MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons.

Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type (WT) and mutant MECP2 molecules. MECP2 occupies CpG-rich promoter-proximal regions in over four thousand genes in human neurons, including a plethora of autism risk genes, together with RNA polymerase II (RNA Pol II). MECP2 directly interacts with RNA Pol II, and genes occupied by both proteins showed reduced expression in neurons with MECP2 patient mutations. We conclude that MECP2 acts as a positive cofactor for RNA Pol II gene expression at many neuronal genes that harbor CpG islands in promoter-proximal regions and that RTT is due, in part, to the loss of gene activity of these genes in neurons.

What Complexity Science Predicts About the Potential of Artificial Intelligence/Machine Learning to Improve Primary Care.

Primary care physicians are likely both excited and apprehensive at the prospects for artificial intelligence (AI) and machine learning (ML). Complexity science may provide insight into which AI/ML applications will most likely affect primary care in the future. AI/ML has successfully diagnosed some diseases from digital images, helped with administrative tasks such as writing notes in the electronic record by converting voice to text, and organized information from multiple sources within a health care system. AI/ML has less successfully recommended treatments for patients with complicated single diseases such as cancer; or improved diagnosing, patient shared decision making, and treating patients with multiple comorbidities and social determinant challenges. AI/ML has magnified disparities in health equity, and almost nothing is known of the effect of AI/ML on primary care physician-patient relationships. An intervention in Victoria, Australia showed promise where an AI/ML tool was used only as an adjunct to complex medical decision making. Putting these findings in a complex adaptive system framework, AI/ML tools will likely work when its tasks are limited in scope, have clean data that are mostly linear and deterministic, and fit well into existing workflows. AI/ML has rarely improved comprehensive care, especially in primary care settings, where data have a significant number of errors and inconsistencies. Primary care should be intimately involved in AI/ML development, and its tools carefully tested before implementation; and unlike electronic health records, not just assumed that AI/ML tools will improve primary care work life, quality, safety, and person-centered clinical decision making.

A Retrospective Review and Comprehensive Tumour Profiling of Advanced Non-Melanomatous Cutaneous Spindle Cell Neoplasms Treated with Immune-Checkpoint Inhibitors.

Non-melanomatous cutaneous spindle cell neoplasms are a rare group of malignancies that present a diagnostic challenge, and for which there is a lack of consensus on how to best manage patients with advanced disease and only limited reports of immune-checkpoint inhibitor (ICI) responses. In this study, we performed a single-center retrospective review of treatment outcomes for all advanced non-melanomatous cutaneous spindle cell neoplasms treated with ICIs. Blinded histopathology reviews occurred to confirm each diagnosis. Comprehensive tumour profiling included whole exome sequencing for tumour mutational burden (TMB) and ultraviolet(UV) signatures, and immunohistochemistry for immune-cell infiltration (CD4/CD3/CD8/CD103/CD20) and immune-checkpoint expression (PD-L1/LAG3/TIGIT). Seven patients were identified. The objective response rate was 86% (6/7) with five complete responses (CR). Responses were durable with two patients in CR > 30 months after ICI commencement. All patients had high TMB and UV signatures. One patient had PD-L1 100% (combined positive score) with abundant immune-cell infiltration and LAG3 expression. In advanced non-melanomatous cutaneous spindle cell neoplasms, excellent responses to ICIs with durable disease control were observed. ICIs are worthy of further exploration in these patients. UV signatures and high TMB could be used to help select patients for treatment.

Protein codes promote selective subcellular compartmentalization.

Cells have evolved mechanisms to distribute ∼10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Here, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. A protein language model, ProtGPS, was developed that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in targeted subcellular compartments. ProtGPS also identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code, but also a previously unrecognized code governing their distribution in specific cellular compartments.

Patient Partnership Tools to Support Medication Safety in Community-Dwelling Older Adults: Protocol for a Nonrandomized Stepped Wedge Clinical Trial.

BACKGROUND: Preventable harms from medications are significant threats to patient safety in community settings, especially among ambulatory older adults on multiple prescription medications. Patients may partner with primary care professionals by taking on active roles in decisions, learning the basics of medication self-management, and working with community resources. OBJECTIVE: This study aims to assess the impact of a set of patient partnership tools that redesign primary care encounters to encourage and empower patients to make more effective use of those encounters to improve medication safety. METHODS: The study is a nonrandomized, cross-sectional stepped wedge cluster-controlled trial with 1 private family medicine clinic and 2 public safety-net primary care clinics each composing their own cluster. There are 2 intervention sequences with 1 cluster per sequence and 1 control sequence with 1 cluster. Cross-sectional surveys will be taken immediately at the conclusion of visits to the clinics during 6 time periods of 6 weeks each, with a transition period of no data collection during intervention implementation. The number of visits to be surveyed will vary by period and cluster. We plan to recruit patients and professionals for surveys during 405 visits. In the experimental periods, visits will be conducted with two partnership tools and associated clinic process changes: (1) a 1-page visit preparation guide given to relevant patients by clinic staff before seeing the provider, with the intention to improve communication and shared decision-making, and (2) a library of short educational videos that clinic staff encourage patients to watch on medication safety. In the control periods, visits will be conducted with usual care. The primary outcome will be patients' self-efficacy in medication use. The secondary outcomes are medication-related issues such as duplicate therapies identified by primary care providers and assessment of collaborative work during visits. RESULTS: The study was funded in September 2019. Data collection started in April 2023 and ended in December 2023. Data was collected for 405 primary care encounters during that period. As of February 15, 2024, initial descriptive statistics were calculated. Full data analysis is expected to be completed and published in the summer of 2024. CONCLUSIONS: This study will assess the impact of patient partnership tools and associated process changes in primary care on medication use self-efficacy and medication-related issues. The study is powered to identify types of patients who may benefit most from patient engagement tools in primary care visits. TRIAL REGISTRATION: ClinicalTrials.gov NCT05880368; https://clinicaltrials.gov/study/NCT05880368. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/57878.

Examination of the mechanisms underlying the discriminative stimulus properties of the atypical antipsychotic amisulpride.

Amisulpride is an atypical benzamide antipsychotic/antidepressant, whose mechanism of action is thought to depend mainly on dopamine D2/3 receptor activity, but also with some serotonin 5-HT2B/7 effects. The present study examined the role of D2/3 receptors and 5-HT2B/7 receptors in amisulpride's discriminative stimulus. Selective agonists and antagonists of the above receptors were tested in adult, male C57BL/6 mice trained to discriminate 10 mg/kg amisulpride from vehicle in a two-lever drug discrimination assay. After acquisition of the two-lever discrimination, the amisulpride generalization curve yielded an ED50 = 0.56 mg/kg (95% CI = 0.42-0.76 mg/kg). Substitution tests found that the D2/3 antagonist raclopride (62.7% Drug Lever Responding), D2/3 agonist quinpirole (56.6% DLR), 5-HT7 agonist LP-44 (50.1% DLR) and 5-HT7 antagonist SB-269970 (36.7% DLR) produced various degrees of partial substitution for the amisulpride stimulus, whereas the 5-HT2B agonist BW 723C86 (17.9% DLR) and 5-HT2B antagonist SB-204741 (21.1% DLR) yielded negligible amisulpride-like effects. In combination tests with amisulpride, quinpirole decreased percent responding from 98.3% to 57.0% DLR, LP-44 decreased percent responding from 97.6% to 76.7% DLR, and BW 723C86 reduced percent responding from 95.66% to 74.11% DLR. Taken together, the results from stimulus generalization and antagonism studies suggest that amisulpride has a complex discriminative cue that involves mainly mixed D2/3 receptor antagonist/agonist effects and, to a lesser degree, mixed 5-HT7 receptor agonist/antagonist and perhaps 5-HT2B receptor antagonist effects.

Characterising B cell expression and prognostic significance in human papillomavirus positive oropharyngeal cancer.

OBJECTIVES: The incidence of human papillomavirus positive oropharyngeal cancer (HPV+OPC) is increasing, and new biomarkers are required to better define prognostic groups and guide treatment. Infiltrating T cells have been well studied in head and neck cancer, however the presence and role of B cells and tertiary lymphoid structures (TLS) in the tumor microenvironment has not, even though the interplay between T and B cells is increasingly being recognised. MATERIALS AND METHODS: Using CD20 immunohistochemistry (IHC) to identify B cells and TLS in a cohort of 159 HPV + OPC patients, we semi-quantitatively scored abundance and location (intra-tumoral or stromal) and correlated findings with patient survival. RESULTS: 32% (51/157) of patients had high intra-tumoral (IT) abundance of CD20+ B cells (≥5%) and this was prognostic for improved overall survival (OS) with an adjusted hazard ratio (HR) of 0.2 (95 % CI 0.0-0.7, p = 0.014). We validated our results in an independent cohort comprising 171 HPV + OPC where 14% (23/171) were IT CD20+ high, again showing improved survival with an adjusted HR for OS of 0.2 (95 % CI 0.0-1.4, p = 0.003). Neither stromal abundance nor the presence of TLS were prognostic in either cohort. B cells were subtyped by multispectral IHC, identifying CD20+CD27+ cells, consistent with memory B cells, as the predominant subtype. Combined with validated biomarker CD103, a marker of tissue-resident memory T cells, IT CD20+ B cells abundance was able to prognostically stratify patients further. CONCLUSIONS: CD20+ B cell abundance has the potential to be used as a biomarker to identify good and poor prognosis HPV + OPC patients.

A Distress-Processing Model for Clients in Suicidal Crisis.

Background: While crisis intervention frameworks have indicated the importance of clients in suicidal crisis better understanding their distress to decrease suicidality, it is unclear how clients in suicidal crisis process their distress. Aims: To develop (Study 1) and validate (Study 2) a sequential distress-processing model for clients in suicidal crisis. Methods: Applying task analysis, Study 1 consisted of three phases, which resulted in a theoretically and empirically informed model. In Study 2, we examined the distress-processing model's validity using a longitudinal design. In both studies, data were online crisis chats with adults in suicidal crisis. Results: In Study 1, we developed a sequential five-stage distress-processing model: (Stage 1) unengaged with distress, (Stage 2) distress awareness, (Stage 3) distress clarity, (Stage 4) distress insight, and (Stage 5) applying distress insight. In Study 2, the model's validity was supported via evidence that (H1) progression through the processing stages was sequential and (H2) clients with good outcomes had greater progression in their processing than clients with poor outcomes. Limitation: Clients who were suicidal but did not disclose their suicidality were not included. Conclusion: Our findings provide a framework for conceptualizing and operationalizing how clients move through suicidal crises, which can facilitate intervention and research developments.

Distinct chemical environments in biomolecular condensates.

Diverse mechanisms have been described for selective enrichment of biomolecules in membrane-bound organelles, but less is known about mechanisms by which molecules are selectively incorporated into biomolecular assemblies such as condensates that lack surrounding membranes. The chemical environments within condensates may differ from those outside these bodies, and if these differed among various types of condensate, then the different solvation environments would provide a mechanism for selective distribution among these intracellular bodies. Here we use small molecule probes to show that different condensates have distinct chemical solvating properties and that selective partitioning of probes in condensates can be predicted with deep learning approaches. Our results demonstrate that different condensates harbor distinct chemical environments that influence the distribution of molecules, show that clues to condensate chemical grammar can be ascertained by machine learning and suggest approaches to facilitate development of small molecule therapeutics with optimal subcellular distribution and therapeutic benefit.

Resident Involvement in Curricular and Clinical Practice Change and Satisfaction With Training According to Length of Training in Family Medicine.

BACKGROUND AND OBJECTIVES: Most research in residency training has focused on quality improvement within a single program. We explored resident involvement in curricular and clinical practice change, the learning environment, and resident satisfaction in 3-year family medicine residencies compared to matched 4-year residencies. METHODS: We used two surveys to capture data. One was for program directors, which assessed the level of resident involvement in curricular and practice transformation. The second was a resident survey, which asked residents to rate their involvement in curricular change and practice transformation, the learning environment, and satisfaction with training. Both were administered annually between 2013 and 2019. Response rates ranged from 84.6% to 100%. RESULTS: Findings revealed no overall difference in resident involvement in curricular change, but the program director survey findings indicated that a higher proportion of residents in 4-year programs were using a broader diversity of approaches to working on quality improvement (QI) projects compared to those in 3-year programs. We also found statistical differences in the number of QI projects completed per year, with 34.1% completing three or more in 4-year programs compared to 13.3% in 3-year programs (P<.001). We found a positive correlation between resident involvement, learning environment, and satisfaction with training for both 3-year (range 0.489-0.666; P=.001) and 4-year residents (range 0.441-0.529; P=.001). CONCLUSIONS: Four-year residents were involved in a greater number of quality improvement projects and had a more diverse profile of involvement than those in 3-year residency programs. Involvement in practice and curricular change and the learning environment were associated with greater levels of resident satisfaction with training in both 3-year and 4-year programs.

Effect of pregnancy on the expression of nutrient-sensors and satiety hormones in mice.

Small intestinal satiation pathways involve nutrient-induced stimulation of chemoreceptors leading to release of satiety hormones from intestinal enteroendocrine cells (ECCs). Whether adaptations in these pathways contribute to increased maternal food intake during pregnancy is unknown. To determine the expression of intestinal nutrient-sensors and satiety hormone transcripts and proteins across pregnancy in mice. Female C57BL/6J mice (10-12 weeks old) were randomized to mating and then tissue collection at early- (6.5 d), mid- (12.5 d) or late-pregnancy (17.5 d), or to an unmated age matched control group. Relative transcript expression of intestinal fatty acid, peptide and amino acid and carbohydrate chemoreceptors, as well as gut hormones was determined across pregnancy. The density of G-protein coupled receptor 93 (GPR93), free fatty acid receptor (FFAR) 4, cholecystokinin (CCK) and glucagon-like peptide1 (GLP-1) immunopositive cells was then compared between non-pregnant and late-pregnant mice. Duodenal GPR93 expression was lower in late pregnant than non-pregnant mice (P < 0.05). Ileal FFAR1 expression was higher at mid- than at early- or late-pregnancy. Ileal FFAR2 expression was higher at mid-pregnancy than in early pregnancy. Although FFAR4 expression was consistently lower in late-pregnant than non-pregnant mice (P < 0.001), the density of FFAR4 immunopositive cells was higher in the jejunum of late-pregnant than non-pregnant mice. A subset of protein and fatty acid chemoreceptor transcripts undergo region-specific change during murine pregnancy, which could augment hormone release and contribute to increased food intake. Further investigations are needed to determine the functional relevance of these changes.

Regulatory architecture of cell identity genes and housekeeping genes.

Gene regulation and chromosome architecture are intimately linked. Genes with prominent roles in cell identity are often regulated by clusters of enhancer elements. By contrast, a recent study shows housekeeping genes are often regulated through clustering of promoters. We discuss here new regulatory insights for these two types of genes.

Primary care teams' reported actions to improve medication safety: a qualitative study with insights in high reliability organising.

BACKGROUND: Our aim was to understand actions by primary care teams to improve medication safety. METHODS: This was a qualitative study using one-on-one, semistructured interviews with the questions guided by concepts from collaborative care and systems engineering models, and with references to the care of older adults. We interviewed 21 primary care physicians and their team members at four primary care sites serving patients with mostly low socioeconomic status in Southwest US during 2019-2020. We used thematic analysis with a combination of inductive and deductive coding. First, codes capturing safety actions were incrementally developed and revised iteratively by a team of multidisciplinary analysts using the inductive approach. Themes that emerged from the coded safety actions taken by primary care professionals to improve medication safety were then mapped to key principles from the high reliability organisation framework using a deductive approach. RESULTS: Primary care teams described their actions in medication safety mainly in making standard-of-care medical decisions, patient-shared decision-making, educating patients and their caregivers, providing asynchronous care separate from office visits and providing clinical infrastructure. Most of the actions required customisation at the individual level, such as limiting the supply of certain medications prescribed and simplifying medication regimens in certain patients. Primary care teams enacted high reliability organisation principles by anticipating and mitigating risks and taking actions to build resilience in patient work systems. The primary care teams' actions reflected their safety organising efforts as responses to many other agents in multiple settings that they could not control nor easily coordinate. CONCLUSIONS: Primary care teams take many actions to shape medication safety outcomes in community settings, and these actions demonstrated that primary care teams are a reservoir of resilience for medication safety in the overall healthcare system. To improve medication safety, primary care work systems require different strategies than those often used in more self-contained systems such as hospital inpatient or surgical services.

A Predictive Decision Analytics Approach for Primary Care Operations Management: A Case Study of Double-Booking Strategy Design and Evaluation.

Primary care plays a vital role for individuals and families in accessing care, keeping well, and improving quality of life. However, the complexities and uncertainties in the primary care delivery system (e.g., patient no-shows/walk-ins, staffing shortage, COVID-19 pandemic) have brought significant challenges in its operations management, which can potentially lead to poor patient outcomes and negative primary care operations (e.g., loss of productivity, inefficiency). This paper presents a decision analytics approach developed based on predictive analytics and hybrid simulation to better facilitate management of the underlying complexities and uncertainties in primary care operations. A case study was conducted in a local family medicine clinic to demonstrate the use of this approach for patient no-show management. In this case study, a patient no-show prediction model was used in conjunction with an integrated agent-based and discrete-event simulation model to design and evaluate double-booking strategies. Using the predicted patient no-show information, a prediction-based double-booking strategy was created and compared against two other strategies, namely random and designated time. Scenario-based experiments were then conducted to examine the impacts of different double-booking strategies on clinic's operational outcomes, focusing on the trade-offs between the clinic productivity (measured by daily patient throughput) and efficiency (measured by visit cycle and patient wait time for doctor). The results showed that the best productivity-efficiency balance was derived under the prediction-based double-booking strategy. The proposed hybrid decision analytics approach has the potential to better support decision-making in primary care operations management and improve the system's performance. Further, it can be generalized in the context of various healthcare settings for broader applications.

The Influence of Transcranial Alternating Current Stimulation on Fatigue Resistance.

Previous research has shown that some forms of non-invasive brain stimulation can increase fatigue resistance. The purpose of this study is to determine the influence of transcranial alternating current stimulation (tACS) on the time to task failure (TTF) of a precision grip task. The study utilized a randomized, double-blind, SHAM-controlled, within-subjects design. Twenty-six young adults completed two experimental sessions (tACS and SHAM) with a 7-day washout period between sessions. Each session involved a fatiguing isometric contraction of the right hand with a precision grip with either a tACS or SHAM stimulation applied to the primary motor cortex (M1) simultaneously. For the fatiguing contraction, the participants matched an isometric target force of 20% of the maximum voluntary contraction (MVC) force until task failure. Pre- and post-MVCs were performed to quantify the force decline due to fatigue. Accordingly, the dependent variables were the TTF and MVC force decline as well as the average EMG activity, force error, and standard deviation (SD) of force during the fatiguing contractions. The results indicate that there were no significant differences in any of the dependent variables between the tACS and SHAM conditions (p value range: 0.256-0.820). These findings suggest that tACS does not increase the TTF during fatiguing contractions in young adults.

Transcription factors interact with RNA to regulate genes.

Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.

Intravenous immunoglobulin is safe and effective in controlling pre-existing paraneoplastic neuromuscular diseases in cancer patients treated with immune checkpoint inhibitors: two case reports and literature review.

Immune checkpoint inhibitors cause rare but potentially fatal neuromuscular complications, leading to a concern to use these agents in cancer patients with pre-existing autoimmune or inflammatory neuromuscular diseases. We report two such patients with paraneoplastic dermatomyositis and "seronegative" paraneoplastic demyelinating neuropathy, respectively, who have been successfully treated with immune checkpoint inhibitor monotherapy as well as maintenance intravenous immunoglobulin. While controlling the paraneoplastic or autoimmune neuromuscular diseases, the use of intravenous immunoglobulin did not compromise the anti-cancer effect of immune checkpoint inhibitor.

Comprehensive profiling identifies tumour and immune microenvironmental differences in clinical subsets of cutaneous squamous cell carcinoma.

BACKGROUND: Cutaneous squamous cell carcinomas (cSCCs) are the second most diagnosed skin cancer worldwide; however, little is known about the pathobiological factors that contribute to the diverse clinical outcomes seen. OBJECTIVES: To profile cSCCs comprehensively and identify the pathological processes that contribute to the disparities seen in their clinical behaviour. METHODS: We characterized the genomic, transcriptomic and immunohistochemical profiles of 211 cSCC tumours, including 37 cSCCs from immunocompromised patients. RESULTS: cSCCs from immunocompromised patients were characterized by a lack of B cells in the peritumoral stroma compared with immunocompetent patients. Further, an abundance of a memory B-cell-like population in the peritumoral stroma was associated with a better prognosis in all patients (immunocompetent and immunocompromised), as well as only immunocompetent patients. No differences in genetic -variants, tumour mutational burden or mutational signatures were observed between cSCCs from immunocompetent and immunocompromised patients. Thus, differences in survival between cSCCs from immunocompromised patients and immunocompetent patients are not likely to be driven by tumour genomic factors, but may be associated with differential host immune response. cSCC not from a primary head and neck site had lower tumour mutational burden and exhibited upregulation of the epithelial-mesenchymal transition programme compared with head and neck cSCC. Both factors were implicated with poorer responses to immune checkpoint inhibition, and the latter with poorer survival. CONCLUSIONS: We identified tumour and host immune factors that contribute to the disparate clinical behaviour of cSCC, with broad translational application, including prognostication, treatment prediction to current therapies and the identification of novel anticancer therapy approaches in cSCC.