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Lactate-driven metabolic reprogramming and histone lactylation play pivotal roles in bladder cancer (BLCA) progression, yet their underlying mechanisms and regulatory genes remain poorly understood. Using transcriptomic data from The Cancer Genome Atlas (TCGA), we identified lactylation-associated genes and constructed a prognostic signature. Comprehensive bioinformatics analyses were conducted to assess immune infiltration, tumor microenvironment characteristics, and the lactylation landscape at the single-cell level. Furthermore, we performed experiments to evaluate the biological functions of key lactylation-related genes in BLCA cells. Six lactylation-related hub genes were identified, among which FASN and RUNX2 were significantly upregulated in BLCA and associated with poor prognosis. Single-cell analyses revealed elevated lactylation signatures in tumor epithelial and immune cells. Knockdown of FASN or RUNX2 in BLCA cell lines significantly suppressed cell proliferation, induced apoptosis, and reduced intracellular lactate levels. Correspondingly, global protein lactylation was diminished, with dominant modification signals observed around 40 kDa, indicating a potential set of non-histone proteins as key functional targets. Our study highlights a metabolic-enzymatic axis wherein FASN and RUNX2 regulate lactate-driven protein lactylation in BLCA. These findings provide new insights into the non-histone functions of lactylation and suggest potential therapeutic targets at the intersection of metabolism and tumor immunity.

Background Knee osteoarthritis is a debilitating disease with a complex pathogenesis. Synovitis, which refers to inflammation of the synovial membrane surrounding the joint, is believed to play an important role in the development and progression of knee osteoarthritis. To better understand the molecular mechanisms underlying knee osteoarthritis, we conducted a comprehensive analysis of gene expression in knee osteoarthritis synovium using machine learning. Methods Differentially expressed genes between knee osteoarthritis and control synovial tissues were analyzed using the GSE55235 dataset. We employed several machine learning algorithms, including least absolute shrinkage and selection operator and support vector machine–recursive feature elimination, to screen for key genes. Then, we validated the key genes using an external dataset (GSE51588) and an in vitro knee osteoarthritis animal model. CIBERSORT was used to compare immune cell infiltration levels between knee osteoarthritis and control synovial tissues and determine their relationship with the key genes. Finally, we performed a Connectivity Map analysis to screen for potential small-molecule compounds. Moreover, we conducted single-cell RNA sequencing analysis using knee joint tissues to annotate different subtypes of cells. Results A total of 930 differentially expressed genes were identified. Least absolute shrinkage and selection operator regression and support vector machine–recursive feature elimination identified FOSL2 and RHoBTB1 as key genes. The expression levels of both genes were further validated in the GSE51588 dataset as well as verified through an in vitro experiment involving a knee osteoarthritis mouse model. Multiple significant correlation pairs were found between the immune cell infiltration levels. We unveiled the genetic basis of knee osteoarthritis using genome-wide association study and specific signaling pathways through gene set enrichment analysis. The GeneCards database was used to obtain 3032 pathogenic genes associated with knee osteoarthritis, and we found that RHoBTB1 expression was significantly negatively correlated and FOSL2 expression was significantly positively correlated with interleukin-1β expression. We predicted several small-molecule compounds based on Connectivity Map analysis. Finally, single-cell RNA sequencing analysis revealed the expression levels of the two key genes in chondrocytes and tissue stem cells. Conclusion FOSL2 and RHoBTB1 may play key roles in the pathogenesis of knee osteoarthritis, exhibiting correlations with immune cell infiltration levels. These findings indicate that these genes have potential as therapeutic targets. However, further research and validation are necessary to confirm their exact roles and therapeutic potential in knee osteoarthritis.

Prolonged exposure to microbial products such as lipopolysaccharide can induce a form of innate immune memory that blunts subsequent responses to unrelated pathogens, known as lipopolysaccharide tolerance. Sepsis is a dysregulated systemic immune response to disseminated infection that has a high mortality rate. In some patients, sepsis results in a period of immunosuppression (known as ‘immunoparalysis’) 1 characterized by reduced inflammatory cytokine output 2 , increased secondary infection 3 and an increased risk of organ failure and mortality 4 . Lipopolysaccharide tolerance recapitulates several key features of sepsis-associated immunosuppression 5 . Although various epigenetic changes have previously been observed in tolerized macrophages 6 – 8 , the molecular basis of tolerance, immunoparalysis and other forms of innate immune memory has remained unclear. Here we perform a screen for tolerance-associated microRNAs and identify miR-221 and miR-222 as regulators of the functional reprogramming of macrophages during lipopolysaccharide tolerization. Prolonged stimulation with lipopolysaccharide in mice leads to increased expression of miR-221 and mir-222, both of which regulate brahma-related gene 1 ( Brg1 , also known as Smarca4 ). This increased expression causes the transcriptional silencing of a subset of inflammatory genes that depend on chromatin remodelling mediated by SWI/SNF (switch/sucrose non-fermentable) and STAT (signal transducer and activator of transcription), which in turn promotes tolerance. In patients with sepsis, increased expression of miR-221 and miR-222 correlates with immunoparalysis and increased organ damage. Our results show that specific microRNAs can regulate macrophage tolerization and may serve as biomarkers of immunoparalysis and poor prognosis in patients with sepsis. The microRNAs miR-221 and miR-222 regulate the reprogramming of macrophages during the development of lipopolysaccharide tolerance, and increased expression of these microRNAs is associated with immunosuppression and poor prognosis in patients with sepsis.

T cell quiescence and tolerance restrain the immune system from becoming overactive and attacking healthy tissue. Negative checkpoint regulators normally limit T cell responses to help safeguard against conditions such as autoimmunity. ElTanbouly et al. report that the checkpoint regulator VISTA (V-type immunoglobulin domain-containing suppressor of T cell activation) restricts early stages of T cell activation by shaping the inherent heterogeneity of the naïve CD4 + T cell compartment to one that is more uniformly quiescent and silent (see the Perspective by Brown and Rudensky). Therapeutic targeting of VISTA using an agonistic antibody in mice curbed the development of graft-versus-host disease and promoted the death of naïve T cells abnormally activated by self-antigen. VISTA thus represents a distinctive immunoregulatory molecule that controls naïve T cell function by maintaining quiescence and peripheral tolerance. Science , this issue p. eaay0524 ; see also p. 247 The immunological checkpoint regulator VISTA silences nonspecific activity of naive CD4 + T cells, limiting immune responses to self-antigens. Negative checkpoint regulators (NCRs) temper the T cell immune response to self-antigens and limit the development of autoimmunity. Unlike all other NCRs that are expressed on activated T lymphocytes, V-type immunoglobulin domain-containing suppressor of T cell activation (VISTA) is expressed on naïve T cells. We report an unexpected heterogeneity within the naïve T cell compartment in mice, where loss of VISTA disrupted the major quiescent naïve T cell subset and enhanced self-reactivity. Agonistic VISTA engagement increased T cell tolerance by promoting antigen-induced peripheral T cell deletion. Although a critical player in naïve T cell homeostasis, the ability of VISTA to restrain naïve T cell responses was lost under inflammatory conditions. VISTA is therefore a distinctive NCR of naïve T cells that is critical for steady-state maintenance of quiescence and peripheral tolerance.

Plants constantly monitor and cope with the fluctuating environment while hosting a diversity of plant-inhabiting microbes. The mode and outcome of plant–microbe interactions, including plant disease epidemics, are dynamically and profoundly influenced by abiotic factors, such as light, temperature, water and nutrients. Plants also utilize associations with beneficial microbes during adaptation to adverse conditions. Elucidation of the molecular bases for the plant–microbe–environment interactions is therefore of fundamental importance in the plant sciences. Following advances into individual stress signaling pathways, recent studies are beginning to reveal molecular intersections between biotic and abiotic stress responses and regulatory principles in combined stress responses. We outline mechanisms underlying environmental modulation of plant immunity and emerging roles for immune regulators in abiotic stress tolerance. Furthermore, we discuss how plants coordinate conflicting demands when exposed to combinations of different stresses, with attention to a possible determinant that links initial stress response to broad-spectrum stress tolerance or prioritization of specific stress tolerance.

Plant growth and development exhibit plasticity, and plants can adapt to environmental changes and stress. Various phytohormones interact synergistically or antagonistically to regulate these responses. Melatonin and indole-3-acetic acid (IAA) are widespread across plant kingdom. Melatonin, an important member of the neuroendocrine immune regulatory network, can confer autoimmunity and protect against viral invasion. Melatonin functions as a plant growth regulator and biostimulant, with an important role in enhancing plant stress tolerance. IAA has a highly complex stress response mechanism, which participates in a series of stress induced physiological changes. This article reviews studies on the signaling pathways of melatonin and IAA, focusing on specific regulatory mechanisms. We discuss how these hormones coordinate plant growth and development and stress responses. Furthermore, the interactions between melatonin and IAA and their upstream and downstream transcriptional regulation are discussed from the perspective of modulating plant development and stress adaptation. The reviewed studies suggest that, at low concentrations, melatonin promotes IAA synthesis, whereas at high levels it reduces IAA levels. Similarly to IAA, melatonin promotes plant growth and development. IAA suppresses the melatonin induced inhibition of germination. IAA signaling plays an important role in plant growth and development, whereas melatonin signaling plays an important role in stress responses.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide–major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4 + T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy. A new technique enabling single-cell analysis of T cell receptor identity and epigenomic state uncovers heterogeneity in normal and leukemic T cells.

Despite impressive durable responses, immune checkpoint inhibitors do not provide a long-term benefit to the majority of patients with cancer. Understanding genomic correlates of response and resistance to checkpoint blockade may enhance benefits for patients with cancer by elucidating biomarkers for patient stratification and resistance mechanisms for therapeutic targeting. Here we review emerging genomic markers of checkpoint blockade response, including those related to neoantigens, antigen presentation, DNA repair, and oncogenic pathways. Compelling evidence also points to a role for T cell functionality, checkpoint regulators, chromatin modifiers, and copy-number alterations in mediating selective response to immune checkpoint blockade. Ultimately, efforts to contextualize genomic correlates of response into the larger understanding of tumor immune biology will build a foundation for the development of novel biomarkers and therapies to overcome resistance to checkpoint blockade. Responders and non-responders to cancer immunotherapy can be identified through a range of genomic markers.

In nature, plants must respond to multiple stresses simultaneously, which likely demands cross-talk between stress-response pathways to minimize fitness costs. Here we provide genetic evidence that biotic and abiotic stress responses are differentially prioritized in Arabidopsis thaliana leaves of different ages to maintain growth and reproduction under combined biotic and abiotic stresses. Abiotic stresses, such as high salinity and drought, blunted immune responses in older rosette leaves through the phytohormone abscisic acid signaling, whereas this antagonistic effect was blocked in younger rosette leaves by PBS3, a signaling component of the defense phytohormone salicylic acid. Plants lacking PBS3 exhibited enhanced abiotic stress tolerance at the cost of decreased fitness under combined biotic and abiotic stresses. Together with this role, PBS3 is also indispensable for the establishment of salt stress- and leaf age-dependent phyllosphere bacterial communities. Collectively, our work reveals a mechanism that balances trade-offs upon conflicting stresses at the organism level and identifies a genetic intersection among plant immunity, leaf microbiota, and abiotic stress tolerance.

Co-inhibitory receptors are important regulators of T-cell function that define the balance between tolerance and autoimmunity. The immune regulatory function of co-inhibitory receptors, including CTLA-4, PD-1, TIM-3, TIGIT, and LAG-3, was first discovered in the setting of autoimmune disease models, in which their blockade or deficiency resulted in induction or exacerbation of the disease. Later on, co-inhibitory receptors on lymphocytes have also been found to influence outcomes in tumor and chronic viral infection settings. These receptors suppress T-cell function in the tumor microenvironment (TME), thereby making the T cells dysfunctional. Based on this observation, blockade of co-inhibitory receptors (also known as checkpoint molecules) has emerged as a successful treatment option for a number of human cancers. However, severe autoimmune-like side effects limit the use of therapeutics that block individual or combinations of co-inhibitory receptors for cancer treatment. In this review we provide an overview of the role of co-inhibitory receptors in autoimmunity and anti-tumor immunity. We then discuss current approaches and future directions to leverage our knowledge of co-inhibitory receptors to target them in tumor immunity without inducing autoimmunity.