LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance.

Targeting autophagy in cancer cells and in the tumor microenvironment are current goals of cancer therapy. However, components of canonical autophagy play roles in other biological processes, adding complexity to this goal. One such alternative function of autophagy proteins is LC3-associated phagocytosis (LAP), which functions in phagosome maturation and subsequent signaling events. Here, we show that impairment of LAP in the myeloid compartment, rather than canonical autophagy, induces control of tumor growth by tumor-associated macrophages (TAM) upon phagocytosis of dying tumor cells. Single-cell RNA sequencing (RNA-seq) analysis revealed that defects in LAP induce pro-inflammatory gene expression and trigger STING-mediated type I interferon responses in TAM. We found that the anti-tumor effects of LAP impairment require tumor-infiltrating T cells, dependent upon STING and the type I interferon response. Therefore, autophagy proteins in the myeloid cells of the tumor microenvironment contribute to immune suppression of T lymphocytes by effecting LAP.

De Novo Epigenetic Programs Inhibit PD-1 Blockade-Mediated T Cell Rejuvenation.

Immune-checkpoint-blockade (ICB)-mediated rejuvenation of exhausted T cells has emerged as a promising approach for treating various cancers and chronic infections. However, T cells that become fully exhausted during prolonged antigen exposure remain refractory to ICB-mediated rejuvenation. We report that blocking de novo DNA methylation in activated CD8 T cells allows them to retain their effector functions despite chronic stimulation during a persistent viral infection. Whole-genome bisulfite sequencing of antigen-specific murine CD8 T cells at the effector and exhaustion stages of an immune response identified progressively acquired heritable de novo methylation programs that restrict T cell expansion and clonal diversity during PD-1 blockade treatment. Moreover, these exhaustion-associated DNA-methylation programs were acquired in tumor-infiltrating PD-1hi CD8 T cells, and approaches to reverse these programs improved T cell responses and tumor control during ICB. These data establish de novo DNA-methylation programming as a regulator of T cell exhaustion and barrier of ICB-mediated T cell rejuvenation.

Critical Role for the DNA Sensor AIM2 in Stem Cell Proliferation and Cancer.

Colorectal cancer is a leading cause of cancer-related deaths. Mutations in the innate immune sensor AIM2 are frequently identified in patients with colorectal cancer, but how AIM2 modulates colonic tumorigenesis is unknown. Here, we found that Aim2-deficient mice were hypersusceptible to colonic tumor development. Production of inflammasome-associated cytokines and other inflammatory mediators was largely intact in Aim2-deficient mice; however, intestinal stem cells were prone to uncontrolled proliferation. Aberrant Wnt signaling expanded a population of tumor-initiating stem cells in the absence of AIM2. Susceptibility of Aim2-deficient mice to colorectal tumorigenesis was enhanced by a dysbiotic gut microbiota, which was reduced by reciprocal exchange of gut microbiota with healthy wild-type mice. These findings uncover a synergy between a specific host genetic factor and gut microbiota in determining the susceptibility to colorectal cancer. Therapeutic modulation of AIM2 expression and microbiota has the potential to prevent colorectal cancer.

Resolving medulloblastoma cellular architecture by single-cell genomics.

Medulloblastoma is a malignant childhood cerebellar tumour type that comprises distinct molecular subgroups. Whereas genomic characteristics of these subgroups are well defined, the extent to which cellular diversity underlies their divergent biology and clinical behaviour remains largely unexplored. Here we used single-cell transcriptomics to investigate intra- and intertumoral heterogeneity in 25 medulloblastomas spanning all molecular subgroups. WNT, SHH and Group 3 tumours comprised subgroup-specific undifferentiated and differentiated neuronal-like malignant populations, whereas Group 4 tumours consisted exclusively of differentiated neuronal-like neoplastic cells. SHH tumours closely resembled granule neurons of varying differentiation states that correlated with patient age. Group 3 and Group 4 tumours exhibited a developmental trajectory from primitive progenitor-like to more mature neuronal-like cells, the relative proportions of which distinguished these subgroups. Cross-species transcriptomics defined distinct glutamatergic populations as putative cells-of-origin for SHH and Group 4 subtypes. Collectively, these data provide insights into the cellular and developmental states underlying subtype-specific medulloblastoma biology.

The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain.

Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Network (BICCN) is applying these technologies at unprecedented scale to map the cell types in the mammalian brain. In an effort to increase data FAIRness (Findable, Accessible, Interoperable, Reusable), the NIH has established repositories to make data generated by the BICCN and related BRAIN Initiative projects accessible to the broader research community. Here, we describe the Neuroscience Multi-Omic Archive (NeMO Archive; nemoarchive.org), which serves as the primary repository for genomics data from the BRAIN Initiative. Working closely with other BRAIN Initiative researchers, we have organized these data into a continually expanding, curated repository, which contains transcriptomic and epigenomic data from over 50 million brain cells, including single-cell genomic data from all of the major regions of the adult and prenatal human and mouse brains, as well as substantial single-cell genomic data from non-human primates. We make available several tools for accessing these data, including a searchable web portal, a cloud-computing interface for large-scale data processing (implemented on Terra, terra.bio), and a visualization and analysis platform, NeMO Analytics (nemoanalytics.org).

Accurate genomic variant detection in single cells with primary template-directed amplification.

Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here, we present primary template-directed amplification (PTA), an isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a tool for mapping genome-wide interactions of mutagens with single living human cells at base-pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate WGA, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.

Streamlining Telecommunications Center and Interfacility Patient Throughput to a Pediatric Emergency Department by Utilizing an Electronic Handoff: A Quality Improvement Initiative.

OBJECTIVE: Effective handoffs are critical for patient safety and high-quality care. The pediatric emergency department serves as the initial reception for patients where optimal communication is crucial. The complexities of interfacility handoffs can result in information loss due to lack of standardization. The aim of our project was a 50% reduction in monthly calls routed through the communication center from 157 to 78, for interfacility transfers to the emergency department from outpatient sites within our organization over a 1-year period, through utilization of an electronic handoff activity. METHODS: We designed a quality improvement project in a tertiary care pediatric hospital to improve the process of interfacility transfer. The initiative aimed to streamline the transfer of patients from ambulatory, urgent care, and nurse triage encounters to the pediatric emergency department by using the electronic health record. The primary outcome measure was number of monthly calls received by the telecommunications center for these transfers.Our process measure was tracked by measuring the utilization of the electronic handoff. In addition, the number of safety events reported because of information lost through using the electronic handoff served as a balancing measure. RESULTS: One year after the enterprise-wide rollout of the handoff, the telecommunications center was receiving an average of 29 calls per month versus 157 at time of study initiation, a decrease of 81.5%. Monthly usage increased from zero to an average of 544 during the same period. The project was continued after the initial 12-month data collection and demonstrated stability. CONCLUSIONS: Our initiative facilitated the safe and efficient transfer of patients and streamlined workflows without sacrificing quality of patient care. Our telecommunications center has been freed up for other tasks with fewer interruptions during patient throughput. Next steps will analyze the encounters of transferred patients to further optimize patient flow at our organization.

Racial discrimination and trauma symptoms: Further support for the Race-Based Traumatic Stress Symptom Scale.

OBJECTIVES: This study provides further validity for scores produced by the Race-Based Traumatic Stress Symptom Scale (RBTSSS), through examining the relationship between perceived discrimination, trauma symptoms, and mental health symptoms with the RBTSSS. METHOD: Participants consisted of 148 people of color (54% women) with an average age of 33.38 years. Study hypotheses were tested using correlational and regression analyses. RESULTS: Validity was supported by strong relations with established symptom scores and perceived discrimination. Regression analysis found RBTSSS to be a significant predictor of trauma symptoms, controlling for general stress. Finally, multivariate analysis found perceived discrimination to be a stronger predictor of RBTSSS symptoms than general stress. CONCLUSIONS: The RBTSSS demonstrates strong relations with other symptom measures and perceived discrimination, supporting the validity of the RBTSSS scores. Both researchers and practitioners may benefit from use of the instrument which captures emotional outcomes specific to racial trauma. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

The actin and tetraspanin networks organize receptor nanoclusters to regulate B cell receptor-mediated signaling.

A key role is emerging for the cytoskeleton in coordinating receptor signaling, although the underlying molecular requirements remain unclear. Here we show that cytoskeleton disruption triggered signaling requiring not only the B cell receptor (BCR), but also the coreceptor CD19 and tetraspanin CD81, thus providing a mechanism for signal amplification upon surface-bound antigen stimulation. By using superresolution microscopy, we demonstrated that endogenous IgM, IgD, and CD19 exhibited distinct nanoscale organization within the plasma membrane of primary B cells. Upon stimulation, we detect a local convergence of receptors, although their global organization was not dramatically altered. Thus, we postulate that cytoskeleton reorganization releases BCR nanoclusters, which can interact with CD19 held in place by the tetraspanin network. These results not only suggest that receptor compartmentalization regulates antigen-induced activation but also imply a potential role for CD19 in mediating ligand-independent "tonic" BCR signaling necessary for B cell survival.

Metrics of color-difference formula improvement.

Metrics of color-difference formula improvement (i.e., standardized residual sum of squares and Pearson product moment correlation) are shown to convey the same information. Furthermore, each metric has two computational forms that assume different linear data models, specifically, with or without an ordinate intercept. It is essential to choose a computational form that matches the data model. We recommend explicitly declaring whether or not the data have been centered, i.e., by subtracting the mean value from each datum, to match the intercept-free data model. Statistical testing of the metrics assumes independent, normally distributed randomness of residuals from the data model, and homogeneous variance. Procedures consistent with these assumptions include robust statistical tests, homogenizing data transformations, and meta-analysis.

Extended Tourniquet Times and the Impact on Wound Healing in Foot Surgery.

OBJECTIVE: The aim of this study was to compare the effect of tourniquet time less than or in excess of 120 minutes on foot surgery wound healing. NULL HYPOTHESIS: A tourniquet time of over 120 minutes will not affect wound healing in foot surgery. DESIGN, SETTING, PARTICIPANTS AND METHOD: A retrospective comparative cohort analysis was performed on 96 patients undergoing complex hindfoot surgery in a large central teaching hospital. Fifty-five patients receiving tourniquet pressure for >120 minutes and 41 receiving <120 minutes of tourniquet pressure were identified from electronic case records. The primary outcome was surgical wound healing. Secondary outcomes were discharge date and complication rate. RESULTS: There was no significant difference in reported time for wounds to heal in the <120-minute or >120-minute cohort. There were no other significant differences in secondary clinical outcomes and no significant variations in patient demographics. CONCLUSION: This study suggests that tourniquet times from 2 to 3 hours in foot and ankle surgery with pressures up to 300 mmHg are not associated with a significant effect on wound healing.

Dynamic Pneumococcal Genetic Adaptations Support Bacterial Growth and Inflammation during Coinfection with Influenza.

Streptococcus pneumoniae (pneumococcus) is one of the primary bacterial pathogens that complicates influenza virus infections. These bacterial coinfections increase influenza-associated morbidity and mortality through a number of immunological and viral-mediated mechanisms, but the specific bacterial genes that contribute to postinfluenza pathogenicity are not known. Here, we used genome-wide transposon mutagenesis (Tn-Seq) to reveal bacterial genes that confer improved fitness in influenza virus-infected hosts. The majority of the 32 genes identified are involved in bacterial metabolism, including nucleotide biosynthesis, amino acid biosynthesis, protein translation, and membrane transport. We generated mutants with single-gene deletions (SGD) of five of the genes identified, SPD1414, SPD2047 (cbiO1), SPD0058 (purD), SPD1098, and SPD0822 (proB), to investigate their effects on in vivo fitness, disease severity, and host immune responses. The growth of the SGD mutants was slightly attenuated in vitro and in vivo, but each still grew to high titers in the lungs of mock- and influenza virus-infected hosts. Despite high bacterial loads, mortality was significantly reduced or delayed with all SGD mutants. Time-dependent reductions in pulmonary neutrophils, inflammatory macrophages, and select proinflammatory cytokines and chemokines were also observed. Immunohistochemical staining further revealed altered neutrophil distribution with reduced degeneration in the lungs of influenza virus-SGD mutant-coinfected animals. These studies demonstrate a critical role for specific bacterial genes and for bacterial metabolism in driving virulence and modulating immune function during influenza-associated bacterial pneumonia.

High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor.

In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion.

Interleukin 17-producing T helper cells and interleukin 17 orchestrate autoreactive germinal center development in autoimmune BXD2 mice.

Interleukin 17 (IL-17) is a cytokine associated with inflammation, autoimmunity and defense against some bacteria. Here we show that IL-17 can promote autoimmune disease through a mechanism distinct from its proinflammatory effects. As compared with wild-type mice, autoimmune BXD2 mice express more IL-17 and show spontaneous development of germinal centers (GCs) before they increase production of pathogenic autoantibodies. We show that blocking IL-17 signaling disrupts CD4+ T cell and B cell interactions required for the formation of GCs and that mice lacking the IL-17 receptor have reduced GC B cell development and humoral responses. Production of IL-17 correlates with upregulated expression of the genes Rgs13 and Rgs16, which encode regulators of G-protein signaling, and results in suppression of the B cell chemotactic response to the chemokine CXCL12. These findings suggest a mechanism by which IL-17 drives autoimmune responses by promoting the formation of spontaneous GCs.

The transcription factor Myc controls metabolic reprogramming upon T lymphocyte activation.

To fulfill the bioenergetic and biosynthetic demand of proliferation, T cells reprogram their metabolic pathways from fatty acid ß-oxidation and pyruvate oxidation via the TCA cycle to the glycolytic, pentose-phosphate, and glutaminolytic pathways. Two of the top-ranked candidate transcription factors potentially responsible for the activation-induced T cell metabolic transcriptome, HIF1α and Myc, were induced upon T cell activation, but only the acute deletion of Myc markedly inhibited activation-induced glycolysis and glutaminolysis in T cells. Glutamine deprivation compromised activation-induced T cell growth and proliferation, and this was partially replaced by nucleotides and polyamines, implicating glutamine as an important source for biosynthetic precursors in active T cells. Metabolic tracer analysis revealed a Myc-dependent metabolic pathway linking glutaminolysis to the biosynthesis of polyamines. Therefore, a Myc-dependent global metabolic transcriptome drives metabolic reprogramming in activated, primary T lymphocytes. This may represent a general mechanism for metabolic reprogramming under patho-physiological conditions.

Dietary modulation of the microbiome affects autoinflammatory disease.

The incidences of chronic inflammatory disorders have increased considerably over the past three decades. Recent shifts in dietary consumption may have contributed importantly to this surge, but how dietary consumption modulates inflammatory disease is poorly defined. Pstpip2(cmo) mice, which express a homozygous Leu98Pro missense mutation in the Pombe Cdc15 homology family protein PSTPIP2 (proline-serine-threonine phosphatase interacting protein 2), spontaneously develop osteomyelitis that resembles chronic recurrent multifocal osteomyelitis in humans. Recent reports demonstrated a crucial role for interleukin-1ß (IL-1ß) in osteomyelitis, but deletion of the inflammasome components caspase-1 and NLRP3 failed to rescue Pstpip2(cmo) mice from inflammatory bone disease. Thus, the upstream mechanisms controlling IL-1ß production in Pstpip2(cmo) mice remain to be identified. In addition, the environmental factors driving IL-1ß-dependent inflammatory bone erosion are unknown. Here we show that the intestinal microbiota of diseased Pstpip2(cmo) mice was characterized by an outgrowth of Prevotella. Notably, Pstpip2(cmo) mice that were fed a diet rich in fat and cholesterol maintained a normal body weight, but were markedly protected against inflammatory bone disease and bone erosion. Diet-induced protection against osteomyelitis was accompanied by marked reductions in intestinal Prevotella levels and significantly reduced pro-IL-1ß expression in distant neutrophils. Furthermore, pro-IL-1ß expression was also decreased in Pstpip2(cmo) mice treated with antibiotics, and in wild-type mice that were kept under germ-free conditions. We further demonstrate that combined deletion of caspases 1 and 8 was required for protection against IL-1ß-dependent inflammatory bone disease, whereas the deletion of either caspase alone or of elastase or neutrophil proteinase 3 failed to prevent inflammatory disease. Collectively, this work reveals diet-associated changes in the intestinal microbiome as a crucial factor regulating inflammasome- and caspase-8-mediated maturation of IL-1ß and osteomyelitis in Pstpip2(cmo) mice.

CIE self-luminous gray-scale calculation: inflections, parameters, and high-contrast limiting behavior.

Wide generalizability of the CIE-recommended gray-scale calculation for self-luminous devices suggests that its parameters, the extrema of the calculation's derivatives, and its limiting behavior are fundamental. The calculation has a negative-contrast point of inflection that is not predicted by any other gray-scale calculation, but that is consistent with data and with the terrestrial luminance histogram. The parameters of the calculation are analyzed, and their significance is explained. High-positive-contrast behavior of the calculation is shown and related to scientific literature. This knowledge represents a clearer understanding of daylight suprathreshold vision, and it enables optimal luminance-coding of contemporary high-resolution, high-contrast, high-luminance displays.

Surgery Performed by Supervised Trainees Does not Affect Outcome in First Metatarsophalangeal Joint (MTPJ) Arthrodesis.

First metatarsophalangeal joint (MTPJ) arthrodesis is an index procedure for orthopedic trainees in the United Kingdom. There is an absence of evidence as to the outcome of surgery when performed by supervised trainees. The aim of this study is to compare the incidence of fusion, complication rate and radiographic outcomes in first MTPJ arthrodesis performed by supervised orthopedic trainees with consultants. This is a retrospective cohort study of 117 patients undergoing first MTPJ arthrodesis from August 2015 to December 2017 in our institute for hallux valgus (HV) deformity with first MPTJ arthrosis or for hallux rigidus. Patients were followed to a minimum of 1-year postsurgery and were given an open appointment thereafter. In the hallux rigidus group, there was no significant difference between the complication rate (p = .477), incidence of fusion (p = .663), postoperatively HVA (p = .763), and postoperative intermetatarsal angle (p = .539) between trainees and consultants. There was a significant difference in mean tourniquet time (p = .563) between trainees and consultants. In the hallux valgus group, there was no significant difference in the complication rate (p = .519), incidence of fusion (p = .786), tourniquet time (p = .075), postoperative HVA (p = .423), and postoperative intermetatarsal angle (p = .143) between the trainees and consultants. This is the first MTPJ fusion series that demonstrates good results can be achieved by supervised trainees performing the procedure. This would suggest that first MTPJ arthrodesis remains an opportunity for trainees to continue learning to perform under supervision whilst ensuring no change in outcome for the patient.

Sickle Cell Trait, Rhabdomyolysis, and Mortality among U.S. Army Soldiers.

BACKGROUND: Studies have suggested that sickle cell trait elevates the risks of exertional rhabdomyolysis and death. We conducted a study of sickle cell trait in relation to these outcomes, controlling for known risk factors for exertional rhabdomyolysis, in a large population of active persons who had undergone laboratory tests for hemoglobin AS (HbAS) and who were subject to exertional-injury precautions. METHODS: We used Cox proportional-hazards models to test whether the risks of exertional rhabdomyolysis and death varied according to sickle cell trait status among 47,944 black soldiers who had undergone testing for HbAS and who were on active duty in the U.S. Army between January 2011 and December 2014. We used the Stanford Military Data Repository, which contains comprehensive medical and administrative data on all active-duty soldiers. RESULTS: There was no significant difference in the risk of death among soldiers with sickle cell trait, as compared with those without the trait (hazard ratio, 0.99; 95% confidence interval [CI], 0.46 to 2.13; P=0.97), but the trait was associated with a significantly higher adjusted risk of exertional rhabdomyolysis (hazard ratio, 1.54; 95% CI, 1.12 to 2.12; P=0.008). This effect was similar in magnitude to that associated with tobacco use, as compared with no use (hazard ratio, 1.54; 95% CI, 1.23 to 1.94; P<0.001), and to that associated with having a body-mass index (BMI; the weight in kilograms divided by the square of the height in meters) of 30.0 or more, as compared with a BMI of less than 25.0 (hazard ratio, 1.39; 95% CI, 1.04 to 1.86; P=0.03). The effect was less than that associated with recent use of a statin, as compared with no use (hazard ratio, 2.89; 95% CI, 1.51 to 5.55; P=0.001), or an antipsychotic agent (hazard ratio, 3.02; 95% CI, 1.34 to 6.82; P=0.008). CONCLUSIONS: Sickle cell trait was not associated with a higher risk of death than absence of the trait, but it was associated with a significantly higher risk of exertional rhabdomyolysis. (Funded by the National Heart, Lung, and Blood Institute and the Uniformed Services University of the Health Sciences.).