Signature Of Transition Research Articles

DDDR-18. SINGLE-CELL FUNCTIONAL GENOMIC ANALYSIS OF PHARMACOLOGIC RESPONSES IN NF1 MUTANT GLIOBLASTOMA REVEALS DISTINCT MECHANISMS OF ACTION FOR MEK AND SHP2 INHIBITION

Abstract BACKGROUND Glioblastomas harbor recurrent mutations in NF1 that activate Ras/Raf/MEK signaling, motivating pharmacologic approaches targeting downstream (MEK) or upstream (SHP2) of Ras signaling. However, the mechanisms underlying therapeutic response remain unclear. Here, we integrate genome wide CRISPRi screens and single cell sequencing in cell lines and mouse xenografts to identify functional genomic mechanisms underlying responses to the MEK inhibitor selumetinib or the SHP2 inhibitor RMC-4550. METHODS Human NF1 mutant GBM43 cells expressing CRISPRi machinery were used for CRISPRi screens with selumetinib or RMC-4550. Intracranial xenografts were established with GBM43 cells and treated with selumetinib or RMC-4550. Tumor growth kinetics were measured with bioluminescent imaging. RESULTS Genome-wide CRISPRi screens with selumetinib or RMC-4550 in NF1 mutant human GBM43 cells identified 39 genes (14 sensitivity, 25 resistance) mediating selumetinib response and 327 genes (51 sensitivity, 276 resistance) mediating RMC-4550 response. While both selumetinib and RMC-4550 hits were enriched for components of Ras/Raf/MEK, hits sensitizing RMC-4550 response were uniquely enriched for PI3K signaling and focal adhesion components while hits mediating resistance were enriched for cell cycle genes. In NF1 mutant GBM43, RMC-4550 significantly reduced tumor volume (p=0.02) while selumetinib did not. Single cell RNA-sequencing (scRNA-seq) analysis of 90,782 tumor cells from NF1 mutant GBM43 xenografts treated with selumetinib or RMC-4550 identified 12 clusters across all samples. RMC-4550, but not selumetinib, resulted in significant depletion of cells expressing an epithelial-mesenchymal transition (EMT) signature marked by expression of focal adhesion genes mediating RMC-4550 sensitivity, suggesting this signature comprises a distinct mechanism of action in response to RMC-4550 but not selumetinib. CONCLUSIONS In NF1 mutant glioblastoma in vitro and in vivo models, cellular response to both upstream (SHP2) and downstream (MEK) inhibition are mediated by Ras/Raf/MEK signaling while RMC-4550 alone uniquely regulates a focal adhesion network associated with EMT and demonstrates improved efficacy in vivo.

Measurement-induced entanglement and teleportation on a noisy quantum processor

Measurement has a special role in quantum theory1: by collapsing the wavefunction, it can enable phenomena such as teleportation2 and thereby alter the ‘arrow of time’ that constrains unitary evolution. When integrated in many-body dynamics, measurements can lead to emergent patterns of quantum information in space–time3–10 that go beyond the established paradigms for characterizing phases, either in or out of equilibrium11–13. For present-day noisy intermediate-scale quantum (NISQ) processors14, the experimental realization of such physics can be problematic because of hardware limitations and the stochastic nature of quantum measurement. Here we address these experimental challenges and study measurement-induced quantum information phases on up to 70 superconducting qubits. By leveraging the interchangeability of space and time, we use a duality mapping9,15–17 to avoid mid-circuit measurement and access different manifestations of the underlying phases, from entanglement scaling3,4 to measurement-induced teleportation18. We obtain finite-sized signatures of a phase transition with a decoding protocol that correlates the experimental measurement with classical simulation data. The phases display remarkably different sensitivity to noise, and we use this disparity to turn an inherent hardware limitation into a useful diagnostic. Our work demonstrates an approach to realizing measurement-induced physics at scales that are at the limits of current NISQ processors.

Uncertainties of critical temperatures based on higher-order fluctuations of the largest fragment charge* *Supported by the National Natural Science Foundation of China (11875328, 12075327), the Key Laboratory of Nuclear Data foundation (JCKY2022201C157), and the Fundamental Research Funds for the Central Universities, Sun Yat-sen University (22lgqb39)

The new signature of liquid-gas phase transition has been well indicated by the higher-order fluctuations of the largest fragment charge, but the uncertainties of critical temperatures based on this signature have not been revealed. This study extracts the critical temperatures of liquid-gas phase transition in nuclear reactions and investigates their uncertainties. Utilizing the isospin-dependent quantum molecular dynamics model in conjunction with the statistical model GEMINI enables us to describe the dynamical path from the initial to the final state. An isotope thermometer and a quantum fluctuation thermometer are employed to extract the nuclear temperature. The higher-order fluctuations of the largest fragment charge and critical temperatures are studied in 124Sn + 120Sn collisions ranging from 400 to 1000 MeV/nucleon and 124Sn + AZ collisions at 600 MeV/nucleon. Observations revealed that the pseudo-critical point is robustly indicated by the higher-order fluctuations of the largest fragment charge. The critical temperatures extracted by the isotope thermometer are relatively consistent, with an uncertainty of 15%, while those obtained by the quantum fluctuation thermometer are heavily influenced by the incident energy and mass number of target nuclei. The excitation energy and bound charge are used for event-sorting. These two ensembles represent the statistical properties of the initial and final states of the system, respectively. The initial-final correlations of statistical properties might lead to two phenomena. First, the size distribution of the largest fragment at the pseudo-critical point based on the ensemble is wide, while that based on ensemble exhibits bimodality, which is a typical characteristic in the liquid-gas coexistence of a finite system. Second, the temperature at the pseudo-critical point based on the ensemble is higher than that based on the ensemble. Furthermore, the projectile-like system exhibits a significant dynamical effect in its evolution path from the initial to final state, closely associated with the fluctuation of critical temperature.

Methanolic Extracts of D. viscosa Specifically Affect the Cytoskeleton and Exert an Antiproliferative Effect on Human Colorectal Cancer Cell Lines, According to Their Proliferation Rate.

Numerous studies have reported the pharmacological effects exhibited by Dittrichia viscosa, (D. viscosa) including antioxidant, cytotoxic, antiproliferative, and anticancer properties. In our research, our primary objective was to validate a prescreening methodology aimed at identifying the fraction that demonstrates the most potent antiproliferative and anticancer effects. Specifically, we investigated the impact of various extract fractions on the cytoskeleton using a screening method involving transgenic plants. Tumors are inherently heterogeneous, and the components of the cytoskeleton, particularly tubulin, are considered a strategic target for antitumor agents. To take heterogeneity into account, we used different lines of colorectal cancer, specifically one of the most common cancers regardless of gender. In patients with metastasis, the effectiveness of chemotherapy has been limited by severe side effects and by the development of resistance. Additional therapies and antiproliferative molecules are therefore needed. In our study, we used colon-like cell lines characterized by the expression of gastrointestinal differentiation markers (such as the HT-29 cell line) and undifferentiated cell lines showing the positive regulation of epithelial-mesenchymal transition and TGFβ signatures (such as the DLD-1, SW480, and SW620 cell lines). We showed that all three of the D. viscosa extract fractions have an antiproliferative effect but the pre-screening on transgenic plants anticipated that the methanolic fraction may be the most promising, targeting the cytoskeleton specifically and possibly resulting in fewer side effects. Here, we show that the preliminary use of screening in transgenic plants expressing subcellular markers can significantly reduce costs and focus the advanced characterization only on the most promising therapeutic molecules.

Single-cell transcriptomic analysis of gingivo-buccal oral cancer reveals two dominant cellular programs.

Oral squamous cell carcinoma of the gingivo-buccal region (OSCC-GB) is the most common cancer among men in India, and is associated with poor prognosis and frequent recurrence. Cellular heterogeneity in OSCC-GB was investigated by single-cell RNA sequencing of tumors derived from the oral cavity of 12 OSCC-GB patients, 3 of whom had concomitant presence of a precancerous lesion (oral submucous fibrosis [OSMF]). Unique malignant cell types, features, and phenotypic shifts in the stromal cell population were identified in oral tumors with associated submucous fibrosis. Expression levels of FOS, ATP1A, and DUSP1 provided robust discrimination between tumors with or without the concomitant presence of OSMF. Malignant cell populations shared between tumors with and without OSMF were enriched with the expression of partial epithelial-mesenchymal transition (pEMT) or fetal cell type signatures indicative of two dominant cellular programs in OSCC-GB-pEMT and fetal cellular reprogramming. Malignant cells exhibiting fetal cellular and pEMT programs were enriched with the expression of immune-related pathway genes known to be involved in antitumor immune response. In the tumor microenvironment, higher infiltration of immune cells than the stromal cells was observed. The T cell population was large in tumors and diverse subtypes of T cells with varying levels of infiltration were found. We also detected double-negative PLCG2+ T cells and cells with intermediate M1-M2 macrophage polarization. Our findings shed light on unique aspects of cellular heterogeneity and cell states in OSCC-GB.

Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants.

The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.

Order–disorder phase transition and elastic-to-plastic vortex creep crossover in a triclinic iron pnictide superconductor (Ca_{0.85}La_{0.15})_{10}(Pt_3As_8)(Fe_2As_2)_5

Vortex matter in layered high-T_c superconductors, including iron-pnictides, undergo several thermodynamic phase transitions due to the complex interplay of pinning energy, thermal energy and elastic energy. Moreover, the presence of anisotropy makes their vortex physics even more intriguing. Here, we report a detailed vortex dynamics study, using dc magnetization measurements, in a triclinic iron-pnictide superconductor (Ca_{0.85}La_{0.15})_{10}(Pt_3As_8)(Fe_2As_2)_5, with a superconducting transition temperature, T_csim 31 K. A second magnetization peak (SMP) feature is observed for magnetic field perpendicular (Hparallelc) and parallel (Hparallelab) to the crystal plane. However, its fundamental origin is quite different in both directions. For Hparallelc, the SMP can be well explained using an elastic-to-plastic vortex creep crossover, using collective creep theory. In addition, a possible rhombic-to-square vortex lattice phase transition is also observed for fields in between the onset-field and peak-field related to the SMP. On the other hand, for Hparallelab, a clear signature of an order-disorder vortex phase transition is observed in the isothermal M(H) measurements at Tge 6 K. The disordered phase exhibits the characteristics of entangled pinned vortex-liquid. We construct a comprehensive vortex phase diagram by displaying characteristic temperatures and magnetic fields for both crystal geometries in this unique superconducting compound. Our study sheds light on the intricate vortex dynamics and pinning in an iron-pnictide superconductor with triclinic symmetry.

An alternatively spliced PD-L1 isoform PD-L1∆3, and PD-L2 expression in breast cancers: implications for eligibility scoring and immunotherapy response.

Targeting PD-1/PD-L1 has shown substantial therapeutic response and unprecedented long-term durable responses in the clinic. However, several challenges persist, encompassing the prediction of treatment effectiveness and patient responses, the emergence of treatment resistance, and the necessity for additional biomarkers. Consequently, we comprehensively explored the often-overlooked isoforms of crucial immunotherapy players, leveraging transcriptomic analysis, structural modeling, and immunohistochemistry (IHC) data. Our investigation has led to the identification of an alternatively spliced isoform of PD-L1 that lacks exon 3 (PD-L1∆3) and the IgV domain required to interact with PD-1. PD-L1∆3 is expressed more than the canonical isoform in a subset of breast cancers and other TCGA tumors. Using the deep learning-based protein modeling tool AlphaFold2, we show the lack of a possible interaction between PD-L1∆3 and PD-1. In addition, we present data on the expression of an additional ligand for PD-1, PD-L2. PD-L2 expression is widespread and positively correlates with PD-L1 levels in breast and other tumors. We report enriched epithelial-mesenchymal transition (EMT) signature in high PD-L2 transcript expressing (PD-L2 > PD-L1) tumors in all breast cancer subtypes, highlighting potential crosstalk between EMT and immune evasion. Notably, the estrogen gene signature is downregulated in ER + breast tumors with high PD-L2. The data on PD-L2 IHC positivity but PD-L1 negativity in breast tumors, together with our results on PD-L1∆3, highlight the need to utilize PD-L2 and PD-L1 isoform-specific antibodies for staining patient tissue sections to offer a more precise prediction of the outcomes of PD-1/PD-L1 immunotherapy.

Intrinsic 1{T}^{{prime} } phase induced in atomically thin 2H-MoTe2 by a single terahertz pulse

The polymorphic transition from 2H to 1{T}^{{prime} }-MoTe2, which was thought to be induced by high-energy photon irradiation among many other means, has been intensely studied for its technological relevance in nanoscale transistors due to the remarkable improvement in electrical performance. However, it remains controversial whether a crystalline 1{T}^{{prime} } phase is produced because optical signatures of this putative transition are found to be associated with the formation of tellurium clusters instead. Here we demonstrate the creation of an intrinsic 1{T}^{{prime} } lattice after irradiating a mono- or few-layer 2H-MoTe2 with a single field-enhanced terahertz pulse. Unlike optical pulses, the low terahertz photon energy limits possible structural damages. We further develop a single-shot terahertz-pump-second-harmonic-probe technique and reveal a transition out of the 2H-phase within 10 ns after photoexcitation. Our results not only provide important insights to resolve the long-standing debate over the light-induced polymorphic transition in MoTe2 but also highlight the unique capability of strong-field terahertz pulses in manipulating quantum materials.

Abstract PO-092: Molecular characterization of the salivary adenoid cystic carcinoma tumor immune landscape by anatomic subsite

Abstract Introduction: Adenoid cystic carcinoma (AdCC) is typically indolent, however tends to behave more aggressively and present with perineural invasion and distant metastasis. Despite an improved understanding of AdCC pathobiology, the impact of anatomic tumor subsite (e.g., major versus minor salivary glands) on survival and response to treatment is relatively understudied. We recently discovered that submandibular AdCC’s exhibit unique differences in prognosis and treatment response to adjuvant radiotherapy. However, the impact of anatomic subsites on gene expression and immune cell composition, has not been investigated. Materials and methods: We used 4 publicly available AdCC molecular datasets (n = 37 AdCCs of different origin: 27 primary and 10 metastatic; 7 parotid (PG), 5 submandibular (SMG), 4 sublingual (SLG), 21 minor salivary gland (mG) and 21 normal salivary gland tissue samples). Data were harmonized between datasets using identical quantification procedures, followed by filtering and normalization performed simultaneously on the pooled data from all cohorts. Gene set enrichment analysis (GSEA) was performed Human Molecular Signatures Database (MSigDB) Hallmark and Oncologic signatures. Tumor immune microenvironment (TIME) decomposition was performed using a non-negative matrix factorization-based approach. GSEA and TIME differences between AdCC subsites were evaluated using Wilcoxon rank-sum and nonparametric equality-of-medians tests. Results: We identified different levels of enrichment for several key tumorigenic pathways between AdCCs arising within different anatomic subsites. Among AdCCs, major glands overexpressed the HALLMARK_SPERMATOGENESIS signature (parotid and sublingual glands), while the HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY (ROS) signature was significantly underexpressed in SMG AdCCs. In addition, the HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION (EMT) signature was significantly underexpressed in both SMG and PG AdCCs. These pathway signatures were not seen in control tissue comparison samples, indicating that these features are AdCC-specific. Additionally, TIME decomposition identified differences in CD4-T cell populations (minor > major gland AdCC) and natural killer (NK) cells (increased in PG and SLG). Meanwhile, normal control comparisons revealed a significant increase in plasma cells only within SM glands. Conclusions: AdCC subsites exhibit survival and treatment-response differences, and in this study demonstrate that these anatomical sites are associated with distinct molecular features. Specifically, these different anatomical sites vary in the expression of spermatogenesis, ROS, and EMT signature-related genes. Also, CD4-T and NK cell populations vary by anatomical site, suggesting that the SMG AdCC tumor-intrinsic pathway differences observed may be responsible for influencing the TIME composition and increased prognosis associated with these tumors following adjuvant radiotherapy. Validation with additional cohorts of primary AdCCs with accurate clinical annotation are required. Citation Format: Jason Tasoulas, Travis Schrank, Steven Johnson, Kimon Divaris, Stamatios Theocharis, Trevor Hackman, Siddharth Sheth, Kedar Kirtane, Juan Hernandez-Prera, Christine Chung, Wendell Gray Yarbrough, Natalia Issaeva, Antonio Amelio. Molecular characterization of the salivary adenoid cystic carcinoma tumor immune landscape by anatomic subsite [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr PO-092.

Spontaneous Raman scattering from vibrational polaritons is obscured by reservoir states.

Vibrational strong coupling results from the interaction between optically allowed molecular vibrational excitations and the resonant mode of an infrared cavity. Strong coupling leads to the formation of hybrid states, known as vibrational polaritons, which are readily observed in transmission measurements and a manifold of the reservoir states. In contrast, Raman spectroscopy of vibrational polaritons is elusive and has recently been the focus of both theoretical and experimental investigations. Because Raman measurements are frequently performed with high-numerical aperture excitation/collection optics, the angular dispersion of the strongly coupled system must be carefully considered. Herein, we experimentally investigated vibrational polaritons involving dispersive collective lattice resonances of infrared antenna arrays. Despite clear indications of the strong coupling to vibrational excitations in the transmission spectrum; we found that Raman spectra do not bear signatures of the polaritonic transitions. Detailed measurements indicate that the disappearance of the Raman signal is not due to the polariton dispersion in our samples. On the other hand, the Tavis-Cummings-Holstein model that we employed to interpret our results suggests that the ratio of the Raman transition strengths between the reservoir and the polariton states scales according to the number of strongly coupled molecules. Because the vibrational transitions are relatively weak, the number of molecules required to achieve strong coupling conditions is about 109 per unit cell of the array of infrared antennas. Therefore, the scaling predicted by the Tavis-Cummings-Holstein model can explain the absence of the polariton signatures in spontaneous Raman scattering experiments.

Pairing Superfluid–Insulator Transition Induced by Atom–Molecule Conversion in Bosonic Mixtures in Optical Lattice

Motivated by the recent experiment on bosonic mixtures of atoms and molecules, we investigate pairing superfluid–insulator (SI) transition for bosonic mixtures of atoms and molecules in a one-dimensional optical lattice, which is described by an extended Bose–Hubbard model with atom–molecule conservation (AMC). It is found that AMC can induce an extra pair–superfluid phase though the system does not demonstrate pair-hopping. In particular, the system may undergo several pairing SI or insulator–superfluid transitions as the detuning from the Feshbach resonance is varied from negative to positive, and the larger positive detuning can bifurcate the pair–superfluid phases into mixed superfluid phases consisting of single-atomic and pair-atomic superfluid. The calculation of the second-order Rényi entropy reveals that the discontinuity in its first-order derivative corresponds to the phase boundary of the pairing SI transition. This means that the residual entanglement in our mean-field treatment can be used to efficiently capture the signature of the pairing SI transition induced by AMC.

Signature of transition in granular flow through apertures

We employ computations to examine transition in granular flow, right above an aperture, in a silo draining under gravity. We show that the energy dissipation rate exhibits a well-defined peak near the aperture. Tracing locations of maximum dissipation rate describes an arch, signifying flow transition. We present a correlation between the transition boundary and outlet using the arguments of self-similarity and geometric similarity, suggesting the spatial non-monotonicity of the dissipation rate to be a signature of flow transition. Utilizing the aforementioned similarity criteria, we also explore the kinetic pressure as a marker of transition in granular flow.

Spatial whole transcriptome profiling of primary tumor from patients with metastatic prostate cancer.

Prostate cancer (PCa) is a highly heterogeneous disease in terms of its molecular makeup and clinical prognosis. The prostate tumor microenvironment (TME) is hypothesized to play an important role in driving disease aggressiveness, but precise mechanisms remain elusive. In our study, we used spatial transcriptomics to explore for the first time the spatial gene expression heterogeneity within primary prostate tumors from patients with metastatic disease. In total, we analyzed 5459 tissue spots from three PCa patients comprising castration-resistant (CRPC) and neuroendocrine (NEPC) disease stages. Within CRPC, we identified a T cell cluster whose activity might be impaired by nearby regulatory T cells, potentially mediating the aggressive disease phenotype. Moreover, we identified Hallmark signatures of epithelial-mesenchymal transition in a cancer-associated fibroblast (CAF) cluster, indicating the aggressive characteristic of the primary TME leading to metastatic dissemination. Within NEPC, we identified active immune-stroma cross-talk exemplified by significant ligand-receptor interactions between CAFs and M2 macrophages. Further, we identified a malignant cell population that was associated with the down-regulation of an immune-related gene signature. Lower expression of this signature was associated with higher levels of genomic instability in advanced PCa patients (SU2C cohort, n = 99) and poor recurrence free survival in early-stage PCa patients (TCGA cohort, n = 395), suggesting prognostic biomarker potential. Taken together, our study reveals the importance of whole transcriptome profiling at spatial resolution for biomarker discovery and for advancing our understanding of tumor biology.

SEM1 promotes tumor progression of glioblastoma via activating the akt signaling pathway

IntroductionSEM1, a 26 S proteasome complex subunit, is an essential regulator of tumor growth. However, the underlying mechanism of SEM1 mediated glioma progression remains to be elucidated. MethodsData from bulk-tumor, single-cell, and spatial sequencing were analyzed to reveal correlations between SEM1 and clinical traits, cell types, and functional enrichment in gliomas. Immunohistochemistry was used to assess SEM1 expression. MTT, flow cytometry, apoptosis signature, epithelial–mesenchymal transition signature, Transwell, and organoid assays were used to study SEM1's effect on the malignant behavior of glioma (U251 and LN229) cells. Weighted gene co-expression network analysis (WGCNA) was conducted to construct an SEM1-mediated malignant regulatory network. Accordingly, survival analysis, therapeutic response, drug prediction, and molecular docking analyses were performed. ResultsHigh SEM1 expression was observed in gliomas and correlated with worse clinical features and prognosis. Moreover, SEM1 is mainly localized in malignant cells (glioma cells). SEM1 knockout inhibited the proliferation, invasion, and migration of glioma cells and promoted their apoptosis. We also constructed an SEM1 malignant regulatory network that was bridged by the PI3K-Akt pathway. The network had a high prognostic value. Finally, drugs potentially targeting SEM1 were screened and docked to SEM1. ConclusionsSEM1 is critically involved in the proliferation, apoptosis, invasion, and migration of glioma cells. The SEM1 malignant regulatory network shows high significance for the prognosis and treatment of gliomas.

Z-Scaling: Search for Signatures of Phase Transition in Nuclear Matter

z-Scaling: Search for Signatures of Phase Transition in Nuclear Matter

Longitudinal immune monitoring of patients with resectable esophageal adenocarcinoma treated with Neoadjuvant PD-L1 checkpoint inhibition

ABSTRACT The analysis of peripheral blood mononuclear cells (PBMCs) by flow cytometry holds promise as a platform for immune checkpoint inhibition (ICI) biomarker identification. Our aim was to characterize the systemic immune compartment in resectable esophageal adenocarcinoma patients treated with neoadjuvant ICI therapy. In total, 24 patients treated with neoadjuvant chemoradiotherapy (nCRT) and anti-PD-L1 (atezolizumab) from the PERFECT study (NCT03087864) were included and 26 patients from a previously published nCRT cohort. Blood samples were collected at baseline, on-treatment, before and after surgery. Response groups for comparison were defined as pathological complete responders (pCR) or patients with pathological residual disease (non-pCR). Based on multicolor flow cytometry of PBMCs, an immunosuppressive phenotype was observed in the non-pCR group of the PERFECT cohort, characterized by a higher percentage of regulatory T cells (Tregs), intermediate monocytes, and a lower percentage of type-2 conventional dendritic cells. A further increase in activated Tregs was observed in non-pCR patients on-treatment. These findings were not associated with a poor response in the nCRT cohort. At baseline, immunosuppressive cytokines were elevated in the non-pCR group of the PERFECT study. The suppressive subsets correlated at baseline with a Wnt/β-Catenin gene expression signature and on-treatment with epithelial–mesenchymal transition and angiogenesis signatures from tumor biopsies. After surgery monocyte activation (CD40), low CD8+Ki67+ T cell rates, and the enrichment of CD206+ monocytes were related to early recurrence. These findings highlight systemic barriers to effective ICI and the need for optimized treatment regimens.

Spectral signatures of symmetry-breaking dynamical phase transitions.

Large deviation theory provides the framework to study the probability of rare fluctuations of time-averaged observables, opening new avenues of research in nonequilibrium physics. Some of the most appealing results within this context are dynamical phase transitions (DPTs), which might occur at the level of trajectories in order to maximize the probability of sustaining a rare event. While macroscopic fluctuation theory has underpinned much recent progress on the understanding of symmetry-breaking DPTs in driven diffusive systems, their microscopic characterization is still challenging. In this work we shed light on the general spectral mechanism giving rise to continuous DPTs not only for driven diffusive systems, but for any jump process in which a discrete Z_{n} symmetry is broken. By means of a symmetry-aided spectral analysis of the Doob-transformed dynamics, we provide the conditions whereby symmetry-breaking DPTs might emerge and how the different dynamical phases arise from the specific structure of the degenerate eigenvectors. In particular, we show explicitly how all symmetry-breaking features are encoded in the subleading eigenvectors of the degenerate subspace. Moreover, by partitioning configuration space into equivalence classes according to a proper order parameter, we achieve a substantial dimensional reduction which allows for the quantitative characterization of the spectral fingerprints of DPTs. We illustrate our predictions in several paradigmatic many-body systems, including (1) the one-dimensional boundary-driven weakly asymmetric exclusion process (WASEP), which exhibits a particle-hole symmetry-breaking DPT for current fluctuations, (2) the three- and four-state Potts model for spin dynamics, which displays discrete rotational symmetry-breaking DPTs for energy fluctuations, and (3) the closed WASEP which presents a continuous symmetry-breaking DPT into a time-crystal phase characterized by a rotating condensate.

Expanding the inventory of spectral lines used to trace atmospheric escape in exoplanets

Escaping exoplanet atmospheres have been observed as deep transit signatures in a few specific spectral lines. Detections have been made in the hydrogen Ly-αline, the metastable helium line at 10 830 Å, and some UV lines of metallic species. Observational challenges, unexpected nondetections, and model degeneracies have generally made it difficult to draw definitive conclusions about the escape process for individual planets. Expanding on the suite of spectral tracers used may help to mitigate these challenges. We present a new framework for modeling the transmission spectrum of hydrodynamically escaping atmospheres. We predict far UV to near infrared spectra for systems with different planet and stellar types and identify new lines that can potentially be used to study their upper atmospheres. Measuring the radius in the atmosphere at which the strongest lines form puts them into context within the upper atmospheric structure. Targeting a set of complementary spectral lines for the same planet will help us to better constrain the outflow properties.

MiR-146a-5p deficiency in extracellular vesicles of glioma-associated macrophages promotes epithelial-mesenchymal transition through the NF-κB signaling pathway

Glioma-associated macrophages (GAMs) are pivotal chains in the tumor immune microenvironment (TIME). GAMs mostly display M2-like phenotypes with anti-inflammatory features related to the malignancy and progression of cancers. Extracellular vesicles derived from immunosuppressive GAMs (M2-EVs), the essential components of the TIME, greatly impact the malignant behavior of GBM cells. M1- or M2-EVs were isolated in vitro, and human GBM cell invasion and migration were reinforced under M2-EV treatment. Signatures of the epithelial-mesenchymal transition (EMT) were also enhanced by M2-EVs. Compared with M1-EVs, miR-146a-5p, considered the key factor in TIME regulation, was deficient in M2-EVs according to miRNA-sequencing. When the miR-146a-5p mimic was added, EMT signatures and the invasive and migratory abilities of GBM cells were correspondingly weakened. Public databases predicted the miRNA binding targets and interleukin 1 receptor-associated kinase 1 (IRAK1) and tumor necrosis factor receptor-associated factor 6 (TRAF6) were screened as miR-146a-5p binding genes. Bimolecular fluorescent complementation and coimmunoprecipitation confirmed interactions between TRAF6 and IRAK1. The correlation between TRAF6 and IRAK1 was evaluated with immunofluorescence (IF)-stained clinical glioma samples. The TRAF6-IRAK1 complex is the switch and the brake that modulates IKK complex phosphorylation and NF-κB pathway activation, as well as the EMT behaviors of GBM cells. Furthermore, a homograft nude mouse model was explored and mice transplanted with TRAF6/IRAK1-overexpressing glioma cells had shorter survival times while mice transplanted with glioma cells with miR-146a-5p overexpression or TRAF6/IRAK1 knockdown lived longer. This work indicated that in the TIME of GBM, the deficiency of miR-146a-5p in M2-EVs enhances tumor EMT through disinhibition of the TRAF6-IRAK1 complex and IKK-dependent NF-κB signaling pathway providing a novel therapeutic strategy targeting the TIME of GBM.