Canonical BAF complex activity shapes the enhancer landscape that licenses CD8+ T cell effector and memory fates.

CD8+ T cells provide host protection against pathogens by differentiating into distinct effector and memory cell subsets, but how chromatin is site-specifically remodeled during their differentiation is unclear. Due to its critical role in regulating chromatin and enhancer accessibility through its nucleosome remodeling activities, we investigated the role of the canonical BAF (cBAF) chromatin remodeling complex in antiviral CD8+ T cells during infection. ARID1A, a subunit of cBAF, was recruited early after activation and established de novo open chromatin regions (OCRs) at enhancers. Arid1a deficiency impaired the opening of thousands of activation-induced enhancers, leading to loss of TF binding, dysregulated proliferation and gene expression, and failure to undergo terminal effector differentiation. Although Arid1a was dispensable for circulating memory cell formation, tissue-resident memory (Trm) formation was strongly impaired. Thus, cBAF governs the enhancer landscape of activated CD8+ T cells that orchestrates TF recruitment and activity and the acquisition of specific effector and memory differentiation states.

CTLA-4 blockade induces a microglia-Th1 cell partnership that stimulates microglia phagocytosis and anti-tumor function in glioblastoma.

The limited efficacy of immunotherapies against glioblastoma underscores the urgency of better understanding immunity in the central nervous system. We found that treatment with αCTLA-4, but not αPD-1, prolonged survival in a mouse model of mesenchymal-like glioblastoma. This effect was lost upon the depletion of CD4+ T cells but not CD8+ T cells. αCTLA-4 treatment increased frequencies of intratumoral IFNγ-producing CD4+ T cells, and IFNγ blockade negated the therapeutic impact of αCTLA-4. The anti-tumor activity of CD4+ T cells did not require tumor-intrinsic MHC-II expression but rather required conventional dendritic cells as well as MHC-II expression on microglia. CD4+ T cells interacted directly with microglia, promoting IFNγ-dependent microglia activation and phagocytosis via the AXL/MER tyrosine kinase receptors, which were necessary for tumor suppression. Thus, αCTLA-4 blockade in mesenchymal-like glioblastoma promotes a CD4+ T cell-microglia circuit wherein IFNγ triggers microglia activation and phagocytosis and microglia in turn act as antigen-presenting cells fueling the CD4+ T cell response.

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of 3D structures for six RNA sequences: four nucleolytic ribozymes and two riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss (i) the comparison between the automated web servers and human experts; (ii) the prediction of coaxial stacking; (iii) the prediction of structural details and ligand binding; (iv) the development of novel prediction methods; and (v) the potential improvements to be made. We show that correct prediction of coaxial stacking and tertiary contacts is essential for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution and simultaneous prediction of RNA structure with accurate ligand binding still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.

The relationship between implicit intergroup attitudes and beliefs.

Intergroup attitudes (evaluations) are generalized valence attributions to social groups (e.g., white-bad/Asian-good), whereas intergroup beliefs (stereotypes) are specific trait attributions to social groups (e.g., white-dumb/Asian-smart). When explicit (self-report) measures are used, attitudes toward and beliefs about the same social group are often related to each other but can also be dissociated. The present work used three approaches (correlational, experimental, and archival) to conduct a systematic investigation of the relationship between implicit (indirectly revealed) intergroup attitudes and beliefs. In study 1 (n = 1,942), we found significant correlations and, in some cases, evidence for redundancy, between Implicit Association Tests (IATs) measuring attitudes toward and beliefs about the same social groups (mean r = 0.31, 95% confidence interval: [0.24; 0.39]). In study 2 (n = 383), manipulating attitudes via evaluative conditioning produced parallel changes in belief IATs, demonstrating that implicit attitudes can causally drive implicit beliefs when information about the specific semantic trait is absent. In study 3, we used word embeddings derived from a large corpus of online text to show that the relative distance of 22 social groups from positive vs. negative words (reflecting generalized attitudes) was highly correlated with their distance from warm vs. cold, and even competent vs. incompetent, words (reflecting specific beliefs). Overall, these studies provide convergent evidence for tight connections between implicit attitudes and beliefs, suggesting that the dissociations observed using explicit measures may arise uniquely from deliberate judgment processes.

Gender Stereotypes in Natural Language: Word Embeddings Show Robust Consistency Across Child and Adult Language Corpora of More Than 65 Million Words.

Stereotypes are associations between social groups and semantic attributes that are widely shared within societies. The spoken and written language of a society affords a unique way to measure the magnitude and prevalence of these widely shared collective representations. Here, we used word embeddings to systematically quantify gender stereotypes in language corpora that are unprecedented in size (65+ million words) and scope (child and adult conversations, books, movies, TV). Across corpora, gender stereotypes emerged consistently and robustly for both theoretically selected stereotypes (e.g., work-home) and comprehensive lists of more than 600 personality traits and more than 300 occupations. Despite underlying differences across language corpora (e.g., time periods, formats, age groups), results revealed the pervasiveness of gender stereotypes in every corpus. Using gender stereotypes as the focal issue, we unite 19th-century theories of collective representations and 21st-century evidence on implicit social cognition to understand the subtle yet persistent presence of collective representations in language.

Integration of cell cycle signals by multi-PAS domain kinases.

Spatial control of intracellular signaling relies on signaling proteins sensing their subcellular environment. In many cases, a large number of upstream signals are funneled to a master regulator of cellular behavior, but it remains unclear how individual proteins can rapidly integrate a complex array of signals within the appropriate spatial niche within the cell. As a model for how subcellular spatial information can control signaling activity, we have reconstituted the cell pole-specific control of the master regulator kinase/phosphatase CckA from the asymmetrically dividing bacterium Caulobacter crescentus CckA is active as a kinase only when it accumulates within a microdomain at the new cell pole, where it colocalizes with the pseudokinase DivL. Both proteins contain multiple PAS domains, a multifunctional class of sensory domains present across the kingdoms of life. Here, we show that CckA uses its PAS domains to integrate information from DivL and its own oligomerization state to control the balance of its kinase and phosphatase activities. We reconstituted the DivL-CckA complex on liposomes in vitro and found that DivL directly controls the CckA kinase/phosphatase switch, and that stimulation of either CckA catalytic activity depends on the second of its two PAS domains. We further show that CckA oligomerizes through a multidomain interaction that is critical for stimulation of kinase activity by DivL, while DivL stimulation of CckA phosphatase activity is independent of CckA homooligomerization. Our results broadly demonstrate how signaling factors can leverage information from their subcellular niche to drive spatiotemporal control of cell signaling.

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

Development and clinical implementation of eclipse scripting-based automated patient-specific collision avoidance software.

PURPOSE: Increased use of Linac-based stereotactic radiosurgery (SRS), which requires highly noncoplanar gantry trajectories, necessitates the development of efficient and accurate methods of collision detection during the treatment planning process. This work outlines the development and clinical implementation of a patient-specific computed tomography (CT) contour-based solution that utilizes Eclipse Scripting to ensure maximum integration with clinical workflow. METHODS: The collision detection application uses triangle mesh structures of the gantry and couch, in addition to the body contour of the patient taken during CT simulation, to virtually simulate patient treatments. Collision detection is performed using Binary Tree Hierarchy detection methods. Algorithm accuracy was first validated for simple cuboidal geometry using a calibration phantom and then extended to an anthropomorphic phantom simulation by comparing the measured minimum distance between structures to the predicted minimum distance for all allowable orientations. The collision space was tested at couch angles every 15° from 90 to 270 with the gantry incremented by 5° through the maximum trajectory. Receiver operating characteristic curve analysis was used to assess algorithm sensitivity and accuracy for predicting collision events. Following extensive validation, the application was implemented clinically for all SRS patients. RESULTS: The application was able to predict minimum distances between structures to within 3 cm. A safety margin of 1.5 cm was sufficient to achieve 100% sensitivity for all test cases. Accuracy obtained was 94.2% with the 5 cm clinical safety margin with 100% true positive collision detection. A total of 88 noncoplanar SRS patients have been currently tested using the application with one collision detected and no undetected collisions occurring. The average time for collision testing per patient was 2 min 58 s. CONCLUSIONS: A collision detection application utilizing patient CT contours was developed and successfully clinically implemented. This application allows collisions to be detected early during the planning process, avoiding patient delays and unnecessary resource utilization if detected during delivery.

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.

This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5-3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson-Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/.

Cell fate regulation governed by a repurposed bacterial histidine kinase.

One of the simplest organisms to divide asymmetrically is the bacterium Caulobacter crescentus. The DivL pseudo-histidine kinase, positioned at one cell pole, regulates cell-fate by controlling the activation of the global transcription factor CtrA via an interaction with the response regulator (RR) DivK. DivL uniquely contains a tyrosine at the histidine phosphorylation site, and can achieve these regulatory functions in vivo without kinase activity. Determination of the DivL crystal structure and biochemical analysis of wild-type and site-specific DivL mutants revealed that the DivL PAS domains regulate binding specificity for DivK∼P over DivK, which is modulated by an allosteric intramolecular interaction between adjacent domains. We discovered that DivL's catalytic domains have been repurposed as a phosphospecific RR input sensor, thereby reversing the flow of information observed in conventional histidine kinase (HK)-RR systems and coupling a complex network of signaling proteins for cell-fate regulation.

On the neural implausibility of the modular mind: Evidence for distributed construction dissolves boundaries between perception, cognition, and emotion.

Firestone & Scholl (F&S) rely on three problematic assumptions about the mind (modularity, reflexiveness, and context-insensitivity) to argue cognition does not fundamentally influence perception. We highlight evidence indicating that perception, cognition, and emotion are constructed through overlapping, distributed brain networks characterized by top-down activity and context-sensitivity. This evidence undermines F&S's ability to generalize from case studies to the nature of perception.

Social-psychological evidence for the effective updating of implicit attitudes.

Recent findings in social psychology show how implicit affective responses can be changed, leading to strong, fast, and durable updating. This work demonstrates that new information viewed as diagnostic or which prompts reinterpretations of previous learning produces fast revision, suggesting two factors that might be leveraged in clinical settings. Reconsolidation provides a plausible route for making such reasoning possible.

Standardization of RNA chemical mapping experiments.

Chemical mapping experiments offer powerful information about RNA structure but currently involve ad hoc assumptions in data processing. We show that simple dilutions, referencing standards (GAGUA hairpins), and HiTRACE/MAPseeker analysis allow rigorous overmodification correction, background subtraction, and normalization for electrophoretic data and a ligation bias correction needed for accurate deep sequencing data. Comparisons across six noncoding RNAs stringently test the proposed standardization of dimethyl sulfate (DMS), 2'-OH acylation (SHAPE), and carbodiimide measurements. Identification of new signatures for extrahelical bulges and DMS "hot spot" pockets (including tRNA A58, methylated in vivo) illustrates the utility and necessity of standardization for quantitative RNA mapping.

Stereotactic Optimized Automated Radiotherapy (SOAR): a novel automated planning solution for multi-metastatic SRS compared to HyperArc™.

Objective.Automated Stereotactic Radiosurgery (SRS) planning solutions improve clinical efficiency and reduce treatment plan variability. Available commercial solutions employ a template-based strategy that may not be optimal for all SRS patients. This study compares a novel beam angle optimized Volumetric Modulated Arc Therapy (VMAT) planning solution for multi-metastatic SRS to the commercial solution HyperArc.Approach.Stereotactic Optimized Automated Radiotherapy (SOAR) performs automated plan creation by combining collision prediction, beam angle optimization, and dose optimization to produce individualized high-quality SRS plans using Eclipse Scripting. In this retrospective study 50 patients were planned using SOAR and HyperArc. Assessed dose metrics included the Conformity Index (CI), Gradient Index (GI), and doses to organs-at-risk. Complexity metrics evaluated the modulation, gantry speed, and dose rate complexity. Plan dosimetric quality, and complexity were compared using double-sided Wilcoxon signed rank tests (α= 0.05) adjusted for multiple comparisons.Main Results.The median target CI was 0.82 with SOAR and 0.79 with HyperArc (p < .001). Median GI was 1.85 for SOAR and 1.68 for HyperArc (p < .001). The median V12Gy normal brain volume for SOAR and HyperArc were 7.76 cm3and 7.47 cm3respectively. Median doses to the eyes, lens, optic nerves, and optic chiasm were statistically significant favoring SOAR. The SOAR algorithm scored lower for all complexity metrics assessed.Significance.In-house developed automated planning solutions are a viable alternative to commercial solutions. SOAR designs high-quality patient-specific SRS plans with a greater degree of versatility than template-based methods.

Fluctuating sea-level and reversing Monsoon winds drive Holocene lagoon infill in Southeast Asia.

Many lagoons surrounded by reefs are partially or completely infilled with reef-derived detrital carbonate sediment. Sediment deposits in such restricted environments are archives of prevailing environmental conditions during lagoon infill. For Indonesia, no paleoenvironmental reconstructions based on Holocene lagoon sediments exist. Here we analyze the sedimentary record obtained from five percussion cores penetrating 10 m into the unconsolidated subsurface of a reef island in the Spermonde Archipelago, Indonesia. The combined compositional, textural and chronostratigraphic analyses reveal that the sedimentary infill of the lagoon underlying the island, starting 6900 years cal BP, was interrupted between 5800 and 4400 years cal BP, when sea level was ~ 0.5 m higher than at present, and monsoon intensity was lower. After the intensity of the monsoons increased to modern levels, and sea level dropped to its present position, lagoonal sedimentation was re-initiated and created the foundation for an island that built up since 3000 years cal BP. Our study provides the first geological evidence for the strong sensitivity of detrital carbonate systems in Indonesia to fluctuations in sea level and dominant wind direction. It thus sheds light on how changing environmental conditions in the context of global warming could affect the morphological development of reef systems, and thereby also habitable coastal areas.

Multiomics atlas-assisted discovery of transcription factors enables specific cell state programming.

The same types of cells can assume diverse states with varying functionalities. Effective cell therapy can be achieved by specifically driving a desirable cell state, which requires the elucidation of key transcription factors (TFs). Here, we integrated epigenomic and transcriptomic data at the systems level to identify TFs that define different CD8 + T cell states in an unbiased manner. These TF profiles can be used for cell state programming that aims to maximize the therapeutic potential of T cells. For example, T cells can be programmed to avoid a terminal exhaustion state (Tex Term ), a dysfunctional T cell state that is often found in tumors or chronic infections. However, Tex Term exhibits high similarity with the beneficial tissue-resident memory T states (T RM ) in terms of their locations and transcription profiles. Our bioinformatic analysis predicted Zscan20 , a novel TF, to be uniquely active in Tex Term . Consistently, Zscan20 knock-out thwarted the differentiation of Tex Term in vivo , but not that of T RM . Furthermore, perturbation of Zscan20 programs T cells into an effector-like state that confers superior tumor and virus control and synergizes with immune checkpoint therapy. We also identified Jdp2 and Nfil3 as powerful Tex Term drivers. In short, our multiomics-based approach discovered novel TFs that enhance anti-tumor immunity, and enable highly effective cell state programming. One sentence summary: Multiomics atlas enables the systematic identification of cell-state specifying transcription factors for therapeutic cell state programming.

Fast stereotactic radiosurgery planning using patient-specific beam angle optimization and automation.

BACKGROUND AND PURPOSE: Linac-based stereotactic radiosurgery (SRS) planning for multi-metastatic cases is a complex and intensive process. A manual planning strategy starts with a template-based set of beam angles and applies modifications though a trial and error process. Beam angle optimization uses patient specific geometric heuristics to determine beam angles that provide optimal target coverage and avoid treating through Organs-at-Risk (OARs). This study expands on a collision prediction application developed using an application programming interface, integrating beam angle optimization and collision prediction into a Stereotactic Optimized Automated Radiotherapy (SOAR) planning algorithm. MATERIALS AND METHODS: Twenty-five patient plans, previously treated with SRS for multi-metastatic intracranial tumors, were selected for a retrospective plan study comparing the manual planning strategy to SOAR. The SOAR algorithm was used to select isocenters, table, collimator, and gantry angles, and target groupings for the optimized plans. Dose-volume metrics for relevant OARs and PTVs were compared using double-sided Wilcoxon signed rank tests (α = 0.05). A subset of five patients were included in an efficiency study comparing manual planning times to SOAR automated times. RESULTS: OAR dose metrics compared between planning strategies showed no statistical difference for the dataset of twenty-five plans. Differences in maximum PTV dose and the conformity index were improved for SOAR planning and statistically significant. The median SOAR planning time was 9.8 min compared to 55 min for the manual planning strategy. CONCLUSIONS: SOAR planning was comparable in plan quality to a manual planning strategy with the possibility for greatly improving planning efficiency through automation.

Ecosystem design as an avenue for improving services provided by carbonate producing marine ecosystems.

Ecosystem Design (ED) is an approach for constructing habitats that places human needs for ecosystem services at the center of intervention, with the overarching goal of establishing self-sustaining habitats which require limited management. This concept was originally developed for use in mangrove ecosystems, and is understandably controversial, as it markedly diverges from other protection approaches that assign human use a minor priority or exclude it. However, the advantage of ED lies within the considered implementation of these designed ecosystems, thus preserving human benefits from potential later disturbances. Here, we outline the concept of ED in tropical carbonate depositional systems and discuss potential applications to aid ecosystem services such as beach nourishment and protection of coastlines and reef islands at risk from environmental and climate change, CO2 sequestration, food production, and tourism. Biological carbonate sediment production is a crucial source of stability of reef islands and reef-rimmed coastlines. Careful implementation of designed carbonate depositional ecosystems could help counterbalance sea-level rise and manage documented erosion effects of coastal constructions. Importantly, adhering to the core ethos of ED, careful dynamic assessments which provide a balanced approach to maximizing ecosystem services (e.g., carbonate production), should identify and avoid any potential damages to existing functioning ecosystems.