LRIG1 engages ligand VISTA and impairs tumor-specific CD8+ T cell responses.

Immune checkpoint blockade is a promising approach to activate antitumor immunity and improve the survival of patients with cancer. V-domain immunoglobulin suppressor of T cell activation (VISTA) is an immune checkpoint target; however, the downstream signaling mechanisms are elusive. Here, we identify leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) as a VISTA binding partner, which acts as an inhibitory receptor by engaging VISTA and suppressing T cell receptor signaling pathways. Mice with T cell-specific LRIG1 deletion developed superior antitumor responses because of expansion of tumor-specific cytotoxic T lymphocytes (CTLs) with increased effector function and survival. Sustained tumor control was associated with a reduction of quiescent CTLs (TCF1+ CD62Lhi PD-1low) and a reciprocal increase in progenitor and memory-like CTLs (TCF1+ PD-1+). In patients with melanoma, elevated LRIG1 expression on tumor-infiltrating CD8+ CTLs correlated with resistance to immunotherapies. These results delineate the role of LRIG1 as an inhibitory immune checkpoint receptor and propose a rationale for targeting the VISTA/LRIG1 axis for cancer immunotherapy.

VISTA promotes the metabolism and differentiation of myeloid-derived suppressor cells by STAT3 and polyamine-dependent mechanisms.

Myeloid-derived suppressor cells (MDSCs) impair antitumor immune responses. Identifying regulatory circuits during MDSC development may bring new opportunities for therapeutic interventions. We report that the V-domain suppressor of T cell activation (VISTA) functions as a key enabler of MDSC differentiation. VISTA deficiency reduced STAT3 activation and STAT3-dependent production of polyamines, which causally impaired mitochondrial respiration and MDSC expansion. In both mixed bone marrow (BM) chimera mice and myeloid-specific VISTA conditional knockout mice, VISTA deficiency significantly reduced tumor-associated MDSCs but expanded monocyte-derived dendritic cells (DCs) and enhanced T cell-mediated tumor control. Correlated expression of VISTA and arginase-1 (ARG1), a key enzyme supporting polyamine biosynthesis, was observed in multiple human cancer types. In human endometrial cancer, co-expression of VISTA and ARG1 on tumor-associated myeloid cells is associated with poor survival. Taken together, these findings unveil the VISTA/polyamine axis as a central regulator of MDSC differentiation and warrant therapeutically targeting this axis for cancer immunotherapy.

Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis.

Transcription factors (TFs) bind combinatorially to genomic cis-regulatory elements (cREs), orchestrating transcription programs. While studies of chromatin state and chromosomal interactions have revealed dynamic neurodevelopmental cRE landscapes, parallel understanding of the underlying TF binding lags. To elucidate the combinatorial TF-cRE interactions driving mouse basal ganglia development, we integrated ChIP-seq for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and transcriptional state, and transgenic enhancer assays. We identified TF-cREs modules with distinct chromatin features and enhancer activity that have complementary roles driving GABAergic neurogenesis and suppressing other developmental fates. While the majority of distal cREs were bound by one or two TFs, a small proportion were extensively bound, and these enhancers also exhibited exceptional evolutionary conservation, motif density, and complex chromosomal interactions. Our results provide new insights into how modules of combinatorial TF-cRE interactions activate and repress developmental expression programs and demonstrate the value of TF binding data in modeling gene regulatory wiring.

The Impact of the Initial Clinical Presentation of Bladder Cancer on Histopathological and Morphological Tumor Characteristics.

This study investigated the impact of the initial clinical presentation of bladder cancer on tumor characteristics. A cross-sectional, retrospective study was performed, and it involved 515 patients who underwent transurethral bladder cancer resection at the University Hospital Center Split between April 2019 and April 2023, excluding recurrent cases. The association between symptomatic versus asymptomatic presentation and bladder cancer characteristics was analyzed. A subgroup analysis compared tumor characteristics between patients with gross and microscopic hematuria. Multiple regression analyses revealed a significant association between symptomatic presentation and the detection of high-grade bladder cancer (OR 3.43, 95% CI 2.22-5.29, p < 0.001), concomitant CIS (OR 3.41, 95% CI 1.31-8.88, p = 0.012), T2 stage bladder cancer (OR 5.79, 95% CI 2.45-13.71, p < 0.001), a higher number of tumors (IRR 1.24, 95% CI 1.07-1.45, p = 0.005), and larger tumor size (B 1.68, 95% CI 1.19-2.18, p < 0.001). In the subgroup analysis, gross hematuria was associated with the detection of high-grade bladder cancer (OR 2.07, 95% CI 1.12-3.84, p = 0.020), T2 stage bladder cancer (OR 6.03, 95% CI 1.42-25.49, p = 0.015), and larger tumor size (B 1.8, 95% CI 0.99-2.6, p < 0.001). The identified associations between symptomatic presentation and unfavorable bladder cancer characteristics, likely attributed to early detection in asymptomatic cases, underscore the importance of additional research in the development of bladder cancer screening strategies.

VENOUS THROMBOEMBOLISM IN THE EMERGENCY DEPARTMENT - SINGLE-CENTER EXPERIENCE.

Given the importance of early recognition of acute venous thromboembolism (VTE) and the nonspecificity of its symptoms and signs, it is essential to follow the guidelines for diagnostic and therapeutic decisions. Ultrasound examination of the entire lower extremity is currently the standard diagnostic method for symptomatic patients with a clinical probability of deep vein thrombosis (DVT) according to the Wells scoring system. The aim of this study is to show the demographic structure and analyze the number of patients in the emergency department with suspected venous thrombosis. In the past 10 years, 2,022 patients with DVT and 686 with pulmonary emboli have been diagnosed. Despite adherence to the diagnostic protocol, nearly two-thirds of patients require early ultrasound diagnosis. One-fifth of patients had thrombosis of the superficial venous system of the leg or arm. Thrombus was present in the veins of the lower leg in 37% of patients with DVT. The presence of thrombi above the knee, involving the deep femoropopliteal venous system, was found in as much as one-third of patients. These findings and current guidelines suggest that there is a paradigm shift toward more frequent use of DOAC in patients with DVT. However, greater educational efforts may be needed for many physicians to become comfortable with the use of DOAC in the outpatient management of patient populations at low risk for pulmonary embolism.

Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity.

Defects in pathways governing genomic fidelity have been linked to improved response to immune checkpoint blockade therapy (ICB). Pathogenic POLE/POLD1 mutations can cause hypermutation, yet how diverse mutations in POLE/POLD1 influence antitumor immunity following ICB is unclear. Here, we comprehensively determined the effect of POLE/POLD1 mutations in ICB and elucidated the mechanistic impact of these mutations on tumor immunity. Murine syngeneic tumors harboring Pole/Pold1 functional mutations displayed enhanced antitumor immunity and were sensitive to ICB. Patients with POLE/POLD1 mutated tumors harboring telltale mutational signatures respond better to ICB than patients harboring wild-type or signature-negative tumors. A mutant POLE/D1 function-associated signature-based model outperformed several traditional approaches for identifying POLE/POLD1 mutated patients that benefit from ICB. Strikingly, the spectrum of mutational signatures correlates with the biochemical features of neoantigens. Alterations that cause POLE/POLD1 function-associated signatures generate T cell receptor (TCR)-contact residues with increased hydrophobicity, potentially facilitating T cell recognition. Altogether, the functional landscapes of POLE/POLD1 mutations shape immunotherapy efficacy.

Transcriptional network orchestrating regional patterning of cortical progenitors.

We uncovered a transcription factor (TF) network that regulates cortical regional patterning in radial glial stem cells. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (Emx2, Nr2f1, and Pax6), which enabled us to define a cortical regionalization TF network (CRTFN). To identify genomic programming underlying this network, we performed TF ChIP-seq and chromatin-looping conformation to identify enhancer-gene interactions. To map enhancers involved in regional patterning of cortical progenitors, we performed assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach has identified a CRTFN and VZ enhancers involved in cortical regional patterning in the mouse.

Resilience and Quality of Life of Patients with Breast Cancer.

INTRODUCTION: Breast cancer is the most common malignancy in women. Modern research attempts to investigate the relationship between psychoemotional parameters and the length of survival of breast cancer patients. Understanding the factors which affect a higher level of resilience can have important clinical implications and can represent a guiding principle for designing psychological interventions that would accelerate recovery and improve the quality of life of cancer patients. To explore the relationship between resilience and quality of life of women with breast cancer. METHODS: The study was conducted at the Clinic of Oncology of the University Clinical Hospital Mostar, which included 60 subjects. Objective realization was achieved through using the socio-demographic questionnaire purposely made for this research, the quality of life questionnaire WHQOL-BREF and the psychological resilience questionnaire CD-RISC-25. RESULTS: Subjects treated with radiotherapy achieved statistically significantly higher scores on subscales of the quality of life: mental health, social relations, and the environment. No statistically significant correlations were found between the level of resilience and results in the domains of quality of life. CONCLUSION: There is not a statistically significant association between resilience levels and quality of life in patients with breast cancer.

Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).

Proximity ligation-assisted ChIP-Seq (PLAC-Seq), also known as HiChIP, is a method to detect and quantify chromatin contacts anchored at genomic regions bound by specific proteins or histone modifications. By combining in situ Hi-C and chromatin immunoprecipitation (ChIP) using antibodies against transcription factors (TFs) or histone marks of interest, the method achieves targeted interrogation of chromatin organization at a subset of genomic regions. PLAC-Seq is able to identify long-range chromatin interactions at kilobase-scale resolution with significantly reduced sequencing cost.

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.

Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.

Papillary thyroid carcinoma in a hyper-functional thyroid nodule.

The authors reported the case of 69 years old woman presented with subclinical hyperthyroidism. 99m-Tc pertechnetate scan showed the abnormal focus of hot uptake in the left lobe, suggestive of a hyperfunctioning toxic thyroid nodule. Surgical treatment was advised because of the size of the nodule as a more applicable solution. Histological findings showed papillary thyroid carcinoma.

Influence of the Interlayer Temperature on Structure and Properties of Wire and Arc Additive Manufactured Duplex Stainless Steel Product.

WAAM (wire and arc additive manufacturing) is becoming an increasingly popular method to produce components from metals, which are usually not so suitable for conventional production methods. One of the good examples is duplex stainless steels (DSSs), which are quite complex for welding and machining. Excessive ferrite amount is a common problem for them and controlling an interlayer temperature could offer a solution. However, using too low interlayer temperature will slow down the whole process and compromise one of the WAAM's main advantages-the high productivity. The aim of this study is to find the relationship between interlayer temperature and process duration and to determine the influence of the interlayer temperature on product structure and other properties. Three samples (walls) were made using different interlayer temperatures (50 °C, 100 °C and 150 °C) and they were tested to analyze their surface texture, chemical composition, ferrite amount, the appearance of porosity and the hardness. Ferrite amount was higher and there was more porosity on lower interlayer temperatures, while there is no significant difference between surface texture and chemical composition for the samples. Considering the fact that higher interlayer temperatures provide a faster process, they should be preferred to produce duplex stainless steel products.

Cell-type-specific 3D epigenomes in the developing human cortex.

Lineage-specific epigenomic changes during human corticogenesis have been difficult to study owing to challenges with sample availability and tissue heterogeneity. For example, previous studies using single-cell RNA sequencing identified at least 9 major cell types and up to 26 distinct subtypes in the dorsal cortex alone1,2. Here we characterize cell-type-specific cis-regulatory chromatin interactions, open chromatin peaks, and transcriptomes for radial glia, intermediate progenitor cells, excitatory neurons, and interneurons isolated from mid-gestational samples of the human cortex. We show that chromatin interactions underlie several aspects of gene regulation, with transposable elements and disease-associated variants enriched at distal interacting regions in a cell-type-specific manner. In addition, promoters with increased levels of chromatin interactivity-termed super-interactive promoters-are enriched for lineage-specific genes, suggesting that interactions at these loci contribute to the fine-tuning of transcription. Finally, we develop CRISPRview, a technique that integrates immunostaining, CRISPR interference, RNAscope, and image analysis to validate cell-type-specific cis-regulatory elements in heterogeneous populations of primary cells. Our findings provide insights into cell-type-specific gene expression patterns in the developing human cortex and advance our understanding of gene regulation and lineage specification during this crucial developmental window.

The Positive Effects of Running on Mental Health.

Working as a team with patients who are also recreational runners and managing a running school in the City of Mostar had made us thinking on how recreational running affects the mental health in individuals. Previous literature is pretty old dated, so we found this even more interesting. We have wondered why there is no more recent literature on this subject. So, while working on this mini review and discussing on this subjects we came up with an idea on a research about self esteem and life quality of individuals pre and post running school experience. Previous studies show that consistent running results in a number of positive psychological changes among diverse populations. In a study of Kenneth E.C. ordinary nonprofessional runners were surveyed about the psychological aspects of running. Many of the respondents had started running to improve their health, and almost all noted mental and emotional benefits including relief of tension, improved self-image, and better mood. Considering therapeutic effects of running Greist et al. define running as not expensive, and unlike sorne other treatments, it has beneficiai physical side effects. Their results compare favorably with those of patients in psychotherapy and have persisted for at !east one year in follow-up. Taking in mind all of the previously published research it can be concluded that running can be a therapeutic tool for a sereies of negative psychological conditions, such ass depression, anxieta, tension, mood changes, low self esteem etc. Although, these research are a few decades old there is still no recipe or dosage for running, especially in the area of physical ilness prevention. There is much to research and to be discovered in this field.

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome.

Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type-specific gene regulatory programs in complex tissues by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain.

Computational modelling predicts substantial carbon assimilation gains for C3 plants with a single-celled C4 biochemical pump.

Achieving global food security for the estimated 9 billion people by 2050 is a major scientific challenge. Crop productivity is fundamentally restricted by the rate of fixation of atmospheric carbon. The dedicated enzyme, RubisCO, has a low turnover and poor specificity for CO2. This limitation of C3 photosynthesis (the basic carbon-assimilation pathway present in all plants) is alleviated in some lineages by use of carbon-concentrating-mechanisms, such as the C4 cycle-a biochemical pump that concentrates CO2 near RubisCO increasing assimilation efficacy. Most crops use only C3 photosynthesis, so one promising research strategy to boost their productivity focuses on introducing a C4 cycle. The simplest proposal is to use the cycle to concentrate CO2 inside individual chloroplasts. The photosynthetic efficiency would then depend on the leakage of CO2 out of a chloroplast. We examine this proposal with a 3D spatial model of carbon and oxygen diffusion and C4 photosynthetic biochemistry inside a typical C3-plant mesophyll cell geometry. We find that the cost-efficiency of C4 photosynthesis depends on the gas permeability of the chloroplast envelope, the C4 pathway having higher quantum efficiency than C3 for permeabilities below 300 µm/s. However, at higher permeabilities the C4 pathway still provides a substantial boost to carbon assimilation with only a moderate decrease in efficiency. The gains would be capped by the ability of chloroplasts to harvest light, but even under realistic light regimes a 100% boost to carbon assimilation is possible. This could be achieved in conjunction with lower investment in chloroplasts if their cell surface coverage is also reduced. Incorporation of this C4 cycle into C3 crops could thus promote higher growth rates and better drought resistance in dry, high-sunlight climates.

Giant infrapatellar ganglion cyst of Hoffa's fat pad.

We present the case of a 36-year-old woman who works as a kindergarten teacher, often she is kneeling on her knees due to the nature of the job. Since a year ago, she noticed that her right knee was swelling. She had an orthopaedic examination when she could no longer bend her knee. Inspection and palpation revealed the swelling of the anterior and anterior-lateral aspect of the knee. MRI imaging revealed a large, sharply defined, lobulated lesion of the infrapatellar fat pad. After the surgical incision, a lobular lesion was found and surgically removed. Histological analysis confirmed a ganglion cyst.

Sensory experience remodels genome architecture in neural circuit to drive motor learning.

Neuronal-activity-dependent transcription couples sensory experience to adaptive responses of the brain including learning and memory. Mechanisms of activity-dependent gene expression including alterations of the epigenome have been characterized1-8. However, the fundamental question of whether sensory experience remodels chromatin architecture in the adult brain in vivo to induce neural code transformations and learning and memory remains to be addressed. Here we use in vivo calcium imaging, optogenetics and pharmacological approaches to show that granule neuron activation in the anterior dorsal cerebellar vermis has a crucial role in a delay tactile startle learning paradigm in mice. Of note, using large-scale transcriptome and chromatin profiling, we show that activation of the motor-learning-linked granule neuron circuit reorganizes neuronal chromatin including through long-distance enhancer-promoter and transcriptionally active compartment interactions to orchestrate distinct granule neuron gene expression modules. Conditional CRISPR knockout of the chromatin architecture regulator cohesin in anterior dorsal cerebellar vermis granule neurons in adult mice disrupts enhancer-promoter interactions, activity-dependent transcription and motor learning. These findings define how sensory experience patterns chromatin architecture and neural circuit coding in the brain to drive motor learning.

Publisher Correction: Sensory experience remodels genome architecture in neural circuit to drive motor learning.

In this Letter, '≥' should be '≤' in the sentence: "Intra-chromosomal reads were further split into short-range reads (≥1 kb) and long-range reads (>1 kb)". This error has been corrected online.An amendment to this paper has been published and can be accessed via a link at the top of the paper.

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.

Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in the analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.