Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment.

Defining genetic factors impacting chemotherapy failure can help to better predict response and identify drug resistance mechanisms. However, there is limited understanding of the contribution of inherited noncoding genetic variation on inter-individual differences in chemotherapy response in childhood acute lymphoblastic leukemia (ALL). Here we map inherited noncoding variants associated with treatment outcome and/or chemotherapeutic drug resistance to ALL cis-regulatory elements and investigate their gene regulatory potential and target gene connectivity using massively parallel reporter assays and three-dimensional chromatin looping assays, respectively. We identify 54 variants with transcriptional effects and high-confidence gene connectivity. Additionally, functional interrogation of the top variant, rs1247117, reveals changes in chromatin accessibility, PU.1 binding affinity and gene expression, and deletion of the genomic interval containing rs1247117 sensitizes cells to vincristine. Together, these data demonstrate that noncoding regulatory variants associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to antileukemic agents.

Associations of seven measures of biological age acceleration with frailty and all-cause mortality among adult survivors of childhood cancer in the St. Jude Lifetime Cohort.

Survivors of childhood cancer may experience accelerated biological aging, resulting in premature frailty and death. We used seven measures of biological age in the St. Jude Lifetime (SJLIFE) Cohort to compare biological age acceleration between the SJLIFE Cohort and the third United States National Health and Nutrition Examination Survey controls, explore trajectories of biological age according to cancer treatment and type, and test associations of biological age acceleration with frailty and death (mean follow-up of 26.5 years) among survivors. Survivors of cancer aged 5% faster per year and measured, on average, 0.6-6.44 years biologically older compared to controls and 5-16 years biologically older compared to age-matched individuals at the population level. Survivors treated with hematopoietic cell transplant and vinca alkaloid chemotherapy evidenced the fastest trajectories of biological aging. Biologically, older and faster-aging survivors consistently and robustly had a higher risk of frailty and died earlier than those with slower biological aging, suggesting a potential opportunity to intervene on excess aging.

3D printed chamber for live cell imaging on an upright epifluorescence microscope.

Live cell imaging is a standard technique in experimental biology that enables the observation of isolated cells and tissue slices in real time; and the testing of cellular responses to changes in buffer composition. However, most live cell imaging devices require the use of dedicated microscopes and/or specialized stage adaptors, and come at a reasonably high cost. We employed 3D printing technology to create a low-cost imaging chamber with side ports to exchange fluids, to be used on upright microscopes. The chamber increased the functionality of a standard upright epifluorescent microscope to allow dynamic, real-time calcium imaging of cultured hypothalamic astrocytes from mice, and to test the effects of ATP stimulation upon calcium signaling. It was also used on slices obtained from mouse brain using a brain matrix slicer. The advantages of this chamber include a very simple design that can be used with upright epifluorescence microscopes, does not require any special stage adaptor, and includes ports to permit fluid exchange during imaging. This chamber is ideal for educational settings with undergraduate laboratories that do not have access to dedicated inverted fluorescent microscopes for tissue culture experiments.

Building Affordable, Durable, Medium-fidelity Ballistic Gel Phantoms for Ultrasound-guided Nerve Block Training.

Ultrasound phantoms - alternatives to live human tissue - give learners the opportunity to practice ultrasound-guided regional anesthesia without introducing undue risk to patients. Gelatin-based phantoms provide educators with durable and reusable task trainers; however, commercially available gel-based phantoms are expensive. Here, we investigate the production of durable, low-cost, ballistic gel-based ultrasound phantoms for median, femoral, suprainguinal fascia iliaca plane, and serratus anterior plane nerve blocks, as well as a methodology for producing a phantom for any ultrasound-guided nerve block procedure. Computer-aided design (CAD) software was utilized to design four phantoms replicating the anatomy of median, femoral, suprainguinal fascia iliaca plane, and serratus anterior plane nerve blocks, including relevant landmarks and tissue planes. Plastic models of the desired tissue planes were 3D printed and used to create silicone molds. Ballistic gel was melted and mixed with flour and dye to create a liquid, echogenic ballistic gel, which was poured into the silicone molds. Vessels were simulated by creating negative space in the ballistic gel using metal rods. Nerves were simulated using yarn submerged in ultrasound gel. Simulated bones were designed using CAD and 3D printed. Ballistic gel is a versatile, durable medium that can be used to simulate a variety of tissues and can be melted and molded into any shape. Under ultrasound, these phantoms provide realistic tissue planes that represent the borders between different layers of skin, muscle, and fascia. The echogenicity of the muscle tissue layers, nerves, vessels, and bones is realistic, and bones have significant posterior shadowing as would be observed in a human subject. These phantoms cost $200 each for the first phantom and $60 for each subsequent phantom. These phantoms require some technical skill to design, but they can be built for just 4% of the cost of their commercial counterparts.

Briefings in surgical teams: a pilot study of experiences and attitudes.

While healthcare should not be compared to other high reliability organisations (HROs), many lessons, attitudes, and transferable practices can be applied and adapted from them to improve patient safety and team morale. Despite briefings improving both patient safety and effective team working, some in healthcare have not valued or actively engaged with them, deeming them to be irrelevant. In this pilot study we explored the experiences of, and attitudes to, briefings using a 10-question Survey Monkey. This was promoted during a human factors session at the 2023 Association of Surgeons in Training Conference (ASiT) and at a large NHS trust. Questions were asked about the number of briefings per day, attitudes, engagement, and respondents' attitudes to them. In total, 109 responses were received. A total of 85% reported at least one briefing on a normal operating day, 65% felt them to be interactive, 67% reported that briefings were led by the most senior surgical team member, and 58% lasted four minutes or more. Eighteen per cent of respondents felt they were of little benefit, and 56% did not routinely de-brief at the end of the day. This study has highlighted variable attitudes to team briefings, with some colleagues still seeing them as a 'tick box' exercise. While culture has changed following the introduction of the WHO checklist, the importance of active engagement and education to improve the delivery and value of effective briefings cannot be overestimated. It is also an opportunity to create a 'safe space' for team members and to confirm zero tolerance for any inappropriate behaviour, including sexual misconduct.

Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators.

B cell lineage acute lymphoblastic leukemia (B-ALL) is composed of diverse molecular subtypes, and while transcriptional and DNA methylation profiling has been extensively examined, the chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq in primary B-ALL cells from 156 patients spanning ten molecular subtypes and present this dataset as a resource. Differential chromatin accessibility and transcription factor (TF) footprint profiling were employed and identified B-ALL cell of origin, TF-target gene interactions enriched in B-ALL, and key TFs associated with accessible chromatin sites preferentially active in B-ALL. We further identified over 20% of accessible chromatin sites exhibiting strong subtype enrichment and candidate TFs that maintain subtype-specific chromatin architectures. Over 9,000 genetic variants were uncovered, contributing to variability in chromatin accessibility among patient samples. Our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants that promote unique gene-regulatory networks.

CRP Monitoring in Early Hospitalization: Implications for Predicting Outcomes in Patients with COVID-19.

Elevated C-reactive protein (CRP) levels have been associated with poorer COVID-19 outcomes. While baseline CRP levels are higher in women, obese individuals, and older adults, the relationship between CRP, sex, body mass index (BMI), age, and COVID-19 outcomes remains unknown. To investigate, we performed a retrospective analysis on 824 adult patients with COVID-19 admitted during the first pandemic wave, of whom 183 (22.2%) died. The maximum CRP value over the first five hospitalization days better predicted hospitalization outcome than the CRP level at admission, as a maximum CRP > 10 mg/dL independently quadrupled the risk of death (p < 0.001). Males (p < 0.001) and patients with a higher BMI (p = 0.001) had higher maximum CRP values, yet CRP levels did not impact their hospitalization outcome. While CRP levels did not statistically mediate any relation between sex, age, or BMI with clinical outcomes, age impacted the association between BMI and the risk of death. For patients 60 or over, a BMI < 25 kg/m2 increased the risk of death (p = 0.017), whereas the reverse was true for patients <60 (p = 0.030). Further impact of age on the association between BMI, CRP, and the risk of death could not be assessed due to a lack of statistical power but should be further investigated.

Effectiveness of rescue Me CPR! smartphone app providing real-time guidance to untrained bystanders performing CPR.

Background: Out-of-hospital cardiac arrest (OHCA) is a persistent global health challenge, owing, in part, to low rates of population CPR training. Smartphone applications have the potential to widely disseminate CPR basic training to a populace, but other studies have found multiple limitations in previously developed CPR guidance applications (CPR-GA). This study aims to use medical simulation to assess the relative CPR performance of novices using the 'Rescue Me CPR!' (RMC) app, a custom CPR-GA designed by this research team, to novices using 'PG-CPR!' (PGC), the most downloaded CPR-GA available in the USA, and to CPR certified medical personnel. Methods: In a prospective randomized experimental trial of 60 individuals, subjects were either given the RMC app, the PGC app, or had active CPR certification. They were presented a cardio-pulmonary arrest scenario and were observed while performing CPR on a high-fidelity manikin. Data was collected through four cycles of CPR, during which time 24 pertinent performance metrics and CPR steps were timed and recorded. These metrics were assessed on their own and used to calculate average time to compressions, average chest compression fraction, and rate of high-quality CPR for each study group. Results: CPR certified subjects called 911 in 100 % of simulation cases, started compressions 34 ± 10 s after first seeing the simulated patient, had an average chest compression fraction of 0.52, and performed high-quality CPR in 25 % of aggregate compression cycles. PGC app users called 911 in 70 % of simulation cases, started compressions 86 ± 17 s after first seeing the simulated patient, had an average chest compression fraction that could not be assessed due to inconsistent pauses during CPR, and performed high-quality CPR in 2.5 % of aggregate compression cycles. RMC app users called 911 in 100 % of simulation cases, started compressions 55 ± 6 s after first seeing the simulated patient, had an average chest compression fraction of 0.48, and performed high-quality CPR in 50 % of aggregate compression cycles. Conclusion: The results of this study demonstrate that in all studied metrics, except time-to-first-compression, CPR provided by individuals using the RMC app is statistically equivalent or superior to CPR performed by a CPR certified individual and, in almost every metric, superior to CPR performed by users of the most downloaded android CPR guidance application, PG-CPR.

Abbreviation use decreases effective clinical communication and can compromise patient safety.

Clear communication is paramount for achieving the safest and best patient outcomes, for maximising time efficiency, and lowering clinician workload. Multiple factors contribute to communication efficacy, including knowledge of topics between those communicating, interpersonal familiarity, and available time. Information exchange is growing faster and more frequent due to evolving communication technology, and communication is expanding as a response to increasing workloads. The number of referrals between specialties and the general practitioner (GP) is rising. The use of abbreviations has expanded in clinical communications and is likely to lead to misunderstanding, increased workload, and worse patient outcomes. In this article, we explore the use of abbreviations in the clinical setting.

Endotracheal tube forces exerted on the larynx and a novel support device to reduce it.

Objective: Endotracheal tubes (ETTs) are commonly associated with laryngeal injury that may be short lasting and temporary or more severe and life altering. Injury is believed to result from forces that these ETTs exert on the larynx. Here we quantify the forces of ETTs of various sizes on the laryngotracheal complex to gain a more quantitative understanding of these potential damaging forces. Here we also perform preclinical testing of a novel support device to offload these forces. Methods: Endotracheal intubation was performed on a fresh human cadaver using various ETT sizes. A strain-sensitive graphene nanosheet sensor and a commercially available force sensing resistor were secured behind the larynx, anterior to the prevertebral fascia. The forces exerted on the larynx were measured for each of the commonly used ETTs. A novel support device, ETT clip (Endo Clip), was attached to the ETTs and changes in these forces were observed. Results: Forces exerted on the laryngotracheal complex by various ETTs were observed to increase with increasing tube size. This pressure can be significantly reduced with a novel ETT clip. Conclusion: Here we demonstrate the first quantitative measurement of forces that ETTs exert on the larynx. We demonstrate a novel device that can easily clip onto an ETT reducing pressure on the laryngotracheal complex. This preclinical test paves the way for a human clinical trial. Level of evidence: 5.

Prenatal Cannabis Use and Offspring Autism-Related Behaviors: Examining Maternal Stress as a Moderator in a Black American Cohort.

Prenatal cannabis use and maternal stress have been proposed as risk factors for autism spectrum disorder (ASD). Black mothers and mothers of lower socioeconomic status (SES) may be especially likely to experience high levels of stress. This study examined the impact of prenatal cannabis use and maternal stress (i.e., prenatal distress, racial discrimination, and lower SES) on child ASD-related behaviors in a sample of 172 Black mother-child pairs. We found that prenatal stress was significantly associated with ASD-related behaviors. Prenatal cannabis use did not predict ASD-related behaviors and did not interact with maternal stress to predict ASD-related behaviors. These findings replicate previous work on prenatal stress-ASD associations and add to the limited literature on prenatal cannabis-ASD associations in Black samples.

Caffeine: benefits and drawbacks for technical performance.

Surgical and minimally-invasive procedures, including cardiac and radiological, have high-stake patient outcomes. Working pressures, altering shift rotas, and ever-increasing demands have led to worsening sleep patterns for surgeons and allied professionals. Sleep deprivation alone has harmful consequences in relation to clinical outcomes and the physical and mental health of the surgeon, and to offset fatigue, some surgeons use legal stimulants such as caffeine and energy drinks. This stimulant use, however, may come at the cost of negative effects on cognitive and physical function. We aimed to explore evidence behind the use of caffeine, and its consequences on technical performance and clinical outcomes.

Relative Effects of Various Factors on Ice Ball Formation and Ablation Zone Size During Ultrasound-Guided Percutaneous Cryoneurolysis: A Laboratory Investigation to Inform Clinical Practice and Future Research.

INTRODUCTION: Ultrasound-guided percutaneous cryoneurolysis provides analgesia using cold temperatures to reversibly ablate peripheral nerves. Cryoneurolysis probes pass a gas through a small internal annulus, rapidly lowering the pressure and temperature, forming an ice ball to envelope the target nerve. Analgesia is compromised if a nerve is inadequately frozen, and laboratory studies suggest that pain may be paradoxically induced with a magnitude and duration in proportion with the incomplete ablation. We therefore investigated the relative effects of various factors that may contribute to the size of the ice ball and the effective cryoneurolysis zone. METHODS: A cryoprobe was inserted into a piece of meat, a gas was passed through for 2 min, and the resulting ice ball width (cross-section) and length (axis parallel to the probe) were measured using ultrasound, with the temperature evaluated in nine concentric locations concurrently. RESULTS: The factor with the greatest influence on ice ball size was probe gauge: in all probe types, a change from 18 to 14 increased ice ball width, length, and volume by up to 70%, 113%, and 512% respectively, with minimum internal temperature decreasing as much as from -5 to -32 °C. In contrast, alternating the type of meat (chicken, beef, pork) and the shape of the probe tip (straight, coudé) affected ice ball dimensions to a negligible degree. The ice ball dimensions and the zone of adequate temperature drop were not always correlated, and, even within a visualized ice ball, the temperature was often inadequate to induce Wallerian degeneration. CONCLUSIONS: Percutaneous probe design can significantly influence the effective cryoneurolysis zone; visualizing a nerve fully encompassed in an ice ball does not guarantee adequate treatment to induce the desired Wallerian degeneration because ice forms at temperatures between 0 and -20 °C, whereas only temperatures below -20 °C induce Wallerian degeneration. The correlation between temperatures in isolated pieces of meat and perfused human tissue remains unknown, and further research to evaluate these findings in situ appears highly warranted.

Epigenomic mapping in B-cell acute lymphoblastic leukemia identifies transcriptional regulators and noncoding variants promoting distinct chromatin architectures.

B-cell lineage acute lymphoblastic leukemia (B-ALL) is comprised of diverse molecular subtypes and while transcriptional and DNA methylation profiling of B-ALL subtypes has been extensively examined, the accompanying chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq for 10 B-ALL molecular subtypes in primary ALL cells from 154 patients. Comparisons with B-cell progenitors identified candidate B-ALL cell-of-origin and AP-1-associated cis-regulatory rewiring in B-ALL. Cis-regulatory rewiring promoted B-ALL-specific gene regulatory networks impacting oncogenic signaling pathways that perturb normal B-cell development. We also identified that over 20% of B-ALL accessible chromatin sites exhibit strong subtype enrichment, with transcription factor (TF) footprint profiling identifying candidate TFs that maintain subtype-specific chromatin architectures. Over 9000 inherited genetic variants were further uncovered that contribute to variability in chromatin accessibility among individual patient samples. Overall, our data suggest that distinct chromatin architectures are driven by diverse TFs and inherited genetic variants which promote unique gene regulatory networks that contribute to transcriptional differences among B-ALL subtypes.

Dietary fatty acids and endometrial cancer risk within the European Prospective Investigation into Cancer and Nutrition.

BACKGROUND: Diet may impact important risk factors for endometrial cancer such as obesity and inflammation. However, evidence on the role of specific dietary factors is limited. We investigated associations between dietary fatty acids and endometrial cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC). METHODS: This analysis includes 1,886 incident endometrial cancer cases and 297,432 non-cases. All participants were followed up for a mean of 8.8 years. Multivariable Cox proportional hazard models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) of endometrial cancer across quintiles of individual fatty acids estimated from various food sources quantified through food frequency questionnaires in the entire EPIC cohort. The false discovery rate (q-values) was computed to control for multiple comparisons. RESULTS: Consumption of n-6 γ-linolenic acid was inversely associated with endometrial cancer risk (HR comparing 5th with 1st quintileQ5-Q1=0.77, 95% CI = 0.64; 0.92, ptrend=0.01, q-value = 0.15). This association was mainly driven by γ-linolenic acid derived from plant sources (HRper unit increment=0.94, 95%CI= (0.90;0.98), p = 0.01) but not from animal sources (HRper unit increment= 1.00, 95%CI = (0.92; 1.07), p = 0.92). In addition, an inverse association was found between consumption of n-3 α-linolenic acid from vegetable sources and endometrial cancer risk (HRper unit increment= 0.93, 95%CI = (0.87; 0.99), p = 0.04). No significant association was found between any other fatty acids (individual or grouped) and endometrial cancer risk. CONCLUSION: Our results suggest that higher consumption of γ-linolenic acid and α-linoleic acid from plant sources may be associated with lower risk of endometrial cancer.

Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment.

Although acute lymphoblastic leukemia (ALL) is the most common childhood cancer, there is limited understanding of the contribution of inherited genetic variation on inter-individual differences in chemotherapy response. Defining genetic factors impacting therapy failure can help better predict response and identify drug resistance mechanisms. We therefore mapped inherited noncoding variants associated with chemotherapeutic drug resistance and/or treatment outcome to ALL cis-regulatory elements and investigated their gene regulatory potential and genomic connectivity using massively parallel reporter assays and promoter capture Hi-C, respectively. We identified 53 variants with reproducible allele-specific effects on transcription and high-confidence gene targets. Subsequent functional interrogation of the top variant (rs1247117) determined that it disrupted a PU.1 consensus motif and PU.1 binding affinity. Importantly, deletion of the genomic interval containing rs1247117 sensitized ALL cells to vincristine. Together, these data demonstrate that noncoding regulatory variation associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to chemotherapeutic agents in ALL.