulmonary disease self-efficacy scale (negative effect -1.22 (95% CI: -2.31 to -0.14), p = 0.027; physical exertion -1.27 (95% CI: -2.52 to -0.02), p = 0.047; behavioural risk factors -0.58 (95% CI: -0.99 to -0.16), p = 0.007). Subgroup analyses revealed that chronic obstructive pulmonary disease education (p < 0.01) was the strongest component with improvements on all aspects of the SGRQ and the six-minute walk test. Providing an exacerbation action plan significantly improved SGRQ activity and impact scores whilst exercise information had a positive effect on activity and symptom scores (p < 0.05). Interventions with a duration of less than five weeks (p < 0.05) significantly improved symptom and activity scores, in addition to the number of patient hospital admissions. Thus, self-management interventions are effective at improving the health outcomes of chronic obstructive pulmonary disease patients, especially when disease education is provided.

A continuum model of transcriptional bursting.

Transcription occurs in stochastic bursts. Early models based upon RNA hybridisation studies suggest bursting dynamics arise from alternating inactive and permissive states. Here we investigate bursting mechanism in live cells by quantitative imaging of actin gene transcription, combined with molecular genetics, stochastic simulation and probabilistic modelling. In contrast to early models, our data indicate a continuum of transcriptional states, with a slowly fluctuating initiation rate converting the gene between different levels of activity, interspersed with extended periods of inactivity. We place an upper limit of 40 s on the lifetime of fluctuations in elongation rate, with initiation rate variations persisting an order of magnitude longer. TATA mutations reduce the accessibility of high activity states, leaving the lifetime of on- and off-states unchanged. A continuum or spectrum of gene states potentially enables a wide dynamic range for cell responses to stimuli.

Structure of Spherulites in Insulin, ß-Lactoglobulin, and Amyloid ß.

Under denaturing conditions such as low pH and elevated temperatures, proteins in vitro can misfold and aggregate to form long rigid rods called amyloid fibrils; further self-assembly can lead to larger structures termed spherulites. Both of these aggregates resemble amyloid tangles and plaques associated with Alzheimer's disease in vivo. The ability to form such aggregates in a multitude of different proteins suggests that it is a generic ability in their mechanism to form. Little is known about the structure of these large spherulites ranging from 5 to 100 microns and whether they can reproducibly form in amyloid ß (1-40) (Aß40), a 40-amino acid residue peptide, which is one of the major components of Alzheimer's amyloid deposits. Here, we show that spherulites can readily form in Aß40 under certain monomerization and denaturing conditions. Using polarized and nonpolarized Raman spectroscopy, we analyzed the secondary structure of spherulites formed from three different proteins: insulin, ß-lactoglobulin (BLG), and Aß40. Visually, these spherulites have a characteristic "Maltese Cross" structure under crossed polarizers through an optical microscope. However, our results indicate that insulin and Aß40 spherulites have similar core structures consisting mostly of random coils with radiating fibrils, whereas BLG mostly contains ß-sheets and fibrils that are likely to be spiraling from the core to the edge.

Multiple cell and population-level interactions with mouse embryonic stem cell heterogeneity.

Much of development and disease concerns the generation of gene expression differences between related cells sharing similar niches. However, most analyses of gene expression only assess population and time-averaged levels of steady-state transcription. The mechanisms driving differentiation are buried within snapshots of the average cell, lacking dynamic information and the diverse regulatory history experienced by individual cells. Here, we use a quantitative imaging platform with large time series data sets to determine the regulation of developmental gene expression by cell cycle, lineage, motility and environment. We apply this technology to the regulation of the pluripotency gene Nanog in mouse embryonic stem cells. Our data reveal the diversity of cell and population-level interactions with Nanog dynamics and heterogeneity, and how this regulation responds to triggers of pluripotency. Cell cycles are highly heterogeneous and cycle time increases with Nanog reporter expression, with longer, more variable cycle times as cells approach ground-state pluripotency. Nanog reporter expression is highly stable over multiple cell generations, with fluctuations within cycles confined by an attractor state. Modelling reveals an environmental component to expression stability, in addition to any cell-autonomous behaviour, and we identify interactions of cell density with both cycle behaviour and Nanog. Rex1 expression dynamics showed shared and distinct regulatory effects. Overall, our observations of multiple partially overlapping dynamic heterogeneities imply complex cell and environmental regulation of pluripotent cell behaviour, and suggest simple deterministic views of stem cell states are inappropriate.

Imaging nascent RNA dynamics in Dictyostelium.

Dictyostelium cells have great utility for live imaging of single gene transcriptional dynamics. The cells allow efficient molecular genetics, for targeting of RNA reporters and fluorescent proteins to individual, defined loci. Dictyostelium cells share many signalling, chromatin and nuclear characteristics of larger eukaryotes, yet the cells have a relatively simple scattered differentiation programme, allowing imaging of transcriptional events in the context of stochastic developmental choices. This review will detail the methods and considerations for imaging nascent RNA dynamics at single genes in living Dictyostelium cells.

Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation.

Transcription of genes can be discontinuous, occurring in pulses or bursts. It is not clear how properties of transcriptional pulses vary between different genes. We compared the pulsing of five housekeeping and five developmentally induced genes by direct imaging of single gene transcriptional events in individual living Dictyostelium cells. Each gene displayed its own transcriptional signature, differing in probability of firing and pulse duration, frequency, and intensity. In contrast to the prevailing view from both prokaryotes and eukaryotes that transcription displays binary behavior, strongly expressed housekeeping genes altered the magnitude of their transcriptional pulses during development. These nonbinary "tunable" responses may be better suited than stochastic switch behavior for housekeeping functions. Analysis of RNA synthesis kinetics using fluorescence recovery after photobleaching implied modulation of housekeeping-gene pulse strength occurs at the level of transcription initiation rather than elongation. In addition, disparities between single cell and population measures of transcript production suggested differences in RNA stability between gene classes. Analysis of stability using RNAseq revealed no major global differences in stability between developmental and housekeeping transcripts, although strongly induced RNAs showed unusually rapid decay, indicating tight regulation of expression.

Spherulites of amyloid-beta42 in vitro and in Alzheimer's disease.

Several amyloidogenic proteins including insulin, beta-lactoglobulin, and albumin form spherulites in vitro under non-physiological conditions. These micrometer-sized, roughly spherical structures are composed of ordered arrays of amyloid fibrils in radial arrangements which, characteristically, show a typical Maltese cross pattern of light extinction under the polarizing microscope. The physiological significance of amyloid spherulites is unknown though in Alzheimer's disease, senile plaques composed primarily of beta sheets of amyloid-beta (Abeta)42 have, very occasionally, been shown to give a Maltese cross pattern of light extinction under crossed polarizers. Herein we describe the first observation of the formation in vitro of spherulites of Abeta42. They were formed under near-physiological conditions in which the beta sheet conformation of pre-formed aggregates of Abeta42 had been abolished following the addition of an excess of copper. Incubation of these preparations at 37 degrees C for up to 9 months resulted in the formation of globular structures, 5-20 microm in diameter, which exhibited a Maltese cross pattern of light extinction typical of spherulites. Near-identical spherulitic structures were also observed in abundance in 30 microm thick sections of Alzheimer's disease brain tissue. Synchrotron x-ray fluorescence showed that the location of these spherulites in AD tissue coincided with locally elevated concentrations of tissue copper. The formation in vitro of spherulites of Abeta42 which morphologically appeared analogous to spherulitic structures observed in vivo strongly supports the hypothesis that spherulites and senile plaques in AD tissue are one and the same structures and that their ultimate formation may involve copper.

Common motifs in protein self-assembly.

The importance of misfolding proteins forming amyloid fibrils for the aetiology of many diseases, particularly those of old age, is well recognized. This phenomenon is now thought to be a universal property of proteins, as long as appropriate conditions for loosening the native folded structure can be found, which may be outside those of normal physiology. However, the beta-sheet-rich structure of the amyloid fibril does not need to exist in isolation. Recent work has shown that higher order assemblies of the fibrils occur into structures resembling spherulites found in common synthetic semi-crystalline polymers. In these, the fibrils grow outwards from an inner core, thought to be amorphous. Data will be presented on the kinetics of growth of these fibrils for different proteins, so that similarities and differences can be revealed, and related to subtle differences in appearance under the microscope. The in vitro assembly of amyloid fibrils is usually thought to occur well away from the isoelectric point of the protein, and these are the conditions under which they have most been studied. Around the isoelectric point, particulate self-assembly is known to occur for beta-lactoglobulin, and we can now show this is also a generic form of protein self-assembly once the net charge on the protein is close to zero. Nevertheless, the charge is not actually zero, and salt in the solution is found to have a significant effect on the growth of the particles. The use of SAXS, thioflavin T staining and FTIR also shows that within the particles there is also clear evidence for amyloid-like beta-sheet structure, particularly in the case when salt is absent, demonstrating that this particular motif underlies this very different form of protein self-assembly.