XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells.

X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.

Species-specific regulation of XIST by the JPX/FTX orthologs.

X chromosome inactivation (XCI) is an essential process, yet it initiates with remarkable diversity in various mammalian species. XIST, the main trigger of XCI, is controlled in the mouse by an interplay of lncRNA genes (LRGs), some of which evolved concomitantly to XIST and have orthologues across all placental mammals. Here, we addressed the functional conservation of human orthologues of two such LRGs, FTX and JPX. By combining analysis of single-cell RNA-seq data from early human embryogenesis with various functional assays in matched human and mouse pluripotent stem- or differentiated post-XCI cells, we demonstrate major functional differences for these orthologues between species, independently of primary sequence conservation. While the function of FTX is not conserved in humans, JPX stands as a major regulator of XIST expression in both species. However, we show that different entities of JPX control the production of XIST at various steps depending on the species. Altogether, our study highlights the functional versatility of LRGs across evolution, and reveals that functional conservation of orthologous LRGs may involve diversified mechanisms of action. These findings represent a striking example of how the evolvability of LRGs can provide adaptative flexibility to constrained gene regulatory networks.

Emergency department care experiences among members of equity-deserving groups: quantitative results from a cross-sectional mixed methods study.

BACKGROUND: Emergency departments (EDs) serve an integral role in healthcare, particularly for vulnerable populations. However, marginalized groups often report negative ED experiences, including stigmatizing attitudes and behaviours. We engaged with historically marginalized patients to better understand their ED care experiences. METHOD: Participants were invited to complete an anonymous mixed-methods survey about a previous ED experience. We analysed quantitative data including controls and equity-deserving groups (EDGs) - those who self-identified as: (a) Indigenous; (b) having a disability; (c) experiencing mental health issues; (d) a person who uses substances; (e) a sexual and gender minority; (f) a visible minority; (g) experiencing violence; and/or (h) facing homelessness - to identify differences in their perspectives. Differences between EDGs and controls were calculated with chi squared tests, geometric means with confidence ellipses, and the Kruskal-Wallis H test. RESULTS: We collected a total of 2114 surveys from 1973 unique participants, 949 controls and 994 who identified as equity-deserving. Members of EDGs were more likely to attribute negative feelings to their ED experience (p < 0.001), to indicate that their identity impacted the care received (p < 0.001), and that they felt disrespected and/or judged while in the ED (p < 0.001). Members of EDGs were also more likely to indicate that they had little control over healthcare decisions (p < 0.001) and that it was more important to be treated with kindness/respect than to receive the best possible care (p < 0.001). CONCLUSION: Members of EDGs were more likely to report negative ED care experiences. Equity-deserving individuals felt judged and disrespected by ED staff and felt disempowered to make decisions about their care. Next steps will include contextualizing findings using participants' qualitative data and identifying how to improve ED care experiences among EDGs to make it more inclusive and better able to meet their healthcare needs.

Identifying Human Naïve Pluripotent Stem Cells - Evaluating State-Specific Reporter Lines and Cell-Surface Markers.

Recent reports that human pluripotent stem cells can be captured in a spectrum of states with variable properties has prompted a re-evaluation of how pluripotency is acquired and stabilised. The latest additions to the stem cell hierarchy open up opportunities for understanding human development, reprogramming, and cell state transitions more generally. Many of the new cell lines have been collectively termed 'naïve' human pluripotent stem cells to distinguish them from the conventional 'primed' cells. Here, several transcriptional and epigenetic hallmarks of human pluripotent states in the recently described cell lines are reviewed and evaluated. Methods to derive and identify human naïve pluripotent stem cells are also discussed, with a focus on the uses and future developments of state-specific reporter cell lines and cell-surface proteins. Finally, opportunities and uncertainties in naïve stem cell biology are highlighted, and the current limitations of human naïve pluripotent stem cells considered, particularly in the context of differentiation.

The strength of gradually accruing probabilistic evidence modulates brain activity during a categorical decision.

The evolution of neural activity during a perceptual decision is well characterized by the evidence parameter in sequential sampling models. However, it is not known whether accumulating signals in human neuroimaging are related to the integration of evidence. Our aim was to determine whether activity accumulates in a nonperceptual task by identifying brain regions tracking the strength of probabilistic evidence. fMRI was used to measure whole-brain activity as choices were informed by integrating a series of learned prior probabilities. Participants first learned the predictive relationship between a set of shape stimuli and one of two choices. During scanned testing, they made binary choices informed by the sum of the predictive strengths of individual shapes. Sequences of shapes adhered to three distinct rates of evidence (RoEs): rapid, gradual, and switch. We predicted that activity in regions informing the decision would modulate as a function of RoE prior to the choice. Activity in some regions, including premotor areas, changed as a function of RoE and response hand, indicating a role in forming an intention to respond. Regions in occipital, temporal, and parietal lobes modulated as a function of RoE only, suggesting a preresponse stage of evidence processing. In all of these regions, activity was greatest on rapid trials and least on switch trials, which is consistent with an accumulation-to-boundary account. In contrast, activity in a set of frontal and parietal regions was greatest on switch and least on rapid trials, which is consistent with an effort or time-on-task account.

A randomized controlled trial of cognitive-behavioral therapy versus treatment as usual for adolescents with autism spectrum disorders and comorbid anxiety.

OBJECTIVE: Examine the efficacy of a personalized, modular cognitive-behavioral therapy (CBT) protocol among early adolescents with high-functioning autism spectrum disorders (ASDs) and co-occurring anxiety relative to treatment as usual (TAU). METHOD: Thirty-one children (11-16 years) with ASD and clinically significant anxiety were randomly assigned to receive 16 weekly CBT sessions or an equivalent duration of TAU. Participants were assessed by blinded raters at screening, posttreatment, and 1-month follow-up. RESULTS: Youth randomized to CBT demonstrated superior improvement across primary outcomes relative to those receiving TAU. Eleven of 16 adolescents randomized to CBT were treatment responders, versus 4 of 15 in the TAU condition. Gains were maintained at 1-month follow-up for CBT responders. CONCLUSIONS: These data extend findings of the promising effects of CBT in anxious youth with ASD to early adolescents.

Frequency and Clinical Correlates of Sleep-Related Problems Among Anxious Youth with Autism Spectrum Disorders.

Sleep-related problems (SRPs) are common and problematic among anxious youth but have not been investigated in anxious youth with autism spectrum disorder (ASD). Participants were 102 youth (ages 7-16 years) with ASD and comorbid anxiety. Youth and their primary caregiver were administered the Pediatric Anxiety Rating Scale. Parents completed the Multidimensional Anxiety Scale for Children-Parent (MASC-P) Report, Social Responsiveness Scale, and the Child Behavior Checklist (CBCL). A measure of SRPs was created from items from the CBCL and MASC-P. Results suggest SRPs were relatively common among youth with ASD and comorbid anxiety. The number of SRPs endorsed directly associated with parent ratings of social deficits, internalizing and externalizing symptoms, and anxiety symptoms, as well as with clinician-rated anxiety symptoms. Parent-rated internalizing symptoms predicted frequency of SRPs over and above social deficits, externalizing symptoms, and parent- and clinician-rated anxiety symptoms. A subset of 40 participants who completed family-based cognitive-behavioral therapy (CBT) experienced reduced SRPs following treatment. Implications, study limitations, and recommendations for future research are discussed.

C'mon get happy: reduced magnitude and duration of response during a positive-affect induction in depression.

BACKGROUND: Depression involves decreased positive affect. Whether this is due to a failure to achieve or maintain positive emotion in response to discrete stimuli is unclear. Understanding the nature of decreased positive affect could help to address how to intervene in the phenomenon, for example, how to structure interventions using positive and rewarding stimuli in depression. Thus, we examined the time course of affect following exposure to positive stimuli in depressed and healthy individuals. METHODS: Seventy-one adults with major depressive disorder and thirty-four never-depressed controls read a self-generated highly positive script and continuously rated their affect for 7 min. RESULTS: Both groups quickly achieved increased positive affect, however, compared to controls, depressed participants did not achieve the same level of positive affect, did not maintain their positive affect, spent less time rating their affect as happy, and demonstrated larger drops in mood. CONCLUSIONS: These data indicate that depressed and nondepressed individuals can generate positive reactions to happy scripts, but depressed individuals cannot achieve or sustain equivalent levels of positive affect. Interventions for depression might fruitfully focus on increasing depressed individuals' ability to maintain initial engagement with positive stimuli over a sustained period of time.

Global Emergency Medicine: A Scoping Review of the Literature from 2022.

OBJECTIVE: The objective was to identify the highest quality global emergency medicine (GEM) research published in 2022. The top articles are compiled in a comprehensive list of all the year's GEM articles and narrative summaries are performed on those included. METHODS: A systematic PubMed search was conducted to identify all GEM articles published in 2022 and included a manual supplemental screen of 11 organizational websites for gray literature (GRAY). A team of trained reviewers and editors screened all identified titles and abstracts, based on three case definition categories: disaster and humanitarian response (DHR), emergency care in resource-limited settings (ECRLS), and emergency medicine development (EMD). Articles meeting these definitions were independently scored by two reviewers using rubrics for original research (OR), review (RE) articles, and GRAY. Articles that scored in the top 5% from each category as well as the overall top 5% of articles were included for narrative summary. RESULTS: The 2022 search identified 58,510 articles in the main review, of which 524 articles screened in for scoring, respectively, 30% and 18% increases from last year. After duplicates were removed, 36 articles were included for narrative summary. The GRAY search identified 7755 articles, of which 33 were scored and one was included for narrative summary. ECRLS remained the largest category (27; 73%), followed by DHR (7; 19%) and EMD (3; 8%). OR articles remained more common than RE articles (64% vs. 36%). CONCLUSIONS: The waning of the COVID-19 pandemic has not affected the continued growth in GEM literature. Articles related to prehospital care, mental health and resilience among patients and health care workers, streamlining pediatric infectious disease care, and disaster preparedness were featured in this year's review. The continued lack of EMD studies despite the global growth of GEM highlights a need for more scholarly dissemination of best practices.

Global emergency medicine: four part series : Paper 4: Global EM education and professionalization.

In 2018, the Canadian Association of Emergency Physicians (CAEP) academic symposium included developing recommendations on supporting global emergency medicine (EM) in Canadian departments and divisions. Members of CAEP's Global EM committee created a four-part series to be published in CJEM that would build upon the symposium recommendations. The objective is to offer practical tools to EM physicians interested in becoming involved in Global EM, as well as provide departments with successful Canadian case examples that foster, facilitate, and grow Global EM efforts. This submission is the fourth paper of the series which focuses on education and continuing professional development for Global EM. It includes resources for resident global EM electives, fellowship training and ongoing or additional CPD training for practicing EM physicians. It also highlights the importance of pre-departure training and other required elements of engaging responsibly in Global EM work.

RéSUMé: En 2018, le symposium universitaire de l'Association canadienne des médecins d'urgence (ACMU) comprenait l'élaboration de recommandations sur le soutien de la médecine d'urgence mondiale (MU) dans les départements et divisions canadiens. Les membres du comité mondial de la GU de l'ACMU proposent une série de quatre articles qui seront publiés dans la MCEM et qui s'appuieront sur les recommandations du symposium. L'objectif est d'offrir des outils pratiques aux médecins en GU qui souhaitent s'impliquer dans la GU mondiale, ainsi que de fournir aux départements des exemples de cas canadiens réussis qui favorisent, facilitent et développent les efforts en GU mondiale. Ce mémoire est le quatrième article de la série qui se concentre sur l'éducation et le développement professionnel continu pour Global EM. Il comprend des ressources pour les cours au choix internationaux de GU des résidents, la formation de fellowship et la formation continue ou supplémentaire de DPC pour les médecins praticiens de GU. Il souligne également l'importance de la formation préalable au départ et d'autres éléments requis pour s'engager de manière responsable dans le travail de gestion des urgences à l'échelle mondiale.

Global emergency medicine: four part series on best practices : Paper 1: Introduction and overview of global emergency medicine.

The Canadian Association of Emergency Physicians' (CAEP) Global Emergency Medicine committee presents a four-part series that builds upon the Academic Symposium recommendations from the CAEP 2018 meeting (Collier et al. in CJEM 21(5):600-606, 2019). This series presents best practices and offers practical tools for the development and practice of Global EM. This is the first paper of the series which provides an overview of current Global EM systems and development. The breadth and scope of the field is described, and key definitions are outlined. International efforts, initiatives, and organizations relating to public health and humanitarian response are introduced. Other key aspects of Global EM are explored in papers 2-4 including: developing partnerships, supporting centers of research and practice, and education and training.

RéSUMé: Le Comité mondial de la médecine d'urgence de l'Association canadienne des médecins d'urgence (ACMU) présente une série en quatre parties qui s'appuie sur les recommandations du Symposium universitaire de la réunion de 2018 de l'ACMU [1]. Cette série présente les meilleures pratiques et propose des outils pratiques pour le développement et la pratique de la ME mondiale. Il s'agit du premier article de la série qui donne un aperçu des systèmes et du développement actuels de la ME mondiale. L'étendue et la portée du domaine sont décrites, ainsi que les définitions clés. Les efforts, les initiatives et les organisations internationales en matière de santé publique et d'intervention humanitaire sont présentés. D'autres aspects clés de la GU mondiale sont explorés dans les documents 2 à 4, notamment : le développement de partenariats, le soutien des centres de recherche et de pratique, et l'éducation et la formation.

Variants in folate pathway genes as modulators of genetic instability and lung cancer risk.

Genetic instability plays a crucial role in cancer development. The genetic stability of the cell as well as DNA methylation status could be modulated by folate levels. Several studies suggested associations between polymorphisms in folate genes and alterations in protein expression and variations in serum levels of the folate. The objective of this study was to investigate the effect of folate pathway polymorphisms on modulating genetic instability and lung cancer risk. Genotyping of 5 SNPs in folate pathway genes and cytokinesis-blocked micronucleus cytome assay analysis (to determine the genetic instability at baseline and following NNK treatment) was conducted on 180 lung cancer cases and 180 age-, gender-, and smoking-matched controls. Our results showed that individually, folate pathway SNPs were not associated with cytogenetic damage or lung cancer risk. However, in a polygenic disease such as lung cancer, gene-gene interactions are expected to play an important role in determining the phenotypic variability of the diseases. We observed that interactions between MTHFR677, MTHFR1298, and SHMT polymorphisms may have a significant impact on genetic instability in lung cancer patients. With regard to cytogenetic alterations, our results showed that lymphocytes from lung cancer patients exposed to the tobacco-specific carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone [NNK] had considerably increased frequency of cytogenetic damage in presence of MTHFR 677, MTHFR 1298, and SHMT allelic variants. These findings support the notion that significant interactions may potentially modulate the lung cancer susceptibility and alter the overall the repair abilities of lung cancer patients when exposed to tobacco carcinogens such as NNK.

Global emergency medicine: A scoping review of the literature from 2021.

OBJECTIVE: The objective was to identify the most important and impactful peer-reviewed global emergency medicine (GEM) articles published in 2021. The top articles are summarized in brief narratives and accompanied by a comprehensive list of all identified articles that address the topic during the year to serve as a reference for clinicians, researchers, and policy makers. METHODS: A systematic PubMed search was carried out to identify all GEM articles published in 2021. Title and abstract screening was performed by trained reviewers and editors to identify articles in one of three categories based on predefined criteria: disaster and humanitarian response (DHR), emergency care in resource-limited settings (ECRLS), and emergency medicine development (EMD). Included articles were each scored by two reviewers using established rubrics for original (OR) and review (RE) articles. The top 5% of articles overall and the top 5% of articles from each category (DHR, ECRLS, EMD, OR, and RE) were included for narrative summary. RESULTS: The 2021 search identified 44,839 articles, of which 444 articles screened in for scoring, 25% and 22% increases from 2020, respectively. After removal of duplicates, 23 articles were included for narrative summary. ECRLS constituted the largest category (n = 16, 70%), followed by EMD (n = 4, 17%) and DHR (n = 3, 13%). The majority of top articles were OR (n = 14, 61%) compared to RE (n = 9, 39%). CONCLUSIONS: The GEM peer-reviewed literature continued to grow at a fast rate in 2021, reflecting the continued expansion and maturation of this subspecialty of emergency medicine. Few high-quality articles focused on DHR and EMD, suggesting a need for further efforts in those fields. Future efforts should focus on improving the diversity of GEM research and equitable representation.

Genome-wide screening identifies Polycomb repressive complex 1.3 as an essential regulator of human naïve pluripotent cell reprogramming.

Uncovering the mechanisms that establish naïve pluripotency in humans is crucial for the future applications of pluripotent stem cells including the production of human blastoids. However, the regulatory pathways that control the establishment of naïve pluripotency by reprogramming are largely unknown. Here, we use genome-wide screening to identify essential regulators as well as major impediments of human primed to naïve pluripotent stem cell reprogramming. We discover that factors essential for cell state change do not typically undergo changes at the level of gene expression but rather are repurposed with new functions. Mechanistically, we establish that the variant Polycomb complex PRC1.3 and PRDM14 jointly repress developmental and gene regulatory factors to ensure naïve cell reprogramming. In addition, small-molecule inhibitors of reprogramming impediments improve naïve cell reprogramming beyond current methods. Collectively, this work defines the principles controlling the establishment of human naïve pluripotency and also provides new insights into mechanisms that destabilize and reconfigure cell identity during cell state transitions.

TGFß superfamily signaling regulates the state of human stem cell pluripotency and capacity to create well-structured telencephalic organoids.

Telencephalic organoids generated from human pluripotent stem cells (hPSCs) are a promising system for studying the distinct features of the developing human brain and the underlying causes of many neurological disorders. While organoid technology is steadily advancing, many challenges remain, including potential batch-to-batch and cell-line-to-cell-line variability, and structural inconsistency. Here, we demonstrate that a major contributor to cortical organoid quality is the way hPSCs are maintained prior to differentiation. Optimal results were achieved using particular fibroblast-feeder-supported hPSCs rather than feeder-independent cells, differences that were reflected in their transcriptomic states at the outset. Feeder-supported hPSCs displayed activation of diverse transforming growth factor ß (TGFß) superfamily signaling pathways and increased expression of genes connected to naive pluripotency. We further identified combinations of TGFß-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSCs and enhance the formation of well-structured brain tissues suitable for disease modeling.

Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction.

Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here we define the chromatin-associated proteome, histone post-translational modifications and transcriptome of human naive and primed pluripotent stem cells. Our integrated analysis reveals differences in the relative abundance and activities of distinct chromatin modules. We identify a strong enrichment of polycomb repressive complex 2 (PRC2)-associated H3K27me3 in the chromatin of naive pluripotent stem cells and H3K27me3 enrichment at promoters of lineage-determining genes, including trophoblast regulators. PRC2 activity acts as a chromatin barrier restricting the differentiation of naive cells towards the trophoblast lineage, whereas inhibition of PRC2 promotes trophoblast-fate induction and cavity formation in human blastoids. Together, our results establish that human naive pluripotent stem cells are not epigenetically unrestricted, but instead possess chromatin mechanisms that oppose the induction of alternative cell fates.

The transcription factor code in iPSC reprogramming.

Transcription factor (TF)-induced reprogramming of somatic cells across lineages and to induced pluripotent stem cells (iPSCs) has revealed a remarkable plasticity of differentiated cells and presents great opportunities for generating clinically relevant cell types for disease modeling and regenerative medicine. The understanding of iPSC reprogramming provides insights into the mechanisms that safeguard somatic cell identity, drive epigenetic reprogramming, and underlie cell fate specification in vivo. The combinatorial action of TFs has emerged as the key mechanism for the direct and indirect effects of reprogramming factors that induce the remodelling of the enhancer landscape. The interplay of TFs in iPSC reprogramming also yields trophectoderm- and extraembryonic endoderm-like cell populations, uncovering an intriguing plasticity of cell states and opening new avenues for exploring cell fate decisions during early embryogenesis.

Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states.

The transition from naive to primed pluripotency is accompanied by an extensive reorganisation of transcriptional and epigenetic programmes. However, the role of transcriptional enhancers and three-dimensional chromatin organisation in coordinating these developmental programmes remains incompletely understood. Here, we generate a high-resolution atlas of gene regulatory interactions, chromatin profiles and transcription factor occupancy in naive and primed human pluripotent stem cells, and develop a network-graph approach to examine the atlas at multiple spatial scales. We uncover highly connected promoter hubs that change substantially in interaction frequency and in transcriptional co-regulation between pluripotent states. Small hubs frequently merge to form larger networks in primed cells, often linked by newly-formed Polycomb-associated interactions. We identify widespread state-specific differences in enhancer activity and interactivity that correspond with an extensive reconfiguration of OCT4, SOX2 and NANOG binding and target gene expression. These findings provide multilayered insights into the chromatin-based gene regulatory control of human pluripotent states.

Last mile research: a conceptual map.

Background: The term 'last mile' has been used across disciplines to refer to populations who are farthest away, most difficult to reach, or last to benefit from a program or service. However, last mile research lacks a shared understanding around its conceptualization.Objectives: This project used a concept mapping process to answer the questions: what is last mile research in global health and, how can it be used to make positive change for health equity in the last mile?Methods: Between July and December 2019, a five-stage concept mapping exercise was undertaken using online concept mapping software and an in-person consensus meeting. The stages were: establishment of an expert group and focus prompt; idea generation; sorting and rating; initial analysis and final consensus meeting.Results: A group of 15 health researchers with experience working with populations in last mile contexts and who were based at the Matariki Network institutions of Queen's University, CAN and Dartmouth College, USA took part. The resulting concept map had 64 unique idea statements and the process resulted in a map with five clusters. These included: (1) Last mile populations; (2) Research methods and approaches; (3) Structural and systemic factors; (4) Health system factors, and (5) Broader environmental factors. Central to the map were the ideas of equity, human rights, health systems, and contextual sensitivity.Conclusion: This is the first time 'last mile research' has been the focus of a formal concept mapping exercise. The resulting map showed consensus about who last mile populations are, how research should be undertaken in the last mile and why last mile health disparities exist. The map can be used to inform research training programs, however, repeating this process with researchers and members from different last mile populations would also add further insight.

TGFß signalling is required to maintain pluripotency of human naïve pluripotent stem cells.

The signalling pathways that maintain primed human pluripotent stem cells (hPSCs) have been well characterised, revealing a critical role for TGFß/Activin/Nodal signalling. In contrast, the signalling requirements of naive human pluripotency have not been fully established. Here, we demonstrate that TGFß signalling is required to maintain naive hPSCs. The downstream effector proteins - SMAD2/3 - bind common sites in naive and primed hPSCs, including shared pluripotency genes. In naive hPSCs, SMAD2/3 additionally bind to active regulatory regions near to naive pluripotency genes. Inhibiting TGFß signalling in naive hPSCs causes the downregulation of SMAD2/3-target genes and pluripotency exit. Single-cell analyses reveal that naive and primed hPSCs follow different transcriptional trajectories after inhibition of TGFß signalling. Primed hPSCs differentiate into neuroectoderm cells, whereas naive hPSCs transition into trophectoderm. These results establish that there is a continuum for TGFß pathway function in human pluripotency spanning a developmental window from naive to primed states.