A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.

We present a multiomic cell atlas of human lung development that combines single-cell RNA and ATAC sequencing, high-throughput spatial transcriptomics, and single-cell imaging. Coupling single-cell methods with spatial analysis has allowed a comprehensive cellular survey of the epithelial, mesenchymal, endothelial, and erythrocyte/leukocyte compartments from 5-22 post-conception weeks. We identify previously uncharacterized cell states in all compartments. These include developmental-specific secretory progenitors and a subtype of neuroendocrine cell related to human small cell lung cancer. Our datasets are available through our web interface (https://lungcellatlas.org). To illustrate its general utility, we use our cell atlas to generate predictions about cell-cell signaling and transcription factor hierarchies which we rigorously test using organoid models.

A Landscape of Pharmacogenomic Interactions in Cancer.

Systematic studies of cancer genomes have provided unprecedented insights into the molecular nature of cancer. Using this information to guide the development and application of therapies in the clinic is challenging. Here, we report how cancer-driven alterations identified in 11,289 tumors from 29 tissues (integrating somatic mutations, copy number alterations, DNA methylation, and gene expression) can be mapped onto 1,001 molecularly annotated human cancer cell lines and correlated with sensitivity to 265 drugs. We find that cell lines faithfully recapitulate oncogenic alterations identified in tumors, find that many of these associate with drug sensitivity/resistance, and highlight the importance of tissue lineage in mediating drug response. Logic-based modeling uncovers combinations of alterations that sensitize to drugs, while machine learning demonstrates the relative importance of different data types in predicting drug response. Our analysis and datasets are rich resources to link genotypes with cellular phenotypes and to identify therapeutic options for selected cancer sub-populations.

Human SARS-CoV-2 challenge uncovers local and systemic response dynamics.

The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the dynamics of early cellular responses to this disease remains limited1. Here in our SARS-CoV-2 human challenge study, we used single-cell multi-omics profiling of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in seronegative individuals challenged with pre-Alpha SARS-CoV-2. Our analyses revealed rapid changes in cell-type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific time points and infection status. We observed that the interferon response in blood preceded the nasopharyngeal response. Moreover, nasopharyngeal immune infiltration occurred early in samples from individuals with only transient infection and later in samples from individuals with sustained infection. High expression of HLA-DQA2 before inoculation was associated with preventing sustained infection. Ciliated cells showed multiple immune responses and were most permissive for viral replication, whereas nasopharyngeal T cells and macrophages were infected non-productively. We resolved 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our new computational pipeline Cell2TCR identifies activated antigen-responding T cells based on a gene expression signature and clusters these into clonotype groups and motifs. Overall, our detailed time series data can serve as a Rosetta stone for epithelial and immune cell responses and reveals early dynamic responses associated with protection against infection.

Spatially resolved multiomics of human cardiac niches.

The function of a cell is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here we combine single-cell and spatial transcriptomics data to discover cellular niches within eight regions of the human heart. We map cells to microanatomical locations and integrate knowledge-based and unsupervised structural annotations. We also profile the cells of the human cardiac conduction system1. The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. We show that the sinoatrial node is compartmentalized, with a core of pacemaker cells, fibroblasts and glial cells supporting glutamatergic signalling. Using a custom CellPhoneDB.org module, we identify trans-synaptic pacemaker cell interactions with glia. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions to provide mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches that may contribute to infection defence. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be applied to other tissues and organs.

Effective drug combinations in breast, colon and pancreatic cancer cells.

Combinations of anti-cancer drugs can overcome resistance and provide new treatments1,2. The number of possible drug combinations vastly exceeds what could be tested clinically. Efforts to systematically identify active combinations and the tissues and molecular contexts in which they are most effective could accelerate the development of combination treatments. Here we evaluate the potency and efficacy of 2,025 clinically relevant two-drug combinations, generating a dataset encompassing 125 molecularly characterized breast, colorectal and pancreatic cancer cell lines. We show that synergy between drugs is rare and highly context-dependent, and that combinations of targeted agents are most likely to be synergistic. We incorporate multi-omic molecular features to identify combination biomarkers and specify synergistic drug combinations and their active contexts, including in basal-like breast cancer, and microsatellite-stable or KRAS-mutant colon cancer. Our results show that irinotecan and CHEK1 inhibition have synergistic effects in microsatellite-stable or KRAS-TP53 double-mutant colon cancer cells, leading to apoptosis and suppression of tumour xenograft growth. This study identifies clinically relevant effective drug combinations in distinct molecular subpopulations and is a resource to guide rational efforts to develop combinatorial drug treatments.

Local and systemic responses to SARS-CoV-2 infection in children and adults.

It is not fully understood why COVID-19 is typically milder in children1-3. Here, to examine the differences between children and adults in their response to SARS-CoV-2 infection, we analysed paediatric and adult patients with COVID-19 as well as healthy control individuals (total n = 93) using single-cell multi-omic profiling of matched nasal, tracheal, bronchial and blood samples. In the airways of healthy paediatric individuals, we observed cells that were already in an interferon-activated state, which after SARS-CoV-2 infection was further induced especially in airway immune cells. We postulate that higher paediatric innate interferon responses restrict viral replication and disease progression. The systemic response in children was characterized by increases in naive lymphocytes and a depletion of natural killer cells, whereas, in adults, cytotoxic T cells and interferon-stimulated subpopulations were significantly increased. We provide evidence that dendritic cells initiate interferon signalling in early infection, and identify epithelial cell states associated with COVID-19 and age. Our matching nasal and blood data show a strong interferon response in the airways with the induction of systemic interferon-stimulated populations, which were substantially reduced in paediatric patients. Together, we provide several mechanisms that explain the milder clinical syndrome observed in children.

Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases shows aberrant immune responses to infection.

In COVID-19, hyperinflammatory and dysregulated immune responses contribute to severity. Patients with pre-existing autoimmune conditions can therefore be at increased risk of severe COVID-19 and/or associated sequelae, yet SARS-CoV-2 infection in this group has been little studied. Here, we performed single-cell analysis of peripheral blood mononuclear cells from patients with three major autoimmune diseases (rheumatoid arthritis, psoriasis, or multiple sclerosis) during SARS-CoV-2 infection. We observed compositional differences between the autoimmune disease groups coupled with altered patterns of gene expression, transcription factor activity, and cell-cell communication that substantially shape the immune response under SARS-CoV-2 infection. While enrichment of HLA-DRlow CD14+ monocytes was observed in all three autoimmune disease groups, type-I interferon signaling as well as inflammatory T cell and monocyte responses varied widely between the three groups of patients. Our results reveal disturbed immune responses to SARS-CoV-2 in patients with pre-existing autoimmunity, highlighting important considerations for disease treatment and follow-up.

A Randomized Control Trial of a Digital Health Tool for Safer Firearm and Medication Storage for Patients with Suicide Risk.

Most patients with suicide risk do not receive recommendations to reduce access to lethal means due to a variety of barriers (e.g., lack of provider time, training). Determine if highly efficient population-based EHR messaging to visit the Lock to Live (L2L) decision aid impacts patient-reported storage behaviors. Randomized trial. Integrated health care system serving Denver, CO. Served by primary care or mental health specialty clinic in the 75-99.5th risk percentile on a suicide attempt or death prediction model. Lock to Live (L2L) is a web-based decision aid that incorporates patients' values into recommendations for safe storage of lethal means, including firearms and medications. Anonymous survey that determined readiness to change: pre-contemplative (do not believe in safe storage), contemplative (believe in safe storage but not doing it), preparation (planning storage changes) or action (safely storing). There were 21,131 patients randomized over a 6-month period with a 27% survey response rate. Many (44%) had access to a firearm, but most of these (81%) did not use any safe firearm storage behaviors. Intervention patients were more likely to be categorized as preparation or action compared to controls for firearm storage (OR = 1.30 (1.07-1.58)). When examining action alone, there were no group differences. There were no statistically significant differences for any medication storage behaviors. Selection bias in those who responded to survey. Efficiently sending an EHR invitation message to visit L2L encouraged patients with suicide risk to consider safer firearm storage practices, but a stronger intervention is needed to change storage behaviors. Future studies should evaluate whether combining EHR messaging with provider nudges (e.g., brief clinician counseling) changes storage behavior.ClinicalTrials.gov: NCT05288517.

Evaluating an Electronic Consultation Platform to Support Pediatric Primary Care Providers in Caring for Transgender and Nonbinary Adolescents.

Background: An electronic consultation (e-consult) platform was implemented to support pediatric primary care providers (PCPs) in providing gender-affirming care to transgender and nonbinary (TNB) adolescents. Following implementation, a study was conducted to (1) explore how access to this e-consult platform impacts PCP confidence and referral patterns, (2) describe the content of questions, and (3) evaluate PCP's perspectives regarding platform usability. Methods: Following each submission, providers completed a 17-item survey. A total of 20 providers submitted 38 e-consults and 26 follow-up surveys between October 2021 and December 2022. Results: All PCPs reported a high overall value and increased confidence caring for TNB adolescents. Nearly one in five (19%) felt it allowed them to avoid submitting a specialty referral. Mean System Usability Scale score was 78.2 indicating good usability. Conclusion: This e-consult platform shows great promise in increasing PCP confidence providing gender-affirming care adolescents. More widespread utilization could help improve access to care and decrease specialty care referrals.

Telemedicine-Based Provision of Adolescent Gender-Affirming Medical Care to Promote Equitable Access.

Purpose: To explore transgender and nonbinary (TNB) young adults' (1) interest in receiving gender-affirming medications through telemedicine before age 18 years and (2) willingness to initiate this care with primary care providers (PCPs). Methods: Data were from a survey of TNB young adults who had not received gender-affirming medications before age 18 years. Chi-square and Wald tests identified demographic differences in telemedicine interest and willingness to initiate medications with their PCP as minors. Results: Among 280 respondents, 82.5% indicated interest in telemedicine and 42.0% were willing to initiate medications with their PCP. Black/African American respondents were more likely to indicate interest in telemedicine than White and multiracial respondents. Respondents from rural areas were more likely to indicate willingness to initiate medications with their PCP than those from urban areas. Conclusions: Telemedicine expansion and further support for PCPs may represent critical opportunities to promote equitable access to adolescent gender-affirming care.

Using the Personality Assessment Inventory to Assess the Alternative Model for Personality Disorders: Criterion Validity in a Clinical Sample.

The Personality Assessment Inventory (PAI) is a broadband measure of psychopathology that is widely used in applied settings. Researchers developed regression-based estimates that use the PAI to measure constructs of the Alternative Model for Personality Disorders (AMPD) - a hybrid dimensional and categorical approach to conceptualizing personality disorders. Although prior work has linked these estimates to formal measures of the AMPD, there is little work investigating the clinical correlates of this scoring approach of the PAI. The current study examines associations between these PAI-based AMPD estimates and life data in a large, archival dataset of psychiatric outpatients and inpatients. We found general support for the criterion validity of AMPD estimate scores, such that a theoretically consistent pattern of associations emerged with indicators such as prior academic achievement, antisocial behavior, psychiatric history, and substance abuse. These results provide preliminary support to this scoring approach for use in clinical samples.

Deriving the Transdiagnostic Scales From the Personality Assessment Inventory and SPECTRA: Indices of Psychopathology: A Demonstration.

Transdiagnostic models of psychopathology address many of the shortcomings common to categorical diagnostic systems. These empirically derived models conceptualize psychopathology as a few broad interrelated and hierarchically arranged dimensions, with an overarching general psychopathology dimension, the p-factor, at the apex. While transdiagnostic models are gaining prominence in mental health research, the lack of available tools has limited their clinical translation. The present study explored the potential of creating transdiagnostic scales from the joint factor structure of the Personality Assessment Inventory, Alternative Model of Personality Disorder trait scales (AMPD), and the clinical scales of the SPECTRA: Indices of Psychopathology (SPECTRA). Exploratory factor analysis in a clinical sample (n = 212) identified five factors corresponding to the Negative Affect/Internalizing, Detachment, Antagonism/Externalizing, Disinhibition/Externalizing, and Thought Disorder transdiagnostic dimensions. Goldberg's "Bass-Ackward" method supported a hierarchical structure. Five composite transdiagnostic scales were created by summing each factor's highest loading PAI and SPECTRA scales. A global psychopathology scale was created by summing the five composite scales. All the composite scales demonstrated adequate internal consistency. Correlations between the composite scales and the NEO Five-Factor Inventory-3 provide initial validity evidence for four composite and global scales. The composite thought disorder scale had no conceptually corresponding NEO domain. Clinical implications and study limitations are discussed.

Telemedicine Utilization Among Transgender and Gender-Diverse Adolescents Before and After the COVID-19 Pandemic.

Introduction: Little is known about how expansion of telemedicine services during the COVID-19 pandemic has affected access to gender-affirming care for transgender and gender-diverse (TGD) youth. The purpose of this study was to explore differences in demographic characteristics and visit completion rates at a multidisciplinary gender clinic before and after telemedicine implementation in March 2020 and among telemedicine users and nonusers. Methods: Data were from electronic health records of Seattle Children's Gender Clinic (SCGC) patients seen between April 2019 and February 2021. We assessed differences in demographic characteristics and care utilization (i.e., encounter type and status) between April 2019 and February 2020 (pre-telemedicine) and April 2020 and February 2021 (post-telemedicine). Results: Of the 1,051 unique patients seen at SCGC during this time period, majority groups were as follows: 62% identified as transmasculine/male, 68% were non-Hispanic White, and 76% resided within 50 miles of the clinic. Statistically significant differences were observed in patient pronouns and insurance type when comparing the pre- and post-telemedicine periods (p < 0.01). Half (52%) of post-telemedicine period encounters were conducted through telemedicine, and telemedicine encounters were significantly more likely to be completed (72% vs. 50%) and less likely to be canceled (21% vs. 46%) compared with in-person encounters. Conclusions: Telemedicine services facilitated continued access to gender-affirming care services for TGD youth during the COVID-19 pandemic. Although the introduction of telemedicine did not exacerbate demographic disparities in access to this care, further research and interventions are warranted to address the ongoing disparities in access to gender-affirming care for youth of color and rural youth.

Changes in Defense Mechanisms in Mothers From Pregnancy to 2 Years Postpregnancy.

ABSTRACT: The objective of this study was to assess changes in maternal defensive functioning from the third trimester of pregnancy to 2 years postpregnancy. A community sample of at-risk mothers ( N = 84; non-White [61%], unmarried [67%], high school or less education [72%], and income less than $20,000 [50%]) were recruited for this longitudinal study. Mothers responded to a semistructured interview during pregnancy and at 2 years postpregnancy about the parent-infant relationship; interview transcripts were coded using the Defense Mechanism Rating Scale (DMRS). Results indicated a significant increase in both total defense mechanisms used and the relative percentage of immature defense mechanisms used over time. A significant decrease in the relative percentage of healthy/adaptive defenses was noted. When all seven levels of defenses of the DMRS were assessed, it was an increase in minor image-distorting defenses, mechanisms that supported vulnerable self-esteem, that accounted for most of the change in immature defenses. Stability coefficients of defense mechanisms were reported, with large effect sizes, for overall defensive functioning, and mature and immature defenses over a 2-year period. These findings lend support to the importance of assessing defense mechanisms to better understand stressful life transitions in mothers.

Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens.

Low success rates during drug development are due, in part, to the difficulty of defining drug mechanism-of-action and molecular markers of therapeutic activity. Here, we integrated 199,219 drug sensitivity measurements for 397 unique anti-cancer drugs with genome-wide CRISPR loss-of-function screens in 484 cell lines to systematically investigate cellular drug mechanism-of-action. We observed an enrichment for positive associations between the profile of drug sensitivity and knockout of a drug's nominal target, and by leveraging protein-protein networks, we identified pathways underpinning drug sensitivity. This revealed an unappreciated positive association between mitochondrial E3 ubiquitin-protein ligase MARCH5 dependency and sensitivity to MCL1 inhibitors in breast cancer cell lines. We also estimated drug on-target and off-target activity, informing on specificity, potency and toxicity. Linking drug and gene dependency together with genomic data sets uncovered contexts in which molecular networks when perturbed mediate cancer cell loss-of-fitness and thereby provide independent and orthogonal evidence of biomarkers for drug development. This study illustrates how integrating cell line drug sensitivity with CRISPR loss-of-function screens can elucidate mechanism-of-action to advance drug development.

Implementation of evidence-based, non-pharmacological interventions addressing behavior and psychological symptoms of dementia: a systematic review focused on implementation strategies.

OBJECTIVE: This study aimed to identify the nature and effects of implementation strategies to increase the use of evidence-based, non-pharmacological interventions designed to reduce the frequency and/or severity of behavioral and psychological symptoms associated with dementia, for people living in the community. DESIGN: This was a systematic review of implementation studies. We searched six databases (in January 2019) and hand-searched reference lists of reports. Studies were included if they used quantitative methods evaluating the use of implementation strategies to increase the use of non-pharmacological interventions. These interventions had to have been tested in a randomized controlled trial (RCT) and found to reduce behavioral and psychological symptoms of dementia, for those living in the community. Studies needed to report the effect of the implementation on clinical practice, for example, a change in practice or the adoption of the intervention in community settings. RESULTS: Twelve studies were included: 11 one-group pre-post design studies and 1 cluster RCT. All studies reported practice change - the majority implementing a new intervention, with six different types of interventions implemented. All studies reported including using partnerships, new funding, educational strategies, and ongoing support and consultation. Seven implementation studies reported positive outcomes for clients on some aspect of behavior or depression for the person with dementia. CONCLUSIONS: Implementation studies using multiple implementation strategies to increase the use of non-pharmacological interventions have demonstrated improvements in behavioral and psychological symptoms common in people with dementia, when provided by clinicians as part of their everyday work routines.

Electronic Health Risk Behavior Screening With Integrated Feedback Among Adolescents in Primary Care: Randomized Controlled Trial.

BACKGROUND: Health risk behaviors are the most common sources of morbidity among adolescents. Adolescent health guidelines (Guidelines for Preventive Services by the AMA and Bright Futures by the Maternal Child Health Bureau) recommend screening and counseling, but the implementation is inconsistent. OBJECTIVE: This study aims to test the efficacy of electronic risk behavior screening with integrated patient-facing feedback on the delivery of adolescent-reported clinician counseling and risk behaviors over time. METHODS: This was a randomized controlled trial comparing an electronic tool to usual care in five pediatric clinics in the Pacific Northwest. A total of 300 participants aged 13-18 years who attended a well-care visit between September 30, 2016, and January 12, 2018, were included. Adolescents were randomized after consent by employing a 1:1 balanced age, sex, and clinic stratified schema with 150 adolescents in the intervention group and 150 in the control group. Intervention adolescents received electronic screening with integrated feedback, and the clinicians received a summary report of the results. Control adolescents received usual care. Outcomes, assessed via online survey methods, included adolescent-reported receipt of counseling during the visit (measured a day after the visit) and health risk behavior change (measured at 3 and 6 months after the visit). RESULTS: Of the original 300 participants, 94% (n=282), 94.3% (n=283), and 94.6% (n=284) completed follow-up surveys at 1 day, 3 months, and 6 months, respectively, with similar levels of attrition across study arms. The mean risk behavior score at baseline was 2.86 (SD 2.33) for intervention adolescents and 3.10 (SD 2.52) for control adolescents (score potential range 0-21). After adjusting for age, gender, and random effect of the clinic, intervention adolescents were 36% more likely to report having received counseling for endorsed risk behaviors than control adolescents (adjusted rate ratio 1.36, 95% CI 1.04 to 1.78) 1 day after the well-care visit. Both the intervention and control groups reported decreased risk behaviors at the 3- and 6-month follow-up assessments, with no significant group differences in risk behavior scores at either time point (3-month group difference: ß=-.15, 95% CI -0.57 to -0.01, P=.05; 6-month group difference: ß=-.12, 95% CI -0.29 to 0.52, P=.57). CONCLUSIONS: Although electronic health screening with integrated feedback improves the delivery of counseling by clinicians, the impact on risk behaviors is modest and, in this study, not significantly different from usual care. More research is needed to identify effective strategies to reduce risk in the context of well-care. TRIAL REGISTRATION: ClinicalTrials.gov NCT02882919; https://clinicaltrials.gov/ct2/show/NCT02882919.

External correlates of the SPECTRA: Indices of psychopathology (SPECTRA) in a clinical sample.

The SPECTRA: Indices of Psychopathology is a broadband assessment inventory compatible with contemporary hierarchical models of psychopathology (internalizing, externalizing, reality impairing dimensions and global psychopathology factor). This study explored the SPECTRA's construct validity using a wide range of life event (extra-test) variables in a clinical sample. The life event variables included the following: education level, school failure, childhood adversity, suicide attempts, psychiatric hospitalizations, depression, psychotic symptoms, self-injury, substance abuse, arrests, physical violence, marital status, employment status and current medications. Results showed that all SPECTRA clinical scales had significant life event correlations. For the higher-order Spectra scales, the global index of psychopathology had the greatest number and range of life event correlations. Correlations for the externalizing and reality impairing Spectra scales provided solid validity evidence, while correlations for the internalizing Spectra scale were more diffuse. These findings provide the first non-test-based evidence of construct validity for the SPECTRA.

Coral species composition drives key ecosystem function on coral reefs.

Rapid and unprecedented ecological change threatens the functioning and stability of ecosystems. On coral reefs, global climate change and local stressors are reducing and reorganizing habitat-forming corals and associated species, with largely unknown implications for critical ecosystem functions such as herbivory. Herbivory mediates coral-algal competition, thereby facilitating ecosystem recovery following disturbance such as coral bleaching events or large storms. However, relationships between coral species composition, the distribution of herbivorous fishes and the delivery of their functional impact are not well understood. Here, we investigate how herbivorous fish assemblages and delivery of two distinct herbivory processes, grazing and browsing, differ among three taxonomically distinct, replicated coral habitats. While grazing on algal turf assemblages was insensitive to different coral configurations, browsing on the macroalga Laurencia cf. obtusa varied considerably among habitats, suggesting that different mechanisms may shape these processes. Variation in browsing among habitats was best predicted by the composition and structural complexity of benthic assemblages (in particular the cover and composition of corals, but not macroalgal cover), and was poorly reflected by visual estimates of browser biomass. Surprisingly, the lowest browsing rates were recorded in the most structurally complex habitat, with the greatest cover of coral (branching Porites habitat). While the mechanism for the variation in browsing is not clear, it may be related to scale-dependent effects of habitat structure on visual occlusion inhibiting foraging activity by browsing fishes, or the relative availability of alternate dietary resources. Our results suggest that maintained functionality may vary among distinct and emerging coral reef configurations due to ecological interactions between reef fishes and their environment determining habitat selection.

Sexual attraction and experiences in the primary care setting: Examining disparities in satisfaction with provider and health self-efficacy.

INTRODUCTION: To test whether sexual minority males and females report lower satisfaction with primary care providers and lower health self-efficacy relative to heterosexual males and females. METHODS: Data from 535 adolescents who participated in one of two randomized clinical trials conducted in a primary care setting were analyzed. Multiple linear regressions controlling for demographic characteristics and treatment condition were used to examine sexual attraction differences in indicators of satisfaction with provider and health self-efficacy. RESULTS: Sexual minority and heterosexual youth both endorsed high satisfaction with providers. Relative to heterosexual males, sexual minority males reported lower self-efficacy in reaching their health goals. Relative to heterosexual females, sexual minority females reported lower confidence in positively impacting their own health, and lower self-efficacy in setting goals and working actively to improve their health. CONCLUSIONS: Sexual minority youth may benefit from additional support from health care providers to enhance their health self-efficacy and reach their health goals.