Age-specific nasal epithelial responses to SARS-CoV-2 infection

Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in infected people over 85 years of age remains high. Here we investigate differences in the cellular landscape and function of paediatric (<12 years), adult (30-50 years) and older adult (>70 years) ex vivo cultured nasal epithelial cells in response to infection with SARS-CoV-2. We show that cell tropism of SARS-CoV-2, and expression of ACE2 and TMPRSS2 in nasal epithelial cell subtypes, differ between age groups. While ciliated cells are viral replication centres across all age groups, a distinct goblet inflammatory subtype emerges in infected paediatric cultures and shows high expression of interferon-stimulated genes and incomplete viral replication. In contrast, older adult cultures infected with SARS-CoV-2 show a proportional increase in basaloid-like cells, which facilitate viral spread and are associated with altered epithelial repair pathways. We confirm age-specific induction of these cell types by integrating data from in vivo COVID-19 studies and validate that our in vitro model recapitulates early epithelial responses to SARS-CoV-2 infection.

Suicide Screening, Risk Assessment, and Lethal Means Counseling During Zero Suicide Implementation

OBJECTIVE

The authors measured implementation of Zero Suicide (ZS) clinical practices that support identification of suicide risk and risk mitigation, including screening, risk assessment, and lethal means counseling, across mental health specialty and primary care settings.

METHODS

Six health care systems in California, Colorado, Michigan, Oregon, and Washington participated. The sample included members ages ≥13 years from 2010 to 2019 (N=7,820,524 patients). The proportions of patients with suicidal ideation screening, suicide risk assessment, and lethal means counseling were estimated.

RESULTS

In 2019, patients were screened for suicidal ideation in 27.1% (range 5.0%-85.0%) of mental health visits and 2.5% (range 0.1%-35.0%) of primary care visits among a racially and ethnically diverse sample (44.9% White, 27.2% Hispanic, 13.4% Asian, and 7.7% Black). More patients screened positive for suicidal ideation in the mental health setting (10.2%) than in the primary care setting (3.8%). Of the patients screening positive for suicidal ideation in the mental health setting, 76.8% received a risk assessment, and 82.4% of those identified as being at high risk received lethal means counseling, compared with 43.2% and 82.4%, respectively, in primary care.

CONCLUSIONS

Six health systems that implemented ZS showed a high level of variation in the proportions of patients receiving suicide screening and risk assessment and lethal means counseling. Two opportunities emerged for further study to increase frequency of these practices: expanding screening beyond patients with regular health care visits and implementing risk assessment with lethal means counseling in the primary care setting directly after a positive suicidal ideation screening.

Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations

Oncology drug combinations can improve therapeutic responses and increase treatment options for patients. The number of possible combinations is vast and responses can be context-specific. Systematic screens can identify clinically relevant, actionable combinations in defined patient subtypes. We present data for 109 anticancer drug combinations from AstraZeneca's oncology small molecule portfolio screened in 755 pan-cancer cell lines. Combinations were screened in a 7 × 7 concentration matrix, with more than 4 million measurements of sensitivity, producing an exceptionally data-rich resource. We implement a new approach using combination Emax (viability effect) and highest single agent (HSA) to assess combination benefit. We designed a clinical translatability workflow to identify combinations with clearly defined patient populations, rationale for tolerability based on tumor type and combination-specific "emergent" biomarkers, and exposures relevant to clinical doses. We describe three actionable combinations in defined cancer types, confirmed in vitro and in vivo, with a focus on hematologic cancers and apoptotic targets.

SIGNIFICANCE

We present the largest cancer drug combination screen published to date with 7 × 7 concentration response matrices for 109 combinations in more than 750 cell lines, complemented by multi-omics predictors of response and identification of "emergent" combination biomarkers. We prioritize hits to optimize clinical translatability, and experimentally validate novel combination hypotheses.

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.

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

The immune system comprises multiple cell lineages and heterogeneous subsets found in blood and tissues throughout the body. While human immune responses differ between sites and over age, the underlying sources of variation remain unclear as most studies are limited to peripheral blood. Here, we took a systems approach to comprehensively profile RNA and surface protein expression of over 1.25 million immune cells isolated from blood, lymphoid organs, and mucosal tissues of 24 organ donors aged 20-75 years. We applied a multimodal classifier to annotate the major immune cell lineages (T cells, B cells, innate lymphoid cells, and myeloid cells) and their corresponding subsets across the body, leveraging probabilistic modeling to define bases for immune variations across donors, tissue, and age. We identified dominant tissue-specific effects on immune cell composition and function across lineages for lymphoid sites, intestines, and blood-rich tissues. Age-associated effects were intrinsic to both lineage and site as manifested by macrophages in mucosal sites, B cells in lymphoid organs, and T and NK cells in blood-rich sites. Our results reveal tissue-specific signatures of immune homeostasis throughout the body and across different ages. This information provides a basis for defining the transcriptional underpinnings of immune variation and potential associations with disease-associated immune pathologies across the human lifespan.

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.

Early human lung immune cell development and its role in epithelial cell fate

Studies of human lung development have focused on epithelial and mesenchymal cell types and function, but much less is known about the developing lung immune cells, even though the airways are a major site of mucosal immunity after birth. An unanswered question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. Here, we profiled human embryonic and fetal lung immune cells using scRNA-seq, smFISH, and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including innate lymphoid cells, natural killer cells, myeloid cells, and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes expressing high levels of cytotoxicity genes and the presence of mature B lymphocytes, including B-1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the presence and diversity of immune cells during development, we also investigated their possible effect on epithelial maturation. We found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1β-producing myeloid cells were found throughout the lung and adjacent to epithelial tips, suggesting that immune cells may direct human lung epithelial development.

A spatial human thymus cell atlas mapped to a continuous tissue axis

T cells develop from circulating precursors, which enter the thymus and migrate throughout specialised sub-compartments to support maturation and selection. This process starts already in early fetal development and is highly active until the involution of the thymus in adolescence. To map the micro-anatomical underpinnings of this process in pre- vs. post-natal states, we undertook a spatially resolved analysis and established a new quantitative morphological framework for the thymus, the Cortico-Medullary Axis. Using this axis in conjunction with the curation of a multimodal single-cell, spatial transcriptomics and high-resolution multiplex imaging atlas, we show that canonical thymocyte trajectories and thymic epithelial cells are highly organised and fully established by post-conception week 12, pinpoint TEC progenitor states, find that TEC subsets and peripheral tissue genes are associated with Hassall's Corpuscles and uncover divergence in the pace and drivers of medullary entry between CD4 vs. CD8 T cell lineages. These findings are complemented with a holistic toolkit for spatial analysis and annotation, providing a basis for a detailed understanding of T lymphocyte development.

Development and initial psychometric properties of the Warwick-Edinburgh Mental Wellbeing Scale-Intellectual Disability version

BACKGROUND

The Warwick-Edinburgh Mental Wellbeing Scale (WEMWBS; Tennant et al., 2007) is yet to be validated in the intellectual disability (ID) population. The aim of this study was to report the development process and assess the psychometric properties of a newly adapted version of the WEMWBS and the Short WEMWBS for individuals with mild to moderate IDs (WEMWBS-ID/SWEMWBS-ID).

METHOD

The WEMWBS item wordings and response options were revised by clinicians and researchers expert in the field of ID, and a visual aid was added to the scale. The adapted version was reviewed by 10 individuals with IDs. The measure was administered by researchers online using screenshare, to individuals aged 16+ years with mild to moderate IDs. Data from three UK samples were collated to evaluate the WEMWBS-ID (n = 96). A subsample (n = 22) completed the measure again 1 to 2 weeks later to assess test-retest reliability, and 95 participants additionally completed an adapted version of the adapted Rosenberg Self-Esteem Scale to examine convergent validity. Additional data from a Canadian sample (n = 27) were used to evaluate the SWEMWBS-ID (n = 123).

RESULTS

The WEMWBS-ID demonstrated good internal consistency (ω = 0.77-0.87), excellent test-retest reliability [intraclass correlation coefficient (ICC) = .88] and good convergent validity with the self-esteem scale (r = .48-.60) across samples. A confirmatory factor analysis for a single factor model demonstrated an adequate fit. The SWEMWBS-ID showed poor to good internal consistency (ω = 0.36-0.74), moderate test-retest reliability (ICC = .67) and good convergent validity (r = .48-.60) across samples, and a confirmatory factor analysis indicated good model fit for a single factor structure.

CONCLUSIONS

The WEMWBS-ID and short version demonstrated promising psychometric properties, when administered virtually by a researcher. Further exploration of the scales with larger, representative samples is warranted.

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.

Utilization of Mental Health Services Among Black Adolescents During the COVID-19 Pandemic: a Narrative Review of the Literature

Purpose of Review

Black youth have disproportionately experienced inequities and barriers to care in accessing mental health services. The purpose of this review is to offer a summary of the currently available literature on mental health service utilization by Black youth during the COVID-19 pandemic, compared to prior. A narrative review was conducted in PubMed, Web of Science, psychINFO, and Embase from March 1, 2020 to September 1, 2022, to find studies that examined differences in the utilization of mental health services among Black youth.

Recent Findings

Our results found only 3 studies which examined pre and during the COVID-19 mental health utilization rates among Black youth. Among these studies, time period, study design, sample size, race data, and change in mental health utilization were evaluated.

Summary

From these results, we found that Black youth were overall less likely to utilize services for mental health during the pandemic. However, there were also findings that offer insights into innovative strategies to meet the needs of this unique population. As mental health service utilization has decreased and been slower to rebound from the pandemic compared to other health services, additional research on this topic is needed to ensure that the mental health needs of Black youth are being met.

Does point-of-care ultrasonography improve diagnostic accuracy in emergency department patients with undifferentiated hypotension? An international randomized controlled trial from the SHOC-ED investigators

PURPOSE

Point-of-care ultrasonography (POCUS) is an established tool in the management of hypotensive patients in the emergency department (ED). We compared the diagnostic accuracy of a POCUS protocol versus standard assessment without POCUS in patients with undifferentiated hypotension.

METHODS

This was an international, multicenter randomized controlled trial included three EDs in North America and three in South Africa from September 2012 to December 2016. Hypotensive patients were randomized to early POCUS protocol plus standard care (POCUS group) or standard care without POCUS (control group). Initial and secondary diagnoses were recorded at 0 and 60 min. The main outcome was measures of diagnostic accuracy of a POCUS protocol in differentiating between cardiogenic and non-cardiogenic shock. Secondary outcomes were diagnostic performance for shock sub-types, as well as changes in perceived category of shock and overall diagnosis.

RESULTS

Follow-up was completed for 270 of 273 patients. For cardiogenic shock, the POCUS-based diagnostic approach (POCUS) performed similarly to the non-POCUS approach (control) for specificity [95.5% (89.9-98.5) vs.93.8% (87.7-97.5)]; positive likelihood ratio (17.92 vs 14.80); negative likelihood ratio (0.21 vs 0.09) and diagnostic odds ratio (85.6 vs 166.57), with a similar overall diagnostic accuracy between the two approaches [93.7% (88-97.2) vs 93.6% (87.8-97.2)]. Diagnostic performance measures were similar across sub-categories of shock.

CONCLUSION

This is the first randomized controlled trial to compare diagnostic performance of a POCUS protocol to standard care without POCUS in undifferentiated hypotensive ED patients. POCUS performed well diagnostically in undifferentiated hypotensive patients, especially as a rule-in test; however, performance did not differ meaningfully from standard assessment.

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.

Electronic Screening for Adolescent Risk Behaviors in the Emergency Department: A Randomized Controlled Trial

Introduction: In this study we aimed to assess the impact of an electronic health assessment with individualized feedback for risk behaviors in adolescents seeking care in a pediatric emergency department (ED). Methods: We conducted a randomized control trial using a tablet-based screening program with a study population of adolescents in a busy pediatric ED. The intervention group received the screening program with individualized feedback. The control group received the screening program without feedback. All participants received one-day and three-month follow-up surveys to assess behaviors and attitudes toward health behaviors. Results: A total of 296 subjects were enrolled and randomized. There was no difference in changes in risky behaviors between the control and experimental groups. A higher proportion of participants in the intervention groups reported that the screener changed the way they thought about their health at one-day follow-up (27.0%, 36/133) compared to the control group (15.5%, 20/129, P = .02). Conclusion: This study successfully tested a multivariable electronic health screener in a real-world setting of a busy pediatric ED. The tool did not significantly change risky health behaviors in the adolescent population screened. However, our finding that the intervention changed adolescents’ perceptions of their health opens a door to the continued development of electronic interventions to screen for and target risk behaviors in adolescents in the ED setting.

“Lock to Live” for firearm and medication safety: Feasibility and acceptability of a suicide prevention tool in a learning healthcare system

Objective

Few patients with suicide risk are counseled on lethal means safety by health providers. This study tested the feasibility of different delivery methods for Lock to Live (L2L), a web-based decision aid of safe storage options for firearms and medications.

Methods

Patients reporting suicide ideation on the PHQ9 depression screener during outpatient health visits were included. Invitation messages to visit L2L were sent via combinations of email, text, Electronic Health Record (EHR) message, mailed letter, or provider referral, followed by a survey about storage behavior and acceptability. Provider interviews evaluated logistical considerations and acceptability.

Results

The population-based method reached 2,729 patients and the best method (EHR message plus 2 email reminders) had 11% uptake (L2L visitation rate). Provider referral had small reach (14 patients) and 100% uptake (all visited). Provider interviews identified several strategies to promote uptake including: EHR reminders, provider training, quality metrics with accountability, a clearly communicated lethal means screening/counseling policy, and strong organizational leadership support.

Conclusion

Despite the low uptake for population-based (11%), far more patients with suicide risk were engaged in the L2L tool through population-based outreach than provider-referral over the same time frame.

Pan-cancer proteomic map of 949 human cell lines

The proteome provides unique insights into disease biology beyond the genome and transcriptome. A lack of large proteomic datasets has restricted the identification of new cancer biomarkers. Here, proteomes of 949 cancer cell lines across 28 tissue types are analyzed by mass spectrometry. Deploying a workflow to quantify 8,498 proteins, these data capture evidence of cell-type and post-transcriptional modifications. Integrating multi-omics, drug response, and CRISPR-Cas9 gene essentiality screens with a deep learning-based pipeline reveals thousands of protein biomarkers of cancer vulnerabilities that are not significant at the transcript level. The power of the proteome to predict drug response is very similar to that of the transcriptome. Further, random downsampling to only 1,500 proteins has limited impact on predictive power, consistent with protein networks being highly connected and co-regulated. This pan-cancer proteomic map (ProCan-DepMapSanger) is a comprehensive resource available at https://cellmodelpassports.sanger.ac.uk.

Search for Subsolar-Mass Binaries in the First Half of Advanced LIGO's and Advanced Virgo's Third Observing Run

We report on a search for compact binary coalescences where at least one binary component has a mass between 0.2  M_{⊙} and 1.0  M_{⊙} in Advanced LIGO and Advanced Virgo data collected between 1 April 2019 1500 UTC and 1 October 2019 1500 UTC. We extend our previous analyses in two main ways: we include data from the Virgo detector and we allow for more unequal mass systems, with mass ratio q≥0.1. We do not report any gravitational-wave candidates. The most significant trigger has a false alarm rate of 0.14  yr^{-1}. This implies an upper limit on the merger rate of subsolar binaries in the range [220-24200]  Gpc^{-3} yr^{-1}, depending on the chirp mass of the binary. We use this upper limit to derive astrophysical constraints on two phenomenological models that could produce subsolar-mass compact objects. One is an isotropic distribution of equal-mass primordial black holes. Using this model, we find that the fraction of dark matter in primordial black holes in the mass range 0.2  M_{⊙}<m_{PBH}<1.0  M_{⊙} is f_{PBH}≡Ω_{PBH}/Ω_{DM}≲6%. This improves existing constraints on primordial black hole abundance by a factor of ∼3. The other is a dissipative dark matter model, in which fermionic dark matter can collapse and form black holes. The upper limit on the fraction of dark matter black holes depends on the minimum mass of the black holes that can be formed: the most constraining result is obtained at M_{min}=1  M_{⊙}, where f_{DBH}≡Ω_{DBH}/Ω_{DM}≲0.003%. These are the first constraints placed on dissipative dark models by subsolar-mass analyses.

Assessing health electronically for adolescent and young adult oncology patients (AHEAD Study)

1568

Background: Screening and counseling for health risk behaviors (RB) are recommended but infrequently performed, particularly in individuals undergoing cancer therapy. Unmet needs among adolescents and young adults (AYAs) with cancer translate to poor physical and psychosocial outcomes. The authors aimed to 1) modify an existing RB electronic health assessment (eHA) and intervention tool and 2) determine the feasibility and acceptability of the RB eHA and intervention tool among AYAs with cancer and their oncology providers. Methods: The internally developed HRB eHA and intervention tool Check Yourself was adapted by a multidisciplinary healthcare professional panel for an AYA oncology population and informed by literature review and AYA stakeholder feedback. “Check Yourself Oncology” assesses risk and health domains including home, education, sexual health, safety, alcohol/drugs, mental health and medication adherence. Optional feedback is provided for sexual health, safety, alcohol/drugs and mental health domains. Eligible AYAs were 13 to 29 years old, diagnosed with cancer, receiving cancer directed therapy, follow-up scheduled with a Seattle Children’s Hospital oncology physician or nurse practitioner, and fluent in English. 72 hours prior to their next oncology clinic visit, participants were text messaged or emailed a personalized link to the Check Yourself Oncology tool to be completed prior to their next visit. Upon completion, a detailed report was sent to the primary clinical oncology team prior to the patient’s visit. Feasibility was defined as 1) ≥70% completion of the RB eHA and 2) a Feasibility of Intervention Measure (FIM) mean score >4. Acceptability was defined as an Acceptability of Intervention Measure (AIM) mean score >4 and qualitatively. The FIM and AIM were sent by REDCap survey following the clinical visit; verbal feedback from AYAs and clinicians was analyzed with qualitative content analysis. Results: Of 30 eligible, approached AYAs, 25 (83%) enrolled in the study and 23 (76%) completed the Check Yourself Oncology tool and follow-up assessments. The AYAs had a mean age of 17 years (SD = 2.9 years) and 50% identified as female. Four AYAs declined participation due to lack of interest, 1 due to declined parental consent, 1 passively declined after enrollment, and 1 declined further participation following the confidentiality terms. The mean FIM and AIM scores were 4.1 (SD=0.6) and 4.0 (SD =0.7) respectively. Seventeen AYAs (74%) felt that the feedback provided was relevant and useful. 74% of visits providers reported that they incorporated the results in the care of the patient and 87% reported the results positively impacted care. Conclusions: Risk behavior screening with motivational feedback though the modified eHA tool Check Yourself Oncology is feasible and acceptable in AYAs undergoing cancer directed therapy. Clinical trial information: NCT04484194.

Cross-tissue immune cell analysis reveals tissue-specific features in humans

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.

Effective drug combinations in breast, colon and pancreatic cancer cells

Combinations of anti-cancer drugs can overcome resistance and provide new treatments^1,2. 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.

A survey of potency and efficacy of 2,025 clinically relevant two-drug combinations against 125 molecularly characterized breast, colorectal and pancreatic cancer cell lines identifies rare synergistic effects of anticancer drugs, informing rational combination treatments for specific cancer subtypes.

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.

Inter-rater reliability of occupational exposure assessment in a case-control study of female breast cancer

The objective of this paper was to estimate the inter-rater reliability of expert assessments of occupational exposures. An inter-rater reliability sub-study was conducted within a population-based case-control study of postmenopausal breast cancer. Detailed information on lifetime occupational histories was obtained from participants and two industrial hygienists assigned exposures to 185 jobs using a checklist of 293 agents. Experts rated exposure for each job-agent combination according to exposure status (unexposed/exposed), confidence that the exposure occurred (possible/probable/definite), intensity (low/medium/high), and frequency (% time per week). The statistical unit of observation was each job-agent assessment (185 jobs × 293 agents = 54,205 assessments per expert). Crude agreement, Gwet AC1/2 statistics, and Cohen's Kappa were used to estimate inter-rater agreement for confidence and intensity; for frequency, the intra-class correlation coefficient (ICC) was used. The majority of job-agent combinations were evaluated by the two experts to be not exposed (crude agreement >98% of decisions). The degree of agreement between the experts for the confidence of exposure status was Gwet AC1/2 = 0.99 (95% CI: 0.99-0.99), and for intensity, a Gwet AC2 = 0.99 (95% CI: 0.99-0.99). For frequency, an ICC of 0.31 (95% CI: 0.26-0.35) was found. A sub-analysis restricted to job-agent combinations for which the two experts agreed on exposure status revealed a moderate agreement for confidence of exposure (Gwet AC2 = 0.66) and high agreement for intensity (Gwet AC2 = 0.96). For frequency, the ICC was 0.52 (95% CI: 0.47-0.57). A high level of inter-rater agreement was found for identifying exposures and for coding intensity, but agreement was lower for the coding of frequency of exposure.

An approach to classifying occupational exposures to endocrine disrupting chemicals by sex hormone function using an expert judgment process

Endocrine disrupting chemicals (EDCs) are exogenous substances that interfere with the endocrine system and cause adverse effects. We aimed to classify the effects of 24 known EDCs, prevalent in certain occupations, according to four modes of action (estrogenic, antiestrogenic, androgenic, and/or antiandrogenic). A literature search, stratified into four types of literature was conducted (namely: national and international agency reports; review articles; primary studies; ToxCast^TM). The state of the evidence of each EDC on sex hormone function was summarized and reviewed by an expert panel. For each mode of action, the experts evaluated the likelihood of endocrine disruption in five categories: "No", "Unlikely", "Possibly", "Probably", and "Yes". Seven agents were categorized as "Yes," or having strong evidence for their effects on sex hormone function (antiandrogenic: lead, arsenic, butylbenzyl phthalate, dibutyl phthalate, dicyclohexyl phthalate; estrogenic: nonylphenol, bisphenol A). Nine agents were categorized as "Probable," or having probable evidence (antiandrogenic: bis(2-ethylhexyl)phthalate, nonylphenol, toluene, bisphenol A, diisononyl phthalate; androgenic: cadmium; estrogenic: copper, cadmium and; anti-estrogenic: lead). Two agents (arsenic, polychlorinated biphenyls) had opposing conclusions supporting both "probably" estrogenic and antiestrogenic effects. This synthesis will allow researchers to evaluate the health effects of selected EDCs with an added level of precision related to the mode of action.

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

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: β=-.15, 95% CI -0.57 to -0.01, P=.05; 6-month group difference: β=-.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.

Cervical mucus sialic acid content determines the ability of frozen-thawed ram sperm to migrate through the cervix

The aim of this study was to investigate the properties and to functionally characterize the cervical mucus that modulates sperm transport through the cervix by using ewe breeds with a divergent pregnancy rate (Belclare and Suffolk; high and low, respectively) following cervical insemination using frozen-thawed semen. Sperm number, as well as sialic acid and fucose content in both the channels and in the lumen of different regions of the cervix were quantified in inseminated Belclare and Suffolk ewes. Expression of glycosyltransferase and MUC genes, glycosidase activity and sialic acid speciation in follicular phase cervical tissue and mucus were assessed. More spermatozoa were found in the cervical channels in the region closest to the cervical os in Belclare than Suffolk ewes (P < 0.05) and Suffolk ewes had a higher sialic acid content in the cervical channels than Belclare ewes (P < 0.05) in all regions of cervix. Suffolk ewes had significantly higher expression of FUT1, ST6GAL1 and MUC5AC than Belclare ewes. There was no difference between the breeds in glycosidase activity (P > 0.05). Levels of Neu5Ac were higher in Belclare than Suffolk ewes (P < 0.05) and levels of Neu5Gc was higher in Suffolk than Belclare ewes (P < 0.05). Competitive sperm penetration assays demonstrated that frozen-thawed sperm progression increased when cervical mucus was incubated with sialyllactose prior to a sperm penetration test (P < 0.05). These results suggest that the difference between Belclare and Suffolk ewes in sperm transport with frozen-thawed semen is due to the higher concentration of sialic acid within channels, which binds to spermatozoa and reduces their ability to traverse the cervix.

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.

Author Correction: Development of a source-exposure matrix for occupational exposure assessment of electromagnetic fields in the INTEROCC study

Corrigendum: This work was also funded by the European Commission grant 603794 (GERoNiMO project).

Dispensation of antiretroviral therapy and methadone maintenance therapy at the same facility in a low-barrier setting linked to optimal adherence to HIV treatment

OBJECTIVES

We sought to examine the association between dispensation of methadone maintenance therapy (MMT) and antiretroviral therapy (ART) at the same facility, across multiple low-barrier dispensing outlets, and achieving optimal adherence to ART among people who use illicit drugs (PWUD).

METHODS

We used data from the AIDS Care Cohort to Evaluate Exposure to Survival Services (ACCESS) study, a long-running study of a community-recruited cohort of HIV-positive PWUD, linked to comprehensive HIV clinical records in Vancouver, Canada, a setting of no-cost, universal access to HIV care. The longitudinal relationship between MMT-ART dispensation at the same facility and the odds of ≥ 95% ART adherence was analysed using multivariable generalized linear mixed-effects modelling. We conducted a further analysis using a marginal structural mode with inverse probability of treatment weights as a sensitivity analysis.

RESULTS

This study included data on 1690 interviews of 345 ART- and MMT-exposed participants carried out between June 2012 and December 2017. In the final multivariable model, MMT-ART dispensation, compared with nondispensation at the same facility, was associated with greater odds of achieving ≥ 95% adherence [adjusted odds ratio (AOR) 1.56; 95% confidence interval (CI) 1.26-1.96]. A marginal structural model estimated a 1.48 (95% CI 1.15-1.80) greater odds of ≥ 95% adherence among participants who reported MMT-ART dispensation at the same facility compared with those who did not.

CONCLUSIONS

The odds of achieving optimal adherence to ART were 56% higher during periods in which MMT and ART medications were dispensed at the same facility, in a low-barrier setting. Our findings highlight the need to consider a simpler integrated approach with medication dispensation at the same facility in low-threshold settings.

Collaborative and Integrated Care for Adolescent Depression

Creative collaborative approaches are required to meet the demands of managing depression in youth. Primary care providers are well positioned to engage depressed youth and their families, yet often lack the training, access to psychiatric providers, and the reimbursement structure to support their efforts. Child and adolescent psychiatrists are encouraged to support pediatricians in establishing more robust systems to provide screening and effective treatment interventions, particularly for youth at higher risk. Several models of collaborative care are described, in addition to their emerging evidence-base, in an effort to disseminate evolving treatment strategies that can drive implementation of effective collaborative approaches.

The validation of biomarkers of metabolic efficacy in infant nutrition

Breastfeeding is regarded as the ideal way to nourish infants. However, feeding with formula milk is also common in much of the West. Despite this, the function of the molecular components of breast and formula milks are not fully understood, less still the relationship between the composition of the milk and the infant's metabolism and how this influences the infant's development. The Biotechnology and Biological Sciences Research Council-funded project 'The validation of biomarkers of metabolic efficacy in infant nutrition' aims to identify lipid biomarkers that can be used to study the effect of diet on growth and development of infants. In this work, we have been able to validate these markers. Here, we present an approach to biomarker discovery that has new depth and will inform research questions about how metabolism is governed, and which species can be used to identify situations where metabolism is becoming defective.

Probabilistic Multiple-Bias Modeling Applied to the Canadian Data From the Interphone Study of Mobile Phone Use and Risk of Glioma, Meningioma, Acoustic Neuroma, and Parotid Gland Tumors

We undertook a re-analysis of the Canadian data from the 13-country case-control Interphone Study (2001-2004), in which researchers evaluated the associations of mobile phone use with the risks of brain, acoustic neuroma, and parotid gland tumors. In the main publication of the multinational Interphone Study, investigators concluded that biases and errors prevented a causal interpretation. We applied a probabilistic multiple-bias model to address possible biases simultaneously, using validation data from billing records and nonparticipant questionnaires as information on recall error and selective participation. In our modeling, we sought to adjust for these sources of uncertainty and to facilitate interpretation. For glioma, when comparing those in the highest quartile of use (>558 lifetime hours) to those who were not regular users, the odds ratio was 2.0 (95% confidence interval: 1.2, 3.4). After adjustment for selection and recall biases, the odds ratio was 2.2 (95% limits: 1.3, 4.1). There was little evidence of an increase in the risk of meningioma, acoustic neuroma, or parotid gland tumors in relation to mobile phone use. Adjustments for selection and recall biases did not materially affect interpretation in our results from Canadian data.