Development and evaluation of three-dimensional transfers to depict skin conditions in simulation-based education.

Modern medical moulages are becoming increasingly important in simulation-based health professions education. Their lifelikeness is important so that simulation engagement is not disrupted while their standardization is crucial in high-stakes exams. This report describes in detail how three-dimensional transfers are developed and produced so that educators will be able to develop their own. In addition, evaluation findings and lessons learnt from deploying transfers in summative assessments are shared. Step-by-step instructions are given for the creation and application of transfers, including materials and photographic visualizations. We also examined feedback on 10 exam stations (out of a total of 81) with self-developed three-dimensional transfers and complement this with additional lessons learnt. By the time of submission, the authors successfully developed and deployed over 40 different three-dimensional transfers representing different clinical findings in high-stakes exams using the techniques explained in this article or variations thereof. Feedback from students and examiners after completing the OSCE is predominantly positive, with lifelikeness being the quality most often commented upon. Caveats derived from feedback and own experiences are included. The step-by-step approach reported can be adapted and replicated by healthcare educators to build their own three-dimensional transfers. This should widen the scope and the lifelikeness of their simulations. At the same time we propose that this level of lifelikeness should be expected by learners as not to disrupt simulation engagement. Our evaluation of their use in high-stakes assessments suggests they are both useful and accepted.

Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism.

Therapeutic prime editing of hematopoietic stem and progenitor cells (HSPCs) holds great potential to remedy blood disorders. Quiescent cells have low nucleotide levels and resist retroviral infection, and it is possible that nucleotide metabolism could limit reverse transcription-mediated prime editing in HSPCs. We demonstrate that deoxynucleoside supplementation and Vpx-mediated degradation of SAMHD1 improve prime editing efficiency in HSPCs, especially when coupled with editing approaches that evade mismatch repair.

Improving prime editing with an endogenous small RNA-binding protein.

Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3' ends of CRISPR-Cas guide RNAs1. To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3' ends of RNA polymerase III transcripts2. We found that La functionally interacts with the 3' ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.

Direct and selective pharmacological disruption of the YAP-TEAD interface by IAG933 inhibits Hippo-dependent and RAS-MAPK-altered cancers.

The YAP-TEAD protein-protein interaction mediates YAP oncogenic functions downstream of the Hippo pathway. To date, available YAP-TEAD pharmacologic agents bind into the lipid pocket of TEAD, targeting the interaction indirectly via allosteric changes. However, the consequences of a direct pharmacological disruption of the interface between YAP and TEADs remain largely unexplored. Here, we present IAG933 and its analogs as potent first-in-class and selective disruptors of the YAP-TEAD protein-protein interaction with suitable properties to enter clinical trials. Pharmacologic abrogation of the interaction with all four TEAD paralogs resulted in YAP eviction from chromatin and reduced Hippo-mediated transcription and induction of cell death. In vivo, deep tumor regression was observed in Hippo-driven mesothelioma xenografts at tolerated doses in animal models as well as in Hippo-altered cancer models outside mesothelioma. Importantly this also extended to larger tumor indications, such as lung, pancreatic and colorectal cancer, in combination with RTK, KRAS-mutant selective and MAPK inhibitors, leading to more efficacious and durable responses. Clinical evaluation of IAG933 is underway.

Development of an algorithm for correct placement of the basal electrode contact in the context of anatomy based cochlear implantation: a proof of concept.

BACKGROUND: Correct individual tonotopic frequency stimulation of the cochlea plays an important role in the further development of anatomy based cochlear implantation. In this context frequency specific fitting of the basal electrode contact with a normal insertion depth can be difficult since it is often placed in a frequency range higher than 10 kHz and current audio processors only stimulate for frequencies up to 8.5 kHz due to microphone characteristics. This results in a mismatch of the high frequencies. Therefore, this study represents a proof of concept for a tonotopic correct insertion and aims to develop an algorithm for a placement of the basal electrode below 8.5 kHz in an experimental setting. METHODS: Pre- and postoperative flat-panel volume CT scans with secondary reconstructions were performed in 10 human temporal bone specimens. The desired frequency location for the most basal electrode contact was set at 8.25 kHz. The distance from the round window to the position where the basal electrode contact was intended to be located was calculated preoperatively using 3D-curved multiplanar reconstruction and a newly developed mathematical approach. A specially designed cochlear implant electrode array with customized markers imprinted on the silicone of the electrode array was inserted in all specimens based on the individually calculated insertion depths. All postoperative measurements were additionally validated using an otological planning software. RESULTS: Positioning of the basal electrode contact was reached with only a small mean deviation of 37 ± 399 Hz and 0.06 ± 0.37 mm from the planned frequency of 8.25 kHz. The mean rotation angle up to the basal electrode contact was 51 ± 5 °. In addition, the inserted electrode array adequately covered the apical regions of the cochleae. CONCLUSION: Using this algorithm, it was possible to position the basal electrode array contact in an area of the cochlea that could be correctly stimulated by the existing speech processors in the context of tonotopic correct fitting.

Ex vivo culture resting time impacts transplantation outcomes of genome-edited human hematopoietic stem and progenitor cells in xenograft mouse models.

Ex vivo resting culture is a standard procedure following genome editing in hematopoietic stem and progenitor cells (HSPCs). However, prolonged culture may critically affect cell viability and stem cell function. We investigated whether varying durations of culture resting times impact the engraftment efficiency of human CD34+ HSPCs edited at the BCL11A enhancer, a key regulator in the expression of fetal hemoglobin. We employed electroporation to introduce CRISPR-Cas9 components for BCL11A enhancer editing and compared outcomes with nonelectroporated (NEP) and electroporated-only (EP) control groups. Post-electroporation, we monitored cell viability, death rates, and the frequency of enriched hematopoietic stem cell (HSC) fractions (CD34+CD90+CD45RA- cells) over a 48-hour period. Our findings reveal that while the NEP group showed an increase in cell numbers 24 hours post-electroporation, both EP and BCL11A-edited groups experienced significant cell loss. Although CD34+ cell frequency remained high in all groups for up to 48 hours post-electroporation, the frequency of the HSC-enriched fraction was significantly lower in the EP and edited groups compared to the NEP group. In NBSGW xenograft mouse models, both conditioned with busulfan and nonconditioned, we found that immediate transplantation post-electroporation led to enhanced engraftment without compromising editing efficiency. Human glycophorin A+ (GPA+) red blood cells (RBCs) sorted from bone marrow of all BCL11A edited mice exhibited similar levels of γ-globin expression, regardless of infusion time. Our findings underscore the critical importance of optimizing the culture duration between genome editing and transplantation. Minimizing this interval may significantly enhance engraftment success and minimize cell loss without compromising editing efficiency. These insights offer a pathway to improve the success rates of genome editing in HSPCs, particularly for conditions like sickle cell disease.

Direct delivery of stabilized Cas-embedded base editors achieves efficient and accurate editing of clinically relevant targets.

Over the last 5 years, cytosine base editors (CBEs) have emerged as a promising therapeutic tool for specific editing of single nucleotide variants and disrupting specific genes associated with disease. Despite this promise, the currently available CBE's have the significant liabilities of off-target and bystander editing activities, in part due to the mechanism by which they are delivered, causing limitations in their potential applications. In this study we engineeredhighly stabilized Cas-embedded CBEs (sCE_CBEs) that integrate several recent advances, andthat are highly expressible and soluble for direct delivery into cells as ribonucleoprotein (RNP) complexes. Our resulting sCE_CBE RNP complexes efficiently and specifically target TC dinucleotides with minimal off-target or bystander mutations. Additional uracil glycosylase inhibitor (UGI) protein in trans further increased C-to-T editing efficiency and target purity in a dose-dependent manner, minimizing indel formation to untreated levels. A single electroporation was sufficient to effectively edit the therapeutically relevant locus for sickle cell disease in hematopoietic stem and progenitor cells (HSPC) in a dose dependent manner without cellular toxicity. Significantly, these sCE_CBE RNPs permitted for the transplantation of edited HSPCs confirming highly efficient editing in engrafting hematopoietic stem cells in mice. The success of the designed sCBE editors, with improved solubility and enhanced on-target editing, demonstrates promising agents for cytosine base editing at other disease-related sites in HSPCs and other cell types.

Digital analysis of the prostate tumor microenvironment with high-order chromogenic multiplexing.

As our understanding of the tumor microenvironment grows, the pathology field is increasingly utilizing multianalyte diagnostic assays to understand important characteristics of tumor growth. In clinical settings, brightfield chromogenic assays represent the gold-standard and have developed significant trust as the first-line diagnostic method. However, conventional brightfield tests have been limited to low-order assays that are visually interrogated. We have developed a hybrid method of brightfield chromogenic multiplexing that overcomes these limitations and enables high-order multiplex assays. However, how compatible high-order brightfield multiplexed images are with advanced analytical algorithms has not been extensively evaluated. In the present study, we address this gap by developing a novel 6-marker prostate cancer assay that targets diverse aspects of the tumor microenvironment such as prostate-specific biomarkers (PSMA and p504s), immune biomarkers (CD8 and PD-L1), a prognostic biomarker (Ki-67), as well as an adjunctive diagnostic biomarker (basal cell cocktail) and apply the assay to 143 differentially graded adenocarcinoma prostate tissues. The tissues were then imaged on our spectroscopic multiplexing imaging platform and mined for proteomic and spatial features that were correlated with cancer presence and disease grade. Extracted features were used to train a UMAP model that differentiated healthy from cancerous tissue with an accuracy of 89% and identified clusters of cells based on cancer grade. For spatial analysis, cell-to-cell distances were calculated for all biomarkers and differences between healthy and adenocarcinoma tissues were studied. We report that p504s positive cells were at least 2× closer to cells expressing PD-L1, CD8, Ki-67, and basal cell in adenocarcinoma tissues relative to the healthy control tissues. These findings offer a powerful insight to understand the fingerprint of the prostate tumor microenvironment and indicate that high-order chromogenic multiplexing is compatible with digital analysis. Thus, the presented chromogenic multiplexing system combines the clinical applicability of brightfield assays with the emerging diagnostic power of high-order multiplexing in a digital pathology friendly format that is well-suited for translational studies to better understand mechanisms of tumor development and growth.

Parenting, Peers, and Alcohol Use Initiation Among Black, White, and Black-White Adolescents: Evidence Using Discrete-Time Survival Analysis.

Alcohol use among Biracial adolescents remains understudied. This study examined how parenting and peer factors relate to age of alcohol use onset among Black, White, and Biracial Black-White adolescents and emerging adults. We used Add Health data to produce a final analytic sample of 13,528 adolescents who self-identified as White, Black, or Biracial Black-White. Discrete-time survival analysis implemented within logistic regression indicated Black adolescents showed the lowest probability of alcohol use onset by age 18, followed by Biracial adolescents, and White adolescents. The probability of alcohol use onset increased for Monoracial Black and White adolescents at ages 16, 18, and 21. Descriptively our model suggest that Biracial adolescents exhibit a sharp decline in their probability of alcohol use onset at age 16 and a sharp increase at age 21. However, this trend did not differ significantly from the other racial groups. Consistent with social control and learning theories, low parental acceptance, high parental control, and peer substance use were associated with alcohol use onset. Alcohol use onset trajectories differed for Monoracial and Biracial adolescents with Biracial individuals reporting greater alcohol onset in adulthood. Prevention efforts should continue to target parental acceptance, parental control, and peer substance use.

Computed tomographic 3D analysis of the cochlear aqueduct-potential and limitations of clinical imaging.

Background: The cochlear aqueduct (CA), which connects the scala tympani and the subarachnoid space, and its accompanying structures appear to have a significant relevance during cochlear implantation and an accurate visualization in clinical imaging is of great interest. Aims and Objective: This study aims to determine which potential and limitations clinically available imaging modalities have in the visualization of the CA. Methods: Micro-CT, flat-panel volume computed tomography with and without secondary reconstruction (fpVCT, fpVCTseco) and multislice computed tomography (MSCT) of 10 temporal bone specimen were used for 3D analysis of the CA. Results: FpVCTseco proved superior in visualizing the associated structures and lateral portions of the CA, which merge into the basal turn of the cochlea. All clinical imaging modalities proved equal in analyzing the length, total volume of the CA and its area of the medial orifice. Conclusion: The choice of the most accurate clinical imaging modality to evaluate the CA and its associated structures depends on the clinical or scientific question. Furthermore, this study should provide a basis for further investigations analyzing the CA.

Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics.

Gene regulatory networks (GRNs) are key determinants of cell function and identity and are dynamically rewired during development and disease. Despite decades of advancement, challenges remain in GRN inference, including dynamic rewiring, causal inference, feedback loop modeling and context specificity. To address these challenges, we develop Dictys, a dynamic GRN inference and analysis method that leverages multiomic single-cell assays of chromatin accessibility and gene expression, context-specific transcription factor footprinting, stochastic process network and efficient probabilistic modeling of single-cell RNA-sequencing read counts. Dictys improves GRN reconstruction accuracy and reproducibility and enables the inference and comparative analysis of context-specific and dynamic GRNs across developmental contexts. Dictys' network analyses recover unique insights in human blood and mouse skin development with cell-type-specific and dynamic GRNs. Its dynamic network visualizations enable time-resolved discovery and investigation of developmental driver transcription factors and their regulated targets. Dictys is available as a free, open-source and user-friendly Python package.

Epitope editing enables targeted immunotherapy of acute myeloid leukaemia.

Despite the considerable efficacy observed when targeting a dispensable lineage antigen, such as CD19 in B cell acute lymphoblastic leukaemia1,2, the broader applicability of adoptive immunotherapies is hampered by the absence of tumour-restricted antigens3-5. Acute myeloid leukaemia immunotherapies target genes expressed by haematopoietic stem/progenitor cells (HSPCs) or differentiated myeloid cells, resulting in intolerable on-target/off-tumour toxicity. Here we show that epitope engineering of donor HSPCs used for bone marrow transplantation endows haematopoietic lineages with selective resistance to chimeric antigen receptor (CAR) T cells or monoclonal antibodies, without affecting protein function or regulation. This strategy enables the targeting of genes that are essential for leukaemia survival regardless of shared expression on HSPCs, reducing the risk of tumour immune escape. By performing epitope mapping and library screenings, we identified amino acid changes that abrogate the binding of therapeutic monoclonal antibodies targeting FLT3, CD123 and KIT, and optimized a base-editing approach to introduce them into CD34+ HSPCs, which retain long-term engraftment and multilineage differentiation ability. After CAR T cell treatment, we confirmed resistance of epitope-edited haematopoiesis and concomitant eradication of patient-derived acute myeloid leukaemia xenografts. Furthermore, we show that multiplex epitope engineering of HSPCs is feasible and enables more effective immunotherapies against multiple targets without incurring overlapping off-tumour toxicities. We envision that this approach will provide opportunities to treat relapsed/refractory acute myeloid leukaemia and enable safer non-genotoxic conditioning.

Enhancing measurement validity in diverse populations: Modern approaches to evaluating differential item functioning.

When developing and evaluating psychometric measures, a key concern is to ensure that they accurately capture individual differences on the intended construct across the entire population of interest. Inaccurate assessments of individual differences can occur when responses to some items reflect not only the intended construct but also construct-irrelevant characteristics, like a person's race or sex. Unaccounted for, this item bias can lead to apparent differences on the scores that do not reflect true differences, invalidating comparisons between people with different backgrounds. Accordingly, empirically identifying which items manifest bias through the evaluation of differential item functioning (DIF) has been a longstanding focus of much psychometric research. The majority of this work has focused on evaluating DIF across two (or a few) groups. Modern conceptualizations of identity, however, emphasize its multi-determined and intersectional nature, with some aspects better represented as dimensional than categorical. Fortunately, many model-based approaches to modelling DIF now exist that allow for simultaneous evaluation of multiple background variables, including both continuous and categorical variables, and potential interactions among background variables. This paper provides a comparative, integrative review of these new approaches to modelling DIF and clarifies both the opportunities and challenges associated with their application in psychometric research.

Phototoxicity─Medicinal Chemistry Strategies for Risk Mitigation in Drug Discovery.

Phototoxicity is a common safety concern encountered by project teams in pharmaceutical research and has the potential to stop progression of an otherwise promising candidate molecule. This perspective aims to provide an overview of the approaches toward mitigation of phototoxicity that medicinal chemists have taken during the lead optimization phase in the context of regulatory standards for photosafety evaluation. Various strategies are laid out based on available literature examples in order to highlight how structural modification can be utilized toward successful mitigation of a phototoxicity liability. A proposed flowchart is presented as a guidance tool to be used by the practicing medicinal chemist when facing a phototoxicity risk. The description of available tools to consider in the drug design process will include an overview of the evolution of in silico methods and their application as well as structure alerts for consideration as potential phototoxicophores.

Alkali metal cations modulate the geometry of different binding sites in HCN4 selectivity filter for permeation or block.

Hyperpolarization-activated cyclic-nucleotide gated (HCN) channels are important for timing biological processes like heartbeat and neuronal firing. Their weak cation selectivity is determined by a filter domain with only two binding sites for K+ and one for Na+. The latter acts as a weak blocker, which is released in combination with a dynamic widening of the filter by K+ ions, giving rise to a mixed K+/Na+ current. Here, we apply molecular dynamics simulations to systematically investigate the interactions of five alkali metal cations with the filter of the open HCN4 pore. Simulations recapitulate experimental data like a low Li+ permeability, considerable Rb+ conductance, a block by Cs+ as well as a punch through of Cs+ ions at high negative voltages. Differential binding of the cation species in specific filter sites is associated with structural adaptations of filter residues. This gives rise to ion coordination by a cation-characteristic number of oxygen atoms from the filter backbone and solvent. This ion/protein interplay prevents Li+, but not Na+, from entry into and further passage through the filter. The site equivalent to S3 in K+ channels emerges as a preferential binding and presumably blocking site for Cs+. Collectively, the data suggest that the weak cation selectivity of HCN channels and their block by Cs+ are determined by restrained cation-generated rearrangements of flexible filter residues.

Identification of Brain-Penetrant ATP-Competitive mTOR Inhibitors for CNS Syndromes.

The allosteric inhibitor of the mechanistic target of rapamycin (mTOR) everolimus reduces seizures in tuberous sclerosis complex (TSC) patients through partial inhibition of mTOR functions. Due to its limited brain permeability, we sought to develop a catalytic mTOR inhibitor optimized for central nervous system (CNS) indications. We recently reported an mTOR inhibitor (1) that is able to block mTOR functions in the mouse brain and extend the survival of mice with neuronal-specific ablation of the Tsc1 gene. However, 1 showed the risk of genotoxicity in vitro. Through structure-activity relationship (SAR) optimization, we identified compounds 9 and 11 without genotoxicity risk. In neuronal cell-based models of mTOR hyperactivity, both corrected aberrant mTOR activity and significantly improved the survival rate of mice in the Tsc1 gene knockout model. Unfortunately, 9 and 11 showed limited oral exposures in higher species and dose-limiting toxicities in cynomolgus macaque, respectively. However, they remain optimal tools to explore mTOR hyperactivity in CNS disease models.

RUNX1 mutations mitigate quiescence to promote transformation of hematopoietic progenitors in Fanconi anemia.

Many inherited bone marrow failure syndromes (IBMFSs) present a high risk of transformation to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). During transformation of IBMFSs, hematopoietic stem and progenitor cells (HSPCs) with poor fitness gain ectopic, dysregulated self-renewal secondary to somatic mutations via undefined mechanisms. Here, in the context of the prototypical IBMFS Fanconi anemia (FA), we performed multiplexed gene editing of mutational hotspots in MDS-associated genes in human induced pluripotent stem cells (iPSCs) followed by hematopoietic differentiation. We observed aberrant self-renewal and impaired differentiation of HSPCs with enrichment of RUNX1 insertions and deletions (indels), generating a model of IBMFS-associated MDS. We observed that compared to the failure state, FA MDS cells show mutant RUNX1-mediated blunting of the G1/S cell cycle checkpoint that is normally activated in FA in response to DNA damage. RUNX1 indels also lead to activation of innate immune signaling, which stabilizes the homologous recombination (HR) effector BRCA1, and this pathway can be targeted to abrogate viability and restore sensitivity to genotoxins in FA MDS. Together, these studies develop a paradigm for modeling clonal evolution in IBMFSs, provide basic understanding of the pathogenesis of MDS, and uncover a therapeutic target in FA-associated MDS.