Bento: a toolkit for subcellular analysis of spatial transcriptomics data.

The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. We demonstrate MERFISH, seqFISH + , Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.

Dendritic Cell - Fibroblast Crosstalk via TLR9 and AHR Signaling Drives Lung Fibrogenesis.

Idiopathic pulmonary fibrosis (IPF) is characterized by progressive scarring and loss of lung function. With limited treatment options, patients succumb to the disease within 2-5 years. The molecular pathogenesis of IPF regarding the immunologic changes that occur is poorly understood. We characterize a role for non-canonical aryl-hydrocarbon receptor signaling (ncAHR) in dendritic cells (DCs) that leads to production of IL-6 and IL-17, promoting fibrosis. TLR9 signaling in myofibroblasts is shown to regulate production of TDO2 which converts tryptophan into the endogenous AHR ligand kynurenine. Mice with augmented ncAHR signaling were created by crossing floxed AHR exon-2 deletion mice (AHR Δex2 ) with mice harboring a CD11c-Cre. Bleomycin was used to study fibrotic pathogenesis. Isolated CD11c+ cells and primary fibroblasts were treated ex-vivo with relevant TLR agonists and AHR modulating compounds to study how AHR signaling influenced inflammatory cytokine production. Human datasets were also interrogated. Inhibition of all AHR signaling rescued fibrosis, however, AHR Δex2 mice treated with bleomycin developed more fibrosis and DCs from these mice were hyperinflammatory and profibrotic upon adoptive transfer. Treatment of fibrotic fibroblasts with TLR9 agonist increased expression of TDO2. Study of human samples corroborate the relevance of these findings in IPF patients. We also, for the first time, identify that AHR exon-2 floxed mice retain capacity for ncAHR signaling.

Multicomponent processes to identify and prioritise low-value care in hospital settings: a scoping review.

OBJECTIVES: This scoping review mapped and synthesised original research that identified low-value care in hospital settings as part of multicomponent processes. DESIGN: Scoping review. DATA SOURCES: Electronic databases (EMBASE, PubMed, CINAHL, PsycINFO and Cochrane CENTRAL) and grey literature were last searched 11 July and 3 June 2022, respectively, with no language or date restrictions. ELIGIBILITY CRITERIA: We included original research targeting the identification and prioritisation of low-value care as part of a multicomponent process in hospital settings. DATA EXTRACTION AND SYNTHESIS: Screening was conducted in duplicate. Data were extracted by one of six authors and checked by another author. A framework synthesis was conducted using seven areas of focus for the review and an overuse framework. RESULTS: Twenty-seven records were included (21 original studies, 4 abstracts and 2 reviews), originating from high-income countries. Benefit or value (11 records), risk or harm (10 records) were common concepts referred to in records that explicitly defined low-value care (25 records). Evidence of contextualisation including barriers and enablers of low-value care identification processes were identified (25 records). Common components of these processes included initial consensus, consultation, ranking exercise or list development (16 records), and reviews of evidence (16 records). Two records involved engagement of patients and three evaluated the outcomes of multicomponent processes. Five records referenced a theory, model or framework. CONCLUSIONS: Gaps identified included applying systematic efforts to contextualise the identification of low-value care, involving people with lived experience of hospital care and initiatives in resource poor contexts. Insights were obtained regarding the theories, models and frameworks used to guide initiatives and ways in which the concept 'low-value care' had been used and reported. A priority for further research is evaluating the effect of initiatives that identify low-value care using contextualisation as part of multicomponent processes.

Consumer Preferences for a Healthcare Appointment Reminder in Australia: A Discrete Choice Experiment.

BACKGROUND: It is essential to consider the evidence of consumer preferences and their specific needs when determining which strategies to use to improve patient attendance at scheduled healthcare appointments. OBJECTIVES: This study aimed to identify key attributes and elicit healthcare consumer preferences for a healthcare appointment reminder system. METHODS: A discrete choice experiment was conducted in a general Australian population sample. The respondents were asked to choose between three options: their preferred reminder (A or B) or a 'neither' option. Attributes were developed through a literature review and an expert panel discussion. Reminder options were defined by four attributes: modality, timing, content and interactivity. Multinomial logit and mixed multinomial logit models were estimated to approximate individual preferences for these attributes. A scenario analysis was performed to estimate the likelihood of choosing different reminder systems. RESULTS: Respondents (n = 361) indicated a significant preference for an appointment reminder to be delivered via a text message (ß = 2.42, p < 0.001) less than 3 days before the appointment (ß = 0.99, p < 0.001), with basic details including the appointment cost (ß = 0.13, p < 0.10), and where there is the ability to cancel or modify the appointment (ß = 1.36, p < 0.001). A scenario analysis showed that the likelihood of choosing an appointment reminder system with these characteristics would be 97%. CONCLUSIONS: Our findings provide evidence on how healthcare consumers trade-off between different characteristics of reminder systems, which may be valuable to inform current or future systems. Future studies may focus on exploring the effectiveness of using patient-preferred reminders alongside other mitigation strategies used by providers.

Estimating the cost of sports injuries: A scoping review.

OBJECTIVES: Provide an overview of the methods used to estimate the cost of sports-related injury published to date, and to highlight considerations and opportunities for future research. DESIGN: Scoping review. METHODS: Scopus, MEDLINE and CINHAL were searched from 1st January 2000 to 1st January 2023. Studies were screened by two independent reviewers and were eligible if they reported on a cost analysis or cost estimation of sports related injury. RESULTS: Thirty-one studies fulfilled the inclusion criteria. Twenty-seven studies (87 %) were published since 2014. The type of costs included direct healthcare costs (12 studies), indirect costs (10 studies) and a combination of both (9 studies). Twenty-one studies (68 %) used a bottom-up costing approach to measure costs of sports injury and estimated direct costs from the service rates or fee schedules of health systems, hospital, insurance companies or national insurance boards. A top-down approach was used in seven studies (23 %) to estimate the indirect salary cost of time-loss injuries using data from publicly available resources. Ten studies were from the cost perspective of a sporting organisation (32 %). There was a lack of explicit reporting of the costing method used and the perspective of those bearing the costs. CONCLUSIONS: Estimating the cost of sports injuries is an emerging area of research, with publications increasing in recent years. However, there remains a lack of methodological guidance to inform or appraise these studies. The expansion of established cost of illness checklists with sport injury explanations to guide future cost of sports injury studies is recommended.

Adrenal-Permissive Germline HSD3B1 Allele and Prostate Cancer Outcomes.

Importance: The adrenal androgen-metabolizing 3ß-hydroxysteroid dehydrogenase-1 enzyme, encoded by the HSD3B1 gene, catalyzes the rate-limiting step necessary for synthesizing nontesticular testosterone and dihydrotestosterone production. The common adrenal-permissive HSD3B1(1245C) allele is responsible for encoding the 3ß-HSD1 protein with decreased susceptibility to degradation resulting in higher extragonadal androgen synthesis. Retrospective studies have suggested an association of the HSD3B1 adrenal-permissive homozygous genotype with androgen deprivation therapy resistance in prostate cancer. Objective: To evaluate differences in mortality outcomes by HSD3B1 genetic status among men with prostate cancer. Design, Setting, and Participants: This cohort study of patients with prostate cancer who were enrolled in the Million Veteran Program within the Veterans Health Administration (VHA) system between 2011 and 2023 collected genotyping and phenotyping information. Exposure: HSD3B1 genotype status was categorized as AA (homozygous adrenal-restrictive), AC (heterozygous adrenal-restrictive), or CC (homozygous adrenal-permissive). Main Outcomes and Measures: The primary outcome of this study was prostate cancer-specific mortality (PCSM), defined as the time from diagnosis to death from prostate cancer, censored at the date of last VHA follow-up. Secondary outcomes included incidence of metastases and PCSM in predefined subgroups. Results: Of the 5287 participants (median [IQR] age, 69 [64-74] years), 402 (7.6%) had the CC genotype, 1970 (37.3%) had the AC genotype, and 2915 (55.1%) had the AA genotype. Overall, the primary cause of death for 91 patients (1.7%) was prostate cancer. Cumulative incidence of PCSM at 5 years after prostate cancer diagnosis was higher among men with the CC genotype (4.0%; 95% CI, 1.7%-6.2%) compared with the AC genotype (2.1%; 95% CI, 1.3%-2.8%) and AA genotype (1.9%; 95% CI, 1.3%-2.4%) (P = .02). In the 619 patients who developed metastatic disease at any time, the cumulative incidence of PCSM at 5 years was higher among patients with the CC genotype (36.0%; 95% CI, 16.7%-50.8%) compared with the AC genotype (17.9%; 95% CI, 10.5%-24.7%) and AA genotype (18.5%; 95% CI, 12.0%-24.6%) (P = .01). Conclusions and Relevance: In this cohort study of US veterans undergoing treatment for prostate cancer at the VHA, the HSD3B1 CC genotype was associated with inferior outcomes. The HSD3B1 biomarker may help identify patients who may benefit from therapeutic targeting of 3ß-hydroxysteroid dehydrogenase-1 and the androgen-signaling axis.

Germline DNA damage response gene mutations as predictive biomarkers of immune checkpoint inhibitor efficacy.

Background: Impaired DNA damage response (DDR) can affect immune checkpoint inhibitors (ICI) efficacy and lead to heightened immune activation. We assessed the impact of pathogenic or likely pathogenic (P/LP) germline DDR mutations on ICI response and toxicity. Materials and methods: A retrospective analysis of 131 cancer patients with germline DNA testing and ICI treatment was performed. Results: Ninety-two patients were DDR-negative (DDR-), and 39 had ≥1 DDR mutation (DDR+). DDR+ patients showed higher objective response rates (ORRs) compared to DDR- in univariate and multivariable analyses, adjusting for age and metastatic disease (62% vs. 23%, unadjusted OR = 5.41; 95% CI, 2.41-12.14; adjusted OR 5.94; 95% CI, 2.35-15.06). Similar results were seen in mismatch repair (MMR), DDR pathways with intact MMR (DDR+MMRi), and homologous recombination (HR) subgroups versus DDR- (adjusted OR MMR = 24.52; 95% CI 2.72-221.38, DDR+MMRi = 4.26; 95% CI, 1.57-11.59, HR = 4.74; 95% CI, 1.49-15.11). DDR+ patients also had higher ORRs with concurrent chemotherapy (82% vs. 39% DDR-, p=0.03) or concurrent tyrosine kinase inhibitors (50% vs. 5% DDR-, p=0.03). No significant differences in immune-related adverse events were observed between DDR+ and DDR- cohorts. Conclusion: P/LP germline DDR mutations may enhance ICI response without significant additional toxicity.

Process evaluation of a tailored nudge intervention to promote appropriate care and treatment of older patients at the end-of-life.

BACKGROUND: Non-beneficial treatment affects a considerable proportion of older people in hospital, and some will choose to decline invasive treatments when they are approaching the end of their life. The Intervention for Appropriate Care and Treatment (InterACT) intervention was a 12-month stepped wedge randomised controlled trial with an embedded process evaluation in three hospitals in Brisbane, Australia. The aim was to increase appropriate care and treatment decisions for older people at the end-of-life, through implementing a nudge intervention in the form of a prospective feedback loop. However, the trial results indicated that the expected practice change did not occur. The process evaluation aimed to assess implementation using the Consolidated Framework for Implementation Research, identify barriers and enablers to implementation and provide insights into the lack of effect of the InterACT intervention. METHODS: Qualitative data collection involved 38 semi-structured interviews with participating clinicians, members of the executive advisory groups overseeing the intervention at a site level, clinical auditors, and project leads. Online interviews were conducted at two times: implementation onset and completion. Data were coded to the Consolidated Framework for Implementation Research and deductively analysed. RESULTS: Overall, clinicians felt the premise and clinical reasoning behind InterACT were strong and could improve patient management. However, several prominent barriers affected implementation. These related to the potency of the nudge intervention and its integration into routine clinical practice, clinician beliefs and perceived self-efficacy, and wider contextual factors at the health system level. CONCLUSIONS: An intervention designed to change clinical practice for patients at or near to end-of-life did not have the intended effect. Future interventions targeting this area of care should consider using multi-component strategies that address the identified barriers to implementation and clinician change of practice. TRIAL REGISTRATION: Australia New Zealand Clinical Trial Registry (ANZCTR), ACTRN12619000675123p (approved 06/05/2019).

Integrated germline and somatic features reveal divergent immune pathways driving ICB response.

Immune Checkpoint Blockade (ICB) has revolutionized cancer treatment, however mechanisms determining patient response remain poorly understood. Here we used machine learning to predict ICB response from germline and somatic biomarkers and interpreted the learned model to uncover putative mechanisms driving superior outcomes. Patients with higher T follicular helper infiltrates were robust to defects in the class-I Major Histocompatibility Complex (MHC-I). Further investigation uncovered different ICB responses in MHC-I versus MHC-II neoantigen reliant tumors across patients. Despite similar response rates, MHC-II reliant responses were associated with significantly longer durable clinical benefit (Discovery: Median OS=63.6 vs. 34.5 months P=0.0074; Validation: Median OS=37.5 vs. 33.1 months, P=0.040). Characteristics of the tumor immune microenvironment reflected MHC neoantigen reliance, and analysis of immune checkpoints revealed LAG3 as a potential target in MHC-II but not MHC-I reliant responses. This study highlights the value of interpretable machine learning models in elucidating the biological basis of therapy responses.

A single-cell atlas of the aging mouse ovary.

Ovarian aging leads to diminished fertility, dysregulated endocrine signaling and increased chronic disease burden. These effects begin to emerge long before follicular exhaustion. Female humans experience a sharp decline in fertility around 35 years of age, which corresponds to declines in oocyte quality. Despite a growing body of work, the field lacks a comprehensive cellular map of the transcriptomic changes in the aging mouse ovary to identify early drivers of ovarian decline. To fill this gap we performed single-cell RNA sequencing on ovarian tissue from young (3-month-old) and reproductively aged (9-month-old) mice. Our analysis revealed a doubling of immune cells in the aged ovary, with lymphocyte proportions increasing the most, which was confirmed by flow cytometry. We also found an age-related downregulation of collagenase pathways in stromal fibroblasts, which corresponds to rises in ovarian fibrosis. Follicular cells displayed stress-response, immunogenic and fibrotic signaling pathway inductions with aging. This report provides critical insights into mechanisms responsible for ovarian aging phenotypes. The data can be explored interactively via a Shiny-based web application.

Stakeholders' preferences for the design and delivery of virtual care services: A systematic review of discrete choice experiments.

This systematic review aimed to synthesise evidence from discrete choice experiments (DCEs) eliciting preferences for virtual models of care, as well as to assess the quality of those DCEs and compare the relative preferences for different stakeholder groups. Articles were included if published between January 2010 and December 2022. Data were synthesised narratively, and attributes were assessed for frequency, significance, and relative importance using a semi-quantitative approach. Overall, 21 studies were included encompassing a wide range of virtual care modalities, with the most common setting being virtual consultations for outpatient management of chronic conditions. A total of 135 attributes were identified and thematically classified into six categories: service delivery, service quality, technical aspects, monetary aspects, health provider characteristics and health consumer characteristics. Attributes related to service delivery were most frequently reported but less highly ranked. Service costs were consistently significant across all studies where they appeared, indicating their importance to the respondents. All studies examining health providers' preferences reported either system performance or professional endorsement attributes to be the most important. Substantial heterogeneity in attribute selection and preference outcomes were observed across studies reporting on health consumers' preferences, suggesting that the consideration of local context is important in the design and delivery of person-centred virtual care services. In general, the experimental design and analysis methods of included studies were clearly reported and justified. An improvement was observed in the quality of DCE design and analysis in recent years, particularly in the attribute development process. Given the continued growth in the use of DCEs within healthcare settings, further research is needed to develop a standardised approach for quantitatively synthesising DCE findings. There is also a need for further research on preferences for virtual care in post-pandemic contexts, where emerging evidence suggests that preferences may differ to those observed in pre-pandemic times.

Session Introduction: Precision Medicine: Innovative methods for advanced understanding of molecular underpinnings of disease.

Precision medicine, also often referred to as personalized medicine, targets the development of treatments and preventative measures specific to the individual's genomic signatures, lifestyle, and environmental conditions. The series of Precision Medicine sessions in PSB has continuously highlighted the advances in this field. Our 2024 collection of manuscripts showcases algorithmic advances that integrate data from distinct modalities and introduce innovative approaches to extract new, medically relevant information from existing data. These evolving technology and analytical methods promise to bring closer the goals of precision medicine to improve health and increase lifespan.

From pilot to a multi-site trial: refining the Early Detection of Deterioration in Elderly Residents (EDDIE +) intervention.

BACKGROUND: Early Detection of Deterioration in Elderly Residents (EDDIE +) is a multi-modal intervention focused on empowering nursing and personal care workers to identify and proactively manage deterioration of residents living in residential aged care (RAC) homes. Building on successful pilot trials conducted between 2014 and 2017, the intervention was refined for implementation in a stepped-wedge cluster randomised trial in 12 RAC homes from March 2021 to May 2022. We report the process used to transition from a small-scale pilot intervention to a multi-site intervention, detailing the intervention to enable future replication. METHODS: The EDDIE + intervention used the integrated Promoting Action on Research Implementation in Health Services (i-PARIHS) framework to guide the intervention development and refinement process. We conducted an environmental scan; multi-level context assessments; convened an intervention working group (IWG) to develop the program logic, conducted a sustainability assessment and deconstructed the intervention components into fixed and adaptable elements; and subsequently refined the intervention for trial. RESULTS: The original EDDIE pilot intervention included four components: nurse and personal care worker education; decision support tools; diagnostic equipment; and facilitation and clinical support. Deconstructing the intervention into core components and what could be flexibly tailored to context was essential for refining the intervention and informing future implementation across multiple sites. Intervention elements considered unsustainable were updated and refined to enable their scalability. Refinements included: an enhanced educational component with a greater focus on personal care workers and interactive learning; decision support tools that were based on updated evidence; equipment that aligned with recipient needs and available organisational support; and updated facilitation model with local and external facilitation. CONCLUSION: By using the i-PARIHS framework in the scale-up process, the EDDIE + intervention was tailored to fit the needs of intended recipients and contexts, enabling flexibility for local adaptation. The process of transitioning from a pilot to larger scale implementation in practice is vastly underreported yet vital for better development and implementation of multi-component interventions across multiple sites. We provide an example using an implementation framework and show it can be advantageous to researchers and health practitioners from pilot stage to refinement, through to larger scale implementation. TRIAL REGISTRATION: The trial was prospectively registered with the Australia New Zealand Clinical Trial Registry (ACTRN12620000507987, registered 23/04/2020).

Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.

Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.

A meta-analysis of epitopes in prostate-specific antigens identifies opportunities and knowledge gaps.

BACKGROUND: The Cancer Epitope Database and Analysis Resource (CEDAR) is a newly developed repository of cancer epitope data from peer-reviewed publications, which includes epitope-specific T cell, antibody, and MHC ligand assays. Here we focus on prostate cancer as our first cancer category to demonstrate the capabilities of CEDAR, and to shed light on the advances of epitope-related prostate cancer research. RESULTS: The meta-analysis focused on a subset of data describing epitopes from 8 prostate-specific (PS) antigens. A total of 460 epitopes were associated with these proteins, 187 T cell, 109B cell, and 271 MHC ligand epitopes. The number of epitopes was not correlated with the length of the protein; however, we found a significant positive correlation between the number of references per specific PS antigen and the number of reported epitopes. Forty-four different class I and 27 class II restrictions were found, with the most epitopes described for HLA-A*02:01 and HLA-DRB1*01:01. Cytokine assays were mostly limited to IFNg assays and a very limited number of tetramer assays were performed. Monoclonal and polyclonal B cell responses were balanced, with the highest number of epitopes studied in ELISA/Western blot assays. Additionally, epitopes were generically described as associated with prostate cancer, with little granularity specifying diseases state. We found that in vivo and tumor recognition assays were sparse, and the number of epitopes with annotated B/T cell receptor information were limited. Potential immunodominant regions were identified by the use of the ImmunomeBrowser tool. CONCLUSION: CEDAR provides a comprehensive repository of epitopes related to prostate-specific antigens. This inventory of epitope data with its wealth of searchable T cell, B cell and MHC ligand information provides a useful tool for the scientific community. At the same time, we identify significant knowledge gaps that could be addressed by experimental analysis.

Incongruence between transcriptional and vascular pathophysiological cell states.

The Notch pathway is a major regulator of endothelial transcriptional specification. Targeting the Notch receptors or Delta-like ligand 4 (Dll4) dysregulates angiogenesis. Here, by analyzing single and compound genetic mutants for all Notch signaling members, we find significant differences in the way ligands and receptors regulate liver vascular homeostasis. Loss of Notch receptors caused endothelial hypermitogenic cell-cycle arrest and senescence. Conversely, Dll4 loss triggered a strong Myc-driven transcriptional switch inducing endothelial proliferation and the tip-cell state. Myc loss suppressed the induction of angiogenesis in the absence of Dll4, without preventing the vascular enlargement and organ pathology. Similarly, inhibition of other pro-angiogenic pathways, including MAPK/ERK and mTOR, had no effect on the vascular expansion induced by Dll4 loss; however, anti-VEGFA treatment prevented it without fully suppressing the transcriptional and metabolic programs. This study shows incongruence between single-cell transcriptional states, vascular phenotypes and related pathophysiology. Our findings also suggest that the vascular structure abnormalization, rather than neoplasms, causes the reported anti-Dll4 antibody toxicity.

Autoimmune HLA Alleles and Neoepitope Presentation Predict Post-Allogenic Transplant Relapse.

Introduction: Allogeneic hematopoietic stem cell transplantation (allo-HSCT) can cure patients with high-risk myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). However, many patients relapse or develop debilitating graft-versus-host disease. Transplant restores T-cell reactivity against tumor cells, implicating patient human leukocyte antigen (HLA)-dependent antigen presentation via the major histocompatibility complex as a determinant of response. We sought to identify characteristics of the HLA genotype that influence response in allo-HSCT patients. Methods: We collected HLA genotype and panel-based somatic mutation profiles for 55 patients with AML and MDS and available data treated at the University of California San Diego Moores Cancer Center between May 2012 and January 2019. We evaluated characteristics of the HLA genotype relative to relapse-free time and overall survival (OS) post-allo-HSCT using univariable and multivariable regression. Results: In multivariable regression, the presence of an autoimmune allele was significantly associated with relapse-free time (hazard ratio [HR], 0.25; p = 0.01) and OS (HR, 0.16; p < 0.005). The better potential of the donor HLA type to present peptides harboring driver mutations trended toward better relapse-free survival (HR, 0.45; p = 0.07) and significantly correlated with longer OS (HR, 0.33; p = 0.01) though only a minority of cases had an HLA mismatch. Conclusion: In this single institution retrospective study of patients receiving allo-HSCT for relapsed AML/MDS, characteristics of an individual's HLA genotype (presence of an autoimmune allele and potential of the donor HLA to better present peptides representing driver mutations) were significantly associated with better outcomes. These findings suggest that HLA type may guide the optimal application of allo-HSCT and merit evaluation in larger cohorts. ClinicalTrials.gov Identifier: NCT02478931.

Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS.

Understanding the consequences of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to investigate the effects of individual mutations on cellular programs. Here we deploy SEUSS, a Perturb-seq like approach, to generate and assay mutations at physical interfaces of the RUNX1 Runt domain. We measured the impact of 115 mutations on RNA profiles in single myelogenous leukemia cells and used the profiles to categorize mutations into three functionally distinct groups: wild-type (WT)-like, loss-of-function (LOF)-like and hypomorphic. Notably, the largest concentration of functional mutations (non-WT-like) clustered at the DNA binding site and contained many of the more frequently observed mutations in human cancers. Hypomorphic variants shared characteristics with loss of function variants but had gene expression profiles indicative of response to neural growth factor and cytokine recruitment of neutrophils. Additionally, DNA accessibility changes upon perturbations were enriched for RUNX1 binding motifs, particularly near differentially expressed genes. Overall, our work demonstrates the potential of targeting protein interaction interfaces to better define the landscape of prospective phenotypes reachable by amino acid substitutions.

Preferences for Palliative and End-of-Life Care: A Systematic Review of Discrete Choice Experiments.

OBJECTIVES: Understanding what matters most to patients and their caregivers is fundamental to delivering high-quality care. This systematic review aimed to characterize and appraise the evidence from discrete choice experiments eliciting preferences for palliative care. METHODS: A systematic literature search was undertaken for publications up until August 2022. Data were synthesized narratively. Thematic analysis was applied to categorize attributes into groups. Attribute development, frequency, and relative importance were analyzed. Subgroup analyses were conducted to compare outcomes between patient and proxy respondents. RESULTS: Seventeen studies spanning 11 countries were included; 59% of studies solely considered preferences for patients with cancer. A range of respondent groups were represented including patients (76%) and proxies (caregivers [35%], health providers [12%], and the public [18%]). A total of 117 individual attributes were extracted and thematically grouped into 8 broad categories and 21 subcategories. Clinical outcomes including quality of life, length of life, and pain control were the most frequently reported attributes, whereas attributes relating to psychosocial components were largely absent. Both patients and proxy respondents prioritized pain control over additional survival time. Nevertheless, there were differences between respondent cohorts in the emphasis on other attributes such as access to care, timely information, and low risk of adverse effects (prioritized by patients), as opposed to cost, quality, and delivery of care (prioritized by proxies). CONCLUSIONS: Our review underscores the vital role of pain control in palliative care; in addition, it shed light on the complexity and relative strength of preferences for various aspects of care from multiple perspectives, which is useful in developing personalized, patient-centered models of care for individuals nearing the end of life.