The rockefeller university

The transporter associated with antigen processing (TAP) delivers peptide antigens from the cytoplasm into the endoplasmic reticulum (ER) for loading onto major histocompatibility complex class I (MHC-I) molecules. To examine the mechanisms of peptide transport and release into the ER, we determined cryo-electron microscopy structures of the human TAP heterodimer in multiple functional states along the transport cycle. In the inward-facing conformation, when the peptide translocation cavity within the TAP heterodimer is exposed to the cytosol, ATP binding strengthened intradomain assembly. Transition to the outward-facing conformation, when the transporter opens to the ER lumen, led to a complete reconfiguration of the peptide-binding site, facilitating peptide release. ATP hydrolysis opened the catalytically active nucleotide-binding consensus site, and the subsequent separation of the nucleotide-binding domains reset the transport cycle. These findings establish a comprehensive structural framework for understanding unilateral peptide transport, vanadate trapping, and trans-inhibition-an internal feedback mechanism that prevents excessive peptide accumulation and activation of the ER stress response.

A goal of data visualization is to advance the understanding of multiparameter, large-scale datasets. In astrophysics, scientists map celestial objects to understand the hierarchical structure of the universe. In biology, genetic sequences and biological characteristics uncover evolutionary relationships and patterns (e.g., variation within species and ecological associations). Our highly interdisciplinary project entitled "A Cosmic View of Life on Earth" adapts an immersive astrophysics visualization platform called OpenSpace to contextualize diverse biological data. Dimensionality reduction techniques harmonize biological information to create spatial representations in which data are interactively explored on flat screens and planetarium domes. Visualizations are enriched with geographic metadata, 3-D scans of specimens, and species-specific sonifications (e.g., bird songs). The "Cosmic View" project eases the dissemination of stories related to biological domains (e.g., insects, birds, mammals, and human migrations) and facilitates scientific discovery.

Neurodegenerative diseases present one of the most significant global health challenges. These disorders are defined by the accumulation of abnormal protein aggregates that impair synaptic function and cause progressive neuronal degeneration. Therefore, stimulating protein clearance mechanisms may be neuroprotective. Variants in FBXO7/ PARK15 cause Parkinsonian Pyramidal Syndrome, an early-onset parkinsonian neurodegenerative disorder in humans, and inactivation of this gene in mice recapitulates many phenotypes seen in patients. The proteasome regulator PI31 is a direct binding partner of Fbxo7 and promotes local protein degradation at synapses by mediating fast proteasome transport in neurites. PI31 protein levels are reduced when the function of Fbxo7 is impaired. Here we show that restoring PI31 levels in Fbxo7 mutant fly and mouse strains prevents neuronal degeneration and significantly improves neuronal function, health, and lifespan. Notably, Fbxo7 inactivation in mouse neurons causes hyperphosphorylation of tau, and this was suppressed by transgenic expression of PI31. Our results demonstrate that PI31 is a crucial biological target through which Fbxo7 deficiency drives pathology. Therefore, targeting the PI31-pathway may represent a promising therapeutic approach for treating neurodegenerative disorders.

The Tyrrhenian tree frog (Hyla sarda) is a small cryptically coloured amphibian found in Corsica, Sardinia, and the Tuscan Archipelago. Investigation into the species' evolutionary history has revealed phenotypic changes triggered by glaciation-induced range expansion, but understanding the genetic basis of this trait variation has been hampered by the lack of a reference genome. To address this, we assembled a chromosome-level genome of Hyla sarda using PacBio HiFi long reads, Bionano optical maps, and Hi-C data. The assembly comprises 13 assembled chromosomes, spanning a total length of 4.15 Gb with a scaffold N50 of 385 Mb, a BUSCO completeness of 94.60%, and a k-mer completeness of 98.30%. Approximately 75% of the genome consists of repetitive elements. We annotated 22,847 protein-coding genes with a BUSCO completeness of 94.60% and an OMArk completeness of 93.74%. This high-quality assembly provides a valuable resource for studying phenotypic evolution and its genomic basis during range expansion, and will assist future investigations into the population and conservation genomics of Hyla sarda.

Wnt signaling plays a crucial role for many developmental processes. It is also pivotal in the generation and limited treatment outcomes of glioblastoma (GBM). Here, we identified Wnt7b, which is markedly upregulated in GBM patients, as a determinant of resistance to immune checkpoint blockers (alpha PD1; anti-Programmed Cell Death Protein 1) in a clinically relevant, alpha PD1-resistant GBM murine model with abundant stem cells. We observed that increased levels of Wnt7b and beta-- catenin correlated with the resistance to alpha PD1. Treatment combining a porcupine inhibitor WNT974 with alpha PD1 reprogrammed the immune suppressive tumor microenvironment (TME) to bolster antitumor immune responses and extended the survival of mice bearing orthotopic GBM, with 25% long-term survivors. Our causal studies revealed that WNT974 potentiated alpha PD1 therapy by the expansion of antigen presenting DC3-like dendritic cells (DCs). Additionally, WNT974 combination with alpha PD1 was associated with a reduction in immune suppressive granulocytic myeloid-derived suppressor cells (MDSCs), an increase in the Ki67+CD8/Ki67+regulatory T cells (Treg) ratio, tilting the CD8:Treg balance in the TME toward antitumor immune response, and more pronounced GrzB+CD8+ effector T cells. Conversely, an increase in monocytic MDSCs and phosphorylation of pro-oncogenic proteins was associated with resistance to the combination therapy. Collectively, our preclinical findings provide a strong rationale to test Wnt7b/beta-- catenin inhibition with alpha PD1 therapy in GBM patients with elevated Wnt7b/beta-- catenin signaling.

Purpose of review Whipple's disease (WD), triggered by Tropheryma whipplei ( T. whipplei ), is a rare, chronic, inflammatory, systemic infectious disease that typically manifests in adults. The most frequent initial manifestations include arthritis, followed by diarrhea, abdominal pain, and weight loss. Half the world's population is exposed to T. whipplei , but only one in a million develop WD. This suggests that acquired or inborn errors of immunity (IEI) may underlie WD. Anti-TNF treatment is a well established risk factor for flare-ups of WD. Recent findings We have also reported two rare IEI in patients with WD. Six WD patients from two unrelated kindreds were found to have autosomal dominant IRF4 deficiency acting via a mechanism of haploinsufficiency. These patients were otherwise healthy. In addition, a single patient with a history of WD and other infections was found to have autosomal recessive CD4 deficiency. Summary Rare IEI can underlie WD. Human genetic studies of patients with WD are warranted for the development of precision medicine for affected kindreds and to improve our understanding of the pathogenesis of this rare infectious disease.

Recent technological advances have facilitated the assembly of telomere-to-telomere (T2T) genomes. The current T2T CHM13 showcases the complete architecture of the human genome, yet its use in functional experiments is limited by discrepancies with the actual genome of the specific biological system under study. Access to reference assemblies for experimentally relevant cell lines is therefore essential in advancing sequencing-based analyses and precise manipulation, particularly in highly variable regions such as centromeres. Here, we present RPE1v1.1, the near-complete diploid genome assembly of the hTERT RPE-1 cell line, a non-cancerous human retinal epithelial model with a stable karyotype. Using high-coverage Pacific Biosciences and Oxford Nanopore Technologies long-read sequencing, we generate a high-quality de novo assembly, validate it through multiple methods, and phase it by integrating high-throughput chromosome conformation capture (Hi-C) data. Our assembly includes chromosome-level scaffolds that span centromeres for all chromosomes. Comparing both haplotypes with the CHM13 genome, we detect haplotype-specific genomic variations, including the translocation between chromosome 10 and chromosome X t(X;10)(Xq28;10q21.2) characteristic of RPE-1 cells, and divergence peaking at centromeres. Altogether, the RPE1v1.1 genome provides a reference-quality diploid assembly of a widely used cell line, supporting high-precision genetic and epigenetic studies in this model system.

In the host-pathogen arms race, herpesviruses and poxviruses encode proteins that sabotage the transporter associated with antigen processing (TAP), thereby suppressing MHC-I antigen presentation and enabling lifelong infection. Of the five known viral TAP inhibitors, only the herpes simplex virus (HSV) protein ICP47 has been structurally resolved. We now report cryoelectron microscopy structures of TAP in complex with the remaining four: BNLF2a (Epstein-Barr virus), hUS6 (human cytomegalovirus), bUL49.5 (bovine herpesvirus 1), and CPXV012 (cowpox virus), assembling a structural atlas of viral TAP evasion. Despite employing divergent sequences, folds, and conformational targets, these viral inhibitors converge on a common strategy: they stall TAP from the alternating access cycle, precluding peptide entry into the ER and shielding infected cells from cytotoxic T cell surveillance. These findings reveal striking functional convergence and provide a structural framework for rational antiviral design.

Tumor cell intravasation is essential for metastatic dissemination, but its exact mechanism is incompletely understood. We have previously shown that in breast cancer, the direct and stable association of a tumor cell expressing Mena, a Tie2hi/VEGFhi macrophage, and a vascular endothelial cell, creates an intravasation portal, called a "tumor microenvironment of metastasis" (TMEM) doorway, for tumor cell intravasation, leading to dissemination to distant sites. The density of TMEM doorways, also called TMEM doorway score, is a clinically validated prognostic marker of distant metastasis in breast cancer patients. Although we know that tumor cells utilize TMEM doorway-associated transient vascular openings to intravasate, the precise signaling mechanisms involved in TMEM doorway function are only partially understood. Using two mouse models of breast cancer and an in vitro assay of intravasation, we report that CSF-1 secreted by the TMEM doorway tumor cell stimulates local secretion of VEGF-A from the Tie2hi TMEM doorway macrophage, leading to the dissociation of endothelial junctions between TMEM doorway-associated endothelial cells, supporting tumor cell intravasation. Acute blockade of CSF-1/CSF-1R signaling decreases macrophage VEGF-A secretion as well as TMEM doorway-associated vascular opening, tumor cell trans-endothelial migration, and dissemination. These new insights into signaling events regulating TMEM doorway function should be explored further as treatment strategies for metastatic disease.

ImportanceHealth care workers (HCW) faced chronic stress during the COVID-19 pandemic and were at high risk of illness, death and burnout.ObjectiveTo understand the experiences of and assess the acceptability and usability of the "Stress First Aid" (SFA) intervention for HCWs.DesignWe used a mixed methods approach to conduct: (1) a quantitative post-intervention survey of experiences with the SFA intervention within a cluster randomized controlled trial (cRCT); and (2) a qualitative descriptive analysis. The intervention was rolled out over three waves from March 2021 - October 2022 simultaneously with the sites' COVID-19 response.SettingOur team engaged and recruited eight pairs of hospitals and six pairs of Federally Qualified Health Centers (FQHCs), balanced across region, including nine states, and matched on size, type, and COVID-19 burden.ParticipantsA total of 862 HCWs received the SFA intervention and completed both the pre- and post-intervention surveys (FQHC n = 245 and hospital n = 617). For the qualitative analysis, among HCWs who agreed to be contacted for a post-intervention interview, we purposively sampled a subset of 35 HCWs balanced by site, gender, age, race/ethnicity and HCW type.InterventionSFA is an evidence-informed intervention adapted to mitigate the psychosocial impact of COVID-19 on HCWs through individual peer support actions.Main Outcome(s) and Measure(s)Quantitative measures are binary indicators of agreement with 6 questions about experiences with the SFA intervention. For the qualitative analysis, we utilized a semi-structured interview protocol to provide additional context on experience with SFA and how SFA affects HCW well-being.ResultsBetween 48.2 and 59.4% of HCWs agreed or strongly agreed that they: found SFA helpful (48.2%), felt comfortable supporting colleagues (59.4%), would recommend SFA (51.2%), and would continue to use SFA principles (57.2%). Non-White HCWs (particularly Black HCWs), those in assistant/technician positions and those who reported attending a greater number of booster sessions were more likely to agree with positive statements about SFA experiences.Conclusions and RelevanceGiven the continued resurgence of public health emergencies, its lasting effects on HCWs, and related emerging challenges, we expect there to be a continued need for support of patient-facing HCWs.Clinical trial registrationClinical Trials.gov Number: NCT04723576 Registered on 01/22/2021 Clinicaltrials.govNCT04723576.