C5aR plus MEK inhibition durably targets the tumor milieu and reveals tumor cell phagocytosis.

Plexiform neurofibromas (PNFs) are nerve tumors caused by loss of NF1 and dysregulation of RAS-MAPK signaling in Schwann cells. Most PNFs shrink in response to MEK inhibition, but targets with increased and durable effects are needed. We identified the anaphylatoxin C5a as increased in PNFs and expressed largely by PNF m acrophages. We defined pharmacokinetic and immunomodulatory properties of a C5aR1/2 antagonist and tested if peptide antagonists augment the effects of MEK inhibition. MEK inhibition recruited C5AR1 to the macrophage surface; short-term inhibition of C5aR elevated macrophage apoptosis and Schwann cell death, without affecting MEK-induced tumor shrinkage. PNF macrophages lacking C5aR1 increased the engulfment of dying Schwann cells, allowing their visualization. Halting combination therapy resulted in altered T-cell distribution, elevated Iba1+ and CD169+ immunoreactivity, and profoundly altered cytokine expression, but not sustained trumor shrinkage. Thus, C5aRA inhibition independently induces macrophage cell death and causes sustained and durable effects on the PNF microenvironment.

A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models.

SINE-VNTR-Alu (SVA) retrotransposons represent mobile regulatory elements that have the potential to influence the surrounding genome when they insert into a locus. Evolutionarily recent mobilisation has resulted in loci in the human genome where a given retrotransposon might be observed to be present or absent, termed a retrotransposon insertion polymorphism (RIP). We previously observed that an SVA RIP ~ 2 kb upstream of LRIG2 on chromosome 1, the 'LRIG2 SVA', was associated with differences in local gene expression and methylation, and that the two were correlated. Here, we have used CRISPR-mediated deletion of the LRIG2 SVA in a cell line model to validate that presence of the retrotransposon is directly affecting local expression and provide evidence that is suggestive of a modest role for the SVA in modulating nearby methylation. Additionally, in leveraging an available Hi-C dataset we observed that the LRIG2 SVA was also involved in long-range chromatin interactions with a cluster of genes ~ 300 kb away, and that expression of these genes was to varying degrees associated with dosage of the SVA in both CRISPR cell line and population models. Altogether, these data support a regulatory role for SVAs in the modulation of gene expression, with the latter potentially involving chromatin looping, consistent with the model that RIPs may contribute to interpersonal differences in transcriptional networks.

Strategies for recruiting adolescents in rural areas in firearm injury research.

BACKGROUND: Participant recruitment is a central aspect of human sciences research. Barriers to participant recruitment can be categorised into participant, recruiter and institutional factors. Firearm injury research poses unique barriers to recruitment. This is especially true for rural adolescents, who are at high risk for firearm-related injury and death, and whose voice is often absent in firearms research. In particular, recruitment strategies targeting adolescents should align with developmental changes occurring during this life stage. Identifying strategies to address recruitment barriers tailored to firearm-related research can help future researchers engage rural adolescents in injury prevention efforts. PURPOSE: The purpose of the current methodology paper is to outline barriers and provide strategies for recruiting rural adolescents in firearms research informed by the Youth Experiences in Rural Washington: Research on Firearm Safety project, a mixed-methods, community-based participatory research study of 13-18 year-olds residing in rural Washington. STRATEGIES: Recruitment barriers and related strategies were organised by participant-related and recruiter-related/institutional-related factors. While carrying out the study, key considerations or strategies which addressed multiple participant and recruiter/institutional factors, emerged with potential to enhance firearm-related research with rural adolescents more broadly. Key considerations included logistics (ie, scheduling flexibility, adequate and aligned incentives), use of a community-based participatory research approach and accounting for developmental stage. CONCLUSION: Reducing the burden of firearm injury and death for rural adolescents and developing effective interventions requires understanding and navigating recruitment barriers. Strategies used in the current project can guide future qualitative or mixed methods data collection informing firearm injury prevention.

Virologic outcomes of antiretroviral therapy in patients with HIV-1 following bariatric surgery: A case series and review of the literature.

BACKGROUND: Selection of an antiretroviral regimen for people living with HIV (PLWH) involves various clinical considerations, such as comorbidities, archived drug resistance mutations, concomitant medications, and potential drug interactions and side effects. Alterations in the surface area and pH of the gastrointestinal tract following bariatric surgery may alter absorption, antiretroviral pharmacokinetics and viral suppression. Data on the efficacy of antiretroviral (ARV) therapy in PLWH who have undergone bariatric surgery are limited or lacking for new antiretrovirals, such as dolutegravir and bictegravir. METHODS: This case series reports virologic outcomes and side effects in eight cases of PLWH receiving ARV therapy who underwent bariatric surgery. A systematic literature review was performed to review the available literature on the efficacy and safety of antiretroviral regimens in PLWH who have undergone bariatric surgery. RESULTS: Virologic suppression was not impacted for obese PLWH who underwent bariatric surgery following failure of life-style modifications and pharmacological therapy. CONCLUSIONS: There were no deleterious effects on HIV progression for PLWH that underwent bariatric surgery. More prospective research is required to validate the effects of bariatric surgery on immunologic and virologic function outcomes. Close involvement of HIV and surgical specialists is recommended to manage ARV therapy in patients undergoing bariatric surgery.

Tools for Genetic Engineering and Gene Expression Control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides.

Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts have the potential to form the backbone of the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans, Rhodobacter sphaeroides, and Zymomonas mobilis, show particular promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis, N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides. We screen a synthetic promoter library to identify inducible promoters with strong, regulated activity in both organisms. Combining Tn7 integration with promoters from our library, we establish CRISPR interference systems for N. aromaticivorans and R. sphaeroides that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these industrially important species and other Alphaproteobacteria.

Complete sequences of conjugal helper plasmids pRK2013 and pEVS104.

We present the complete sequences of two commonly used conjugal helper plasmids: pRK2013 and pEVS104. These sequences will enable engineering of custom helper plasmids, for example, with different antibiotic markers or origins of replication. We provide both sequence information and plasmid maps to aid future engineering efforts.

Perioperative changes in neurocognitive and Alzheimer's disease-related cerebrospinal fluid biomarkers in older patients randomised to isoflurane or propofol for anaesthetic maintenance.

BACKGROUND: Animal studies have shown that isoflurane and propofol have differential effects on Alzheimer's disease (AD) pathology and memory, although it is unclear whether this occurs in humans. METHODS: This was a nested randomised controlled trial within a prospective cohort study; patients age ≥60 yr undergoing noncardiac/non-neurological surgery were randomised to isoflurane or propofol for anaesthetic maintenance. Cerebrospinal fluid (CSF) was collected via lumbar puncture before, 24 h, and 6 weeks after surgery. Cognitive testing was performed before and 6 weeks after surgery. Nonparametric methods and linear regression were used to evaluate CSF biomarkers and cognitive function, respectively. RESULTS: There were 107 subjects (54 randomised to isoflurane and 53 to propofol) who completed the 6-week follow-up and were included in the analysis. There was no significant effect of anaesthetic treatment group, time, or group-by-time interaction for CSF amyloid-beta (Aß), tau, or phospho-tau181p levels, or on the tau/Aß or p-tau181p/Aß ratios (all P>0.05 after Bonferroni correction). In multivariable-adjusted intention-to-treat analyses, there were no significant differences between the isoflurane and propofol groups in 6-week postoperative change in overall cognition (mean difference [95% confidence interval]: 0.01 [-0.12 to 0.13]; P=0.89) or individual cognitive domains (P>0.05 for each). Results remained consistent across as-treated and per-protocol analyses. CONCLUSIONS: Intraoperative anaesthetic maintenance with isoflurane vs propofol had no significant effect on postoperative cognition or CSF Alzheimer's disease-related biomarkers within 6 weeks after noncardiac, non-neurological surgery in older adults. CLINICAL TRIAL REGISTRATION: NCT01993836.

Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans.

The genes that encode ribosomal RNAs are present in several hundred copies in most eukaryotes. These vast arrays of repetitive ribosomal DNA (rDNA) have been implicated not just in ribosome biogenesis, but also aging, cancer, genome stability, and global gene expression. rDNA copy number is highly variable among and within species; this variability is thought to associate with traits relevant to human health and disease. Here we investigate the phenotypic consequences of multicellular life at the lower bounds of rDNA copy number. We use the model Caenorhabditis elegans, which has previously been found to complete embryogenesis using only maternally provided ribosomes. We find that individuals with rDNA copy number reduced to ∼5% of wild type are capable of further development with variable penetrance. Such individuals are sterile and exhibit severe morphological defects, particularly in post-embryonically dividing tissues such as germline and vulva. Developmental completion and fertility are supported by an rDNA copy number ∼10% of wild type, with substantially delayed development. Worms with rDNA copy number reduced to ∼33% of wild type display a subtle developmental timing defect that was absent in worms with higher copy numbers. Our results support the hypothesis that rDNA requirements vary across tissues and indicate that the minimum rDNA copy number for fertile adulthood is substantially less than the lowest naturally observed total copy number. The phenotype of individuals with severely reduced rDNA copy number is highly variable in penetrance and presentation, highlighting the need for continued investigation into the biological consequences of rDNA copy number variation.

Quantifying DNA loss in laboratory-created latent prints due to fingerprint processing.

Fingerprints, which are associated with touch samples, typically contain a limited amount of DNA. The amount of available DNA can be further reduced when the same touch samples undergo fingerprint processing [1]. The fingerprint development process consists of high-powered lighting (inherent luminescence and UV light) and chemical compounds (ninhydrin, black powder, cyanoacrylate, and rhodamine 6 G) which could reduce DNA quality and quantity. Therefore, forensic scientists often must select one type of analysis over the other due to the destructive nature of processing. DNA and latent fingerprinting are both useful sources for identification, although both can produce partial results. A partial DNA profile may only contain a few alleles, limiting the ability to identify a potential suspect to perform comparisons. A partial fingerprint generally means that only a very small part of the fingerprint is present, which makes comparisons difficult. Because partial results are common, combining data from both fingerprinting and DNA analysis would increase the confidence of an identification of a person. Significant research has been performed to determine if a DNA profile can be obtained from latent processed fingerprints; however, there has yet to be research done in a standardized manner. In this study, we used standardized mock "fingerprints" in order to reduce fingerprint DNA variability and specifically focused on DNA quantitation after each step in the fingerprinting process. Results suggest that latent print processing techniques used on non-porous surfaces (plastic, duct-tape, metal, and rubber) do not affect DNA quantity or quality. In contrast, ninhydrin, a chemical used for processing fingerprints present on porous surfaces (wood and paper), significantly reduced DNA recovery. Together these results suggest that DNA can still be performed on latent print processed items, unless ninhydrin has been used.

Runx1/3-driven adaptive endoplasmic reticulum stress pathways contribute to neurofibromagenesis.

Neurofibromatosis type 1 (NF1) patients are predisposed to develop plexiform neurofibromas (PNFs). Three endoplasmic reticulum (ER) stress response pathways restore cellular homeostasis. The unfolded protein response (UPR) sensors contribute to tumor initiation in many cancers. We found that all three UPR pathways were activated in mouse and human PNFs, with protein kinase RNA [PKR]-like ER kinase (PERK) the most highly expressed. We tested if neurofibroma cells adapt to ER stress, leading to their growth. Pharmacological or genetic inhibition of PERK reduced mouse neurofibroma-sphere number, and genetic inhibition in PERK in Schwann cell precursors (SCPs) decreased tumor-like lesion numbers in a cell transplantation model. Further, in a PNF mouse model, deletion of PERK in Schwann cells (SCs) and SCPs reduced tumor size, number, and increased survival. Mechanistically, loss of Nf1 activated PERK-eIF2α-ATF4 signaling and increased ATF4 downstream target gene p21 translocation from nucleus to cytoplasm. This nucleus-cytoplasm translocation was mediated by exportin-1. Runx transcriptionally activated ribosome gene expression and increased protein synthesis to allow SCs to adapt to ER stress and tumor formation. We propose that targeting proteostasis might provide cytotoxic and/or potentially durable novel therapy for PNFs.

ED point-of-care ultrasonography is associated with earlier drainage of pericardial effusion: A retrospective cohort study.

OBJECTIVES: To determine the association between emergency department point-of-care cardiac ultrasonography (POCUS) utilization and time to pericardial effusion drainage during an 8-year period when the emergency ultrasound program was established at our institution. METHODS: We performed a single-center retrospective cohort study in patients undergoing pericardiocentesis or other procedure for evacuation of pericardial effusion. Data was collected using both direct queries to the electronic health record database and two-examiner chart review. The primary outcome was time to intervention for pericardial effusion drainage. Multivariable Cox regression, with and without inverse probability weighting for likelihood to receive POCUS, was used to determine the association between POCUS and time to intervention. Secondary outcomes included 28-day mortality. RESULTS: 257 patient encounters were included with 137 receiving POCUS and 120 who did not. The proportion of patients receiving POCUS increased from 18.5% to 69.5% during the early to late periods of the study. POCUS was associated with an earlier median time to intervention of 21.6 h (95% CI 17.2, 24.2) compared to 34.6 h (27.0, 50.5) in the No POCUS group. After adjustment for patient demographics, anticoagulation, time of presentation and hemodynamic instability, POCUS was associated with earlier intervention (HR 2.08 [95% CI 1.56, 2.77]). POCUS use was not associated with a difference in 28-day mortality, which was evaluated as a secondary outcome. However, diagnosis of pericardial effusion by the ED physician using any means (POCUS or other imaging) was associated with decreased 28-day mortality (9.7% vs. 26.0%, -16.3% for POCUS [95% CI -29.1, -3.5]). CONCLUSION: POCUS was associated with an earlier time to intervention for pericardial effusions after adjustment for multiple confounding factors. Failure to diagnose pericardial effusion in the ED using any diagnostic testing including POCUS, was associated with increased 28-day mortality.

Can early introduction of gluten reduce risk of celiac disease?

This UK study revealed the benefits of introducing gluten at age 4 months.

EMBRACE: One Small Story in Lupus-One Giant Challenge in Clinical Trials.

Clinical trials of novel therapeutics in the United States have not been adequately representative of diverse populations, particularly racial and ethnic minorities. The challenges and consequences of underrepresentation in clinical trial recruitment are exemplified by the case of belimumab, a biologic treatment for systemic lupus erythematosus (SLE), a disease that is more prevalent in patients of Black African ancestry and of Hispanic/Latino ethnicity than in other patient populations. Although belimumab was found to be effective in phase 2 and 3 clinical trials in the general population, post hoc analyses of efficacy data in patients of Black African ancestry showed inconsistent results. Consequently, a cautionary statement regarding belimumab use in this population was added to the product label. To alleviate concerns that belimumab may not be safe and effective for patients of Black African ancestry, the Efficacy and Safety of Belimumab in Black Race Patients with SLE (EMBRACE) study was conducted in a post-marketing commitment to the Food and Drug Administration. The study recruited only patients who self-identified as being of Black race; its findings led to the removal of the cautionary labeling of belimumab use in patients of Black African ancestry. Our manuscript highlights the critical lessons learned from the successes and failures of the EMBRACE study. It also provides suggestions for overcoming health disparities, highlighting strategies for conducting well-designed clinical trials to overcome systematic barriers to diversity in recruitment, with a focus on enacting long-term support to ensure equity in the process, products, and benefits from drug development and clinical trials.

Detection of Hemodynamic Status Using an Analytic Based on an Electrocardiogram Lead Waveform.

OBJECTIVES: Delayed identification of hemodynamic deterioration remains a persistent issue for in-hospital patient care. Clinicians continue to rely on vital signs associated with tachycardia and hypotension to identify hemodynamically unstable patients. A novel, noninvasive technology, the Analytic for Hemodynamic Instability (AHI), uses only the continuous electrocardiogram (ECG) signal from a typical hospital multiparameter telemetry monitor to monitor hemodynamics. The intent of this study was to determine if AHI is able to predict hemodynamic instability without the need for continuous direct measurement of blood pressure. DESIGN: Retrospective cohort study. SETTING: Single quaternary care academic health system in Michigan. PATIENTS: Hospitalized adult patients between November 2019 and February 2020 undergoing continuous ECG and intra-arterial blood pressure monitoring in an intensive care setting. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: One million two hundred fifty-two thousand seven hundred forty-two 5-minute windows of the analytic output were analyzed from 597 consecutive adult patients. AHI outputs were compared with vital sign indications of hemodynamic instability (heart rate > 100 beats/min, systolic blood pressure < 90 mm Hg, and shock index of > 1) in the same window. The observed sensitivity and specificity of AHI were 96.9% and 79.0%, respectively, with an area under the curve (AUC) of 0.90 for heart rate and systolic blood pressure. For the shock index analysis, AHI's sensitivity was 72.0% and specificity was 80.3% with an AUC of 0.81. CONCLUSIONS: The AHI-derived hemodynamic status appropriately detected the various gold standard indications of hemodynamic instability (hypotension, tachycardia and hypotension, and shock index > 1). AHI may provide continuous dynamic hemodynamic monitoring capabilities in patients who traditionally have intermittent static vital sign measurements.

First discovered, long out of sight, finally visible: ribosomal DNA.

With the advent of long-read sequencing, previously unresolvable genomic elements are being revisited in an effort to generate fully complete reference genomes. One such element is ribosomal DNA (rDNA), the highly conserved genomic region that encodes rRNAs. Genomic structure and content of the rDNA are variable in both prokarya and eukarya, posing interesting questions about the biology of rDNA. Here, we consider the types of variation observed in rDNA - including locus structure and number, copy number, and sequence variation - and their known phenotypic consequences. With recent advances in long-read sequencing technology, incorporating the full rDNA sequence into reference genomes is within reach. This knowledge will have important implications for understanding rDNA biology within the context of cell physiology and whole-organism phenotypes.