Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that escape convalescent and vaccine-induced antibody responses has renewed focus on the development of broadly protective T-cell-based vaccines. Here, we apply structure-based network analysis and assessments of HLA class I peptide stability to define mutationally constrained CD8+ T cell epitopes across the SARS-CoV-2 proteome. Highly networked residues are conserved temporally among circulating variants and sarbecoviruses and disproportionately impair spike pseudotyped lentivirus infectivity when mutated. Evaluation of HLA class I stabilizing activity for 18 globally prevalent alleles identifies CD8+ T cell epitopes within highly networked regions with limited mutational frequencies in circulating SARS-CoV-2 variants and deep-sequenced primary isolates. Moreover, these epitopes elicit demonstrable CD8+ T cell reactivity in convalescent individuals but reduced recognition in recipients of mRNA-based vaccines. These data thereby elucidate key mutationally constrained regions and immunogenic epitopes in the SARS-CoV-2 proteome for a global T-cell-based vaccine against emerging variants and SARS-like coronaviruses.

Intragenic DNA inversions expand bacterial coding capacity.

Bacterial populations that originate from a single bacterium are not strictly clonal and often contain subgroups with distinct phenotypes1. Bacteria can generate heterogeneity through phase variation-a preprogrammed, reversible mechanism that alters gene expression levels across a population1. One well-studied type of phase variation involves enzyme-mediated inversion of specific regions of genomic DNA2. Frequently, these DNA inversions flip the orientation of promoters, turning transcription of adjacent coding regions on or off2. Through this mechanism, inversion can affect fitness, survival or group dynamics3,4. Here, we describe the development of PhaVa, a computational tool that identifies DNA inversions using long-read datasets. We also identify 372 'intragenic invertons', a novel class of DNA inversions found entirely within genes, in genomes of bacterial and archaeal isolates. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We validate ten intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, and experimentally characterize an intragenic inverton in the thiamine biosynthesis gene thiC.

Effects of contralateral noise on envelope-following responses, auditory-nerve compound action potentials, and otoacoustic emissions measured simultaneously.

This study assessed whether the effects of contralateral acoustic stimulation (CAS) are consistent with eliciting the medial olivocochlear (MOC) reflex for measurements sensitive to outer hair cell (otoacoustic emissions, OAEs), auditory-nerve (AN; compound action potential, CAP), and brainstem/cortical (envelope-following response, EFR) function. The effects of CAS were evaluated for simultaneous measurement of OAEs, CAPs, and EFRs in participants with normal hearing. Clicks were presented at 40 or 98 Hz in three ipsilateral noise conditions (no noise, 45 dB SPL, and 55 dB SPL). For the no noise condition, CAS suppressed or enhanced EFR amplitudes for 40- and 98-Hz clicks, respectively, while CAS had no significant effect on CAP amplitudes. A follow-up experiment using slower rates (4.4-22.2 Hz) assessed whether this insignificant CAS effect on CAPs was from ipsilateral MOC stimulation or AN adaptation; however, CAS effects remained insignificant despite favorable signal-to-noise ratios. CAS-related enhancements of EFR and CAP amplitudes in ipsilateral noise were not observed, contrary to the anti-masking effect of the MOC reflex. EFR and OAE suppression from CAS were not significantly correlated. Thus, the effects of CAS on EFRs may not be solely mediated by the MOC reflex and may be partially mediated by higher auditory centers.

The Characteristics and Ethics of Sham Surgeries: A Systematic Review of Randomized Controlled Trials.

OBJECTIVE: We sought to perform a large-scale systematic review across all sham-controlled studies currently present in the literature to better characterize the ethical considerations of these studies. BACKGROUND: Innovative surgical procedures are often introduced into the clinical setting without the robust clinical trials required for medicinal treatments. Sham surgeries serve as placebos by performing all steps of a surgical intervention aside from those deemed therapeutically necessary. Yet, sham trials are underutilized because of ethical controversy. METHODS: Ovid MEDLINE was queried through April 2022 with combinations of the Medical Subject (MeSH) headings and keywords including, but not limited to, "surgery," "endoscopy," "randomized controlled trial," and "sham procedure." Primary outcomes were surgical indications and characteristics, outcome measurements, and whether the investigational treatment was offered to the sham cohort. RESULTS: One hundred seventy-two articles fit our inclusion criteria, with gastrointestinal pathologies being the most common surgical indication. Participants, personnel, and outcome assessment were all blinded in 8.7% of trials (n=15). Study populations included adult subjects (age ≥18) in 170 studies (98.8%), and two involved children. The most common level of dissection and type of anesthesia were deep (n=66, 38.4%) and general (n=49, 28.5%), respectively. An open surgical approach was utilized in 20.9% of studies (n=36). Primary outcomes were objective in 75 studies (43.6%) and subjective in 97 (56.4%), 62 of which used validated outcome measures (36.0%). Four trials explicitly did not offer the surgery to the sham arm (2.3%), whereas 106 had no mention of whether the intervention was offered (61.6%). CONCLUSIONS: Our systematic review of 172 randomized, sham-controlled trials highlights the ethical considerations that must be considered in these studies, namely the importance of transparent study design and objective outcome reporting, the difficulty of informed consent, and the inherent risks associated with surgical interventions.

GNAI1 and GNAI3 Reduce Colitis-Associated Tumorigenesis in Mice by Blocking IL6 Signaling and Down-regulating Expression of GNAI2.

BACKGROUND & AIMS: Interleukin 6 (IL6) and tumor necrosis factor contribute to the development of colitis-associated cancer (CAC). We investigated these signaling pathways and the involvement of G protein subunit alpha i1 (GNAI1), GNAI2, and GNAI3 in the development of CAC in mice and humans. METHODS: B6;129 wild-type (control) or mice with disruption of Gnai1, Gnai2, and/or Gnai3 or conditional disruption of Gnai2 in CD11c+ or epithelial cells were given dextran sulfate sodium (DSS) to induce colitis followed by azoxymethane (AOM) to induce carcinogenesis; some mice were given an antibody against IL6. Feces were collected from mice, and the compositions of microbiomes were analyzed by polymerase chain reactions. Dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs) isolated from spleen and colon tissues were analyzed by flow cytometry. We performed immunoprecipitation and immunoblot analyses of colon tumor tissues, MDSCs, and mouse embryonic fibroblasts to study the expression levels of GNAI1, GNAI2, and GNAI3 and the interactions of GNAI1 and GNAI3 with proteins in the IL6 signaling pathway. We analyzed the expression of Gnai2 messenger RNA by CD11c+ cells in the colonic lamina propria by PrimeFlow, expression of IL6 in DCs by flow cytometry, and secretion of cytokines in sera and colon tissues by enzyme-linked immunosorbent assay. We obtained colon tumor and matched nontumor tissues from 83 patients with colorectal cancer having surgery in China and 35 patients with CAC in the United States. Mouse and human colon tissues were analyzed by histology, immunoblot, immunohistochemistry, and/or RNA-sequencing analyses. RESULTS: GNAI1 and GNAI3 (GNAI1;3) double-knockout (DKO) mice developed more severe colitis after administration of DSS and significantly more colonic tumors than control mice after administration of AOM plus DSS. Development of increased tumors in DKO mice was not associated with changes in fecal microbiomes but was associated with activation of nuclear factor (NF) κB and signal transducer and activator of transcription (STAT) 3; increased levels of GNAI2, nitric oxide synthase 2, and IL6; increased numbers of CD4+ DCs and MDSCs; and decreased numbers of CD8+ DCs. IL6 was mainly produced by CD4+/CD11b+, but not CD8+, DCs in DKO mice. Injection of DKO mice with a blocking antibody against IL6 reduced the expansion of MDSCs and the number of tumors that developed after CAC induction. Incubation of MDSCs or mouse embryonic fibroblasts with IL6 induced activation of either NF-κB by a JAK2-TRAF6-TAK1-CHUK/IKKB signaling pathway or STAT3 by JAK2. This activation resulted in expression of GNAI2, IL6 signal transducer (IL6ST, also called GP130) and nitric oxide synthase 2, and expansion of MDSCs; the expression levels of these proteins and expansion of MDSCs were further increased by the absence of GNAI1;3 in cells and mice. Conditional disruption of Gnai2 in CD11c+ cells of DKO mice prevented activation of NF-κB and STAT3 and changes in numbers of DCs and MDSCs. Colon tumor tissues from patients with CAC had reduced levels of GNAI1 and GNAI3 and increased levels of GNAI2 compared with normal tissues. Further analysis of a public human colorectal tumor DNA microarray database (GSE39582) showed that low Gani1 and Gnai3 messenger RNA expression and high Gnai2 messenger RNA expression were significantly associated with decreased relapse-free survival. CONCLUSIONS: GNAI1;3 suppresses DSS-plus-AOM-induced colon tumor development in mice, whereas expression of GNAI2 in CD11c+ cells and IL6 in CD4+/CD11b+ DCs appears to promote these effects. Strategies to induce GNAI1;3, or block GNAI2 and IL6, might be developed for the prevention or therapy of CAC in patients.

Preclinical evaluation of a 64Cu-labeled disintegrin for PET imaging of prostate cancer.

A novel recombinant disintegrin, vicrostatin (VCN), displays high binding affinity to a broad range of human integrins in substantial competitive biological advantage over other integrin-based antagonists. In this study, we synthesized a new 64Cu-labeled VCN probe and evaluated its imaging properties for prostate cancer in PC-3 tumor-bearing mice. Macrocyclic chelating agent 1,8-diamino-3,6,10,13,16,19-hexaazabicyclo[6.6.6]-eicosine (DiAmSar) was conjugated with PEG unit and followed by coupling with VCN. The precursor was then radiolabeled with positron emitter 64Cu (t1/2 = 12.7 h) in ammonium acetate buffer to provide 64Cu-Sar-PEG-VCN, which was subsequently subjected to in vitro studies, small animal PET, and biodistribution studies. The PC-3 tumor-targeting efficacy of 64Cu-Sar-PEG-VCN was compared to a cyclic RGD peptide-based PET probe (64Cu-Sar-RGD). 64Cu labeling was achieved in 75% decay-corrected yield with radiochemical purity of > 98%. The specific activity of 64Cu-Sar-PEG-VCN was estimated to be 37 MBq/nmol. MicroPET imaging results showed that 64Cu-Sar-PEG-VCN has preferential tumor uptake and good tumor retention in PC-3 tumor xenografts. As compared to 64Cu-Sar-RGD, 64Cu-Sar-PEG-VCN produces higher tumor-to-muscle (T/M) imaging contrast ratios at 2 h (4.66 ± 0.34 vs. 2.88 ± 0.46) and 24 h (4.98 ± 0.80 vs. 3.22 ± 0.30) post-injection (pi) and similar tumor-to-liver ratios at 2 h (0.43 ± 0.09 vs. 0.37 ± 0.04) and 24 h (0.57 ± 0.13 vs. 0.52 ± 0.07) pi. The biodistribution results were consistent with the quantitative analysis of microPET imaging, demonstrating good T/M ratio (2.73 ± 0.36) of 64Cu-Sar-PEG-VCN at 48 h pi in PC-3 tumor xenografts. For both microPET and biodistribution studies at 48 h pi, the PC-3 tumor uptake of 64Cu-Sar-PEG-VCN is lower than that of 64Cu-Sar-RGD. 64Cu-Sar-PEG-VCN has the potential for in vivo imaging of prostate cancer with PET, which may provide a unique non-invasive method to quantitatively localize and characterize prostate cancer.

A Nanoscale Tool for Photoacoustic-Based Measurements of Clotting Time and Therapeutic Drug Monitoring of Heparin.

Heparin anticoagulation therapy is an indispensable feature of clinical care yet has a narrow therapeutic window and is the second most common intensive care unit (ICU) medication error. The active partial thromboplastin time (aPTT) monitors heparin but suffers from long turnaround times, a variable reference range, limited utility with low molecular weight heparin, and poor correlation to dose. Here, we describe a photoacoustic imaging technique to monitor heparin concentration using methylene blue as a simple and Federal Drug Administration-approved contrast agent. We found a strong correlation between heparin concentration and photoacoustic signal measured in phosphate buffered saline (PBS) and blood. Clinically relevant heparin concentrations were detected in blood in 32 s with a detection limit of 0.28 U/mL. We validated this imaging approach by correlation to the aPTT (Pearson's r = 0.86; p < 0.05) as well as with protamine sulfate treatment. This technique also has good utility with low molecular weight heparin (enoxaparin) including a blood detection limit of 72 µg/mL. We then used these findings to create a nanoparticle-based hybrid material that can immobilize methylene blue for potential applications as a wearable/implantable heparin sensor to maintain drug levels in the therapeutic window. To the best of our knowledge, this is the first use of photoacoustics to image anticoagulation therapy with significant potential implications to the cardiovascular and surgical community.

How we used a patient visit tracker tool to advance experiential learning in systems-based practice and quality improvement in a medical student clinic.

Poorly designed healthcare systems increase costs and preventable medical errors. To address these issues, systems-based practice (SBP) education provides future physicians with the tools to identify systemic errors and implement quality improvement (QI) initiatives to enhance the delivery of cost-effective, safe and multi-disciplinary care. Although SBP education is being implemented in residency programs and is mandated by the Accreditation Council for Graduate Medical Education (ACGME) as one of its core competencies, it has largely not been integrated into undergraduate medical education. We propose that Medical Student-Faculty Collaborative Clinics (MSFCCs) may be the ideal environment in which to train medical students in SBPs and QI initiatives, as they allow students to play pivotal roles in project development, administration, and management. Here we describe a process of experiential learning that was developed within a newly established MSFCC, which challenged students to identify inefficiencies, implement interventions, and track the results. After identifying bottlenecks in clinic operations, our students designed a patient visit tracker tool to monitor clinic flow and implemented solutions to decrease patient visit times. Our model allowed students to drive their own active learning in a practical clinical setting, providing early and unique training in crucial QI skills.

Dynamin triple knockout cells reveal off target effects of commonly used dynamin inhibitors.

Dynamin, which is encoded by three genes in mammals, is a GTPase implicated in endocytic membrane fission. Dynamin 1 and 3 are predominantly expressed in brain, whereas dynamin 2 is ubiquitously expressed. With the goal of assessing the impact of the lack of dynamin on cell physiology, we previously generated and characterized dynamin 1 and 2 double knockout (DKO) fibroblasts. These DKO cells were unexpectedly viable in spite of a severe impairment of clathrin-mediated endocytosis. As low-level expression of the dynamin 3 gene in these cells could not be excluded, we have now engineered dynamin 1, 2 and 3 triple KO (TKO) fibroblasts. These cells did not reveal any additional defects beyond what was previously observed in DKO fibroblasts. Surprisingly, although fluid-phase endocytosis and peripheral membrane ruffling were not impaired by the lack of all three dynamins, two structurally similar, widely used dynamin inhibitors, dynasore and Dyngo-4a, robustly inhibited these two processes both in wild-type and TKO cells. Dynamin TKO cells will be useful tools for the further exploration of dynamin-dependent processes and the development of more specific dynamin inhibitors.

Comparing Satisfaction Among Providers Treating Both Pediatric and Adult Otolaryngology Patients.

Objective: Although pediatric otolaryngology providers are reported to garner lower patient satisfaction than adults, this difference is not well characterized. This study investigates whether patient satisfaction differences exist in providers who treat both pediatric and adult patients. Study Design: Retrospective review. Setting: Tertiary medical center. Methods: In this cross-sectional study, Press Ganey surveys (PGS) completed by patients or parents on their first-time visit with 5 general otolaryngology providers from July 2014 to March 2022 were analyzed. Surveys were categorized by child (<18 years old) or adult and consisted of 14 items including 6 service domains of access, visit, nursing, provider, personal issues, and assessment. Analysis was performed with Walsh's t test and analysis of variance. Multivariable logistic regression, controlling for wait times and provider, evaluated the likelihood of highest satisfaction scores (HI-SCORES) based on age. Results: A total of 2549 patients (135 pediatric, 2414 adults) completed the PGS on their initial visit. There was no significant difference in the mean overall satisfaction scores between pediatric and adult patients. Further analysis of service domains among pediatric patients found the mean score in the access domain to be higher for the 6- to 11-year-old age group (0-5 years old: 85.5 ± 20.5 [mean ± SD], 6-11 years old: 94.7 ± 11.5, 12-17 years old: 87.3 ± 15.4, P = .03). Pediatric patients did not have a significantly higher likelihood (odds ratio = 1.1, 95% confidence interval: 0.8-1.6, P > .05) of reporting HI-SCORES compared to adults after covariate adjustment. Conclusion: There was no significant difference in patient satisfaction scores for providers who treat pediatric and adult patients utilizing the same facility and scheduling team.