Immune Network Research Articles

Novel Diagnostic Biomarkers Related to Necroptosis and Immune Infiltration in Coronary Heart Disease.

Necroptosis, a monitored form of inflammatory cell death, contributes to coronary heart disease (CHD) progression. This study examined the potential of using necroptosis genes as diagnostic markers for CHD and sought to elucidate the underlying roles. Through bioinformatic analysis of GSE20680 and GSE20681, we first identified the differentially expressed genes (DEGs) related to necroptosis in CHD. Hub genes were identified using least absolute shrinkage and selection operator (LASSO) regression and random forest analysis after studying immune infiltration and transcription factor-miRNA interaction networks according to the DEGs. Quantitative polymerase chain reaction and immunohistochemistry were used to further investigate hub gene expression in vivo, for which a diagnostic model was constructed and the predictive efficacy was validated. Finally, the CHD group was categorized into high- and low-score groups in accordance with the single-sample gene set enrichment analysis (ssGSEA) score of the necroptosis genes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, GSEA, and further immune infiltration analyses were performed on the two groups to explore the possible roles of hub genes. Based on the results of the LASSO regression and random forest analyses, four genes were used to construct a diagnostic model to establish a nomogram. Additionally, an extensive analysis of all seventeen necroptosis genes revealed notable distinctions in expression between high-risk and low-risk groups. Evaluation of immune infiltration revealed that neutrophils, monocytes, B cells, and activated dendritic cells were highly distributed in the peripheral blood of patients with CHD. Specifically, the high CHD score group exhibited greater neutrophil and monocyte infiltration. Conversely, the high-score group showed lower infiltration of M0 and M2 macrophages, CD8+ T, plasma, and resting mast cells. TLR3, MLKL, HMGB1, and NDRG2 may be prospective biomarkers for CHD diagnosis. These findings offer plausible explanations for the role of necroptosis in CHD progression through immune infiltration and inflammatory response.

Commensal microbiome and gastrointestinal mucosal immunity: Harmony and conflict with our closest neighbor.

The gastrointestinal tract contains a wide range of microorganisms that have evolved alongside the immune system of the host. The intestinal mucosa maintains balance within the intestines by utilizing the mucosal immune system, which is controlled by the complex gut mucosal immune network. This review aims to comprehensively introduce current knowledge of the gut mucosal immune system, focusing on its interaction with commensal bacteria. The gut mucosal immune network includes gut-associated lymphoid tissue, mucosal immune cells, cytokines, and chemokines. The connection between microbiota and the immune system occurs through the engagement of bacterial components with pattern recognition receptors found in the intestinal epithelium and antigen-presenting cells. This interaction leads to the activation of both innate and adaptive immune responses. The interaction between the microbial community and the host is vital for maintaining the balance and health of the host's mucosal system. The gut mucosal immune network maintains a delicate equilibrium between active immunity, which defends against infections and damaging non-self antigens, and immunological tolerance, which allows for the presence of commensal microbiota and dietary antigens. This balance is crucial for the maintenance of intestinal health and homeostasis. Disturbance of gut homeostasis leads to enduring or severe gastrointestinal ailments, such as colorectal cancer and inflammatory bowel disease. Utilizing these factors can aid in the development of cutting-edge mucosal vaccines that have the ability to elicit strong protective immune responses at the primary sites of pathogen invasion.

Lipids and Lipid-Mediated Signaling in Plant-Pathogen Interactions.

Plant lipids are essential cell constituents with many structural, storage, signaling, and defensive functions. During plant-pathogen interactions, lipids play parts in both the preexisting passive defense mechanisms and the pathogen-induced immune responses at the local and systemic levels. They interact with various components of the plant immune network and can modulate plant defense both positively and negatively. Under biotic stress, lipid signaling is mostly associated with oxygenated natural products derived from unsaturated fatty acids, known as oxylipins; among these, jasmonic acid has been of great interest as a specific mediator of plant defense against necrotrophic pathogens. Although numerous studies have documented the contribution of oxylipins and other lipid-derived species in plant immunity, their specific roles in plant-pathogen interactions and their involvement in the signaling network require further elucidation. This review presents the most relevant and recent studies on lipids and lipid-derived signaling molecules involved in plant-pathogen interactions, with the aim of providing a deeper insight into the mechanisms underpinning lipid-mediated regulation of the plant immune system.

Moniezia benedeni drives the SNAP-25 expression of the enteric nerves in sheep's small intestine

BackgroundThe neuroimmune network plays a crucial role in regulating mucosal immune homeostasis within the digestive tract. Synaptosome-associated protein 25 (SNAP-25) is a presynaptic membrane-binding protein that activates ILC2s, initiating the host's anti-parasitic immune response.MethodsTo investigate the effect of Moniezia benedeni (M. benedeni) infection on the distribution of SNAP-25 in the sheep's small intestine, the recombinant plasmid pET-28a-SNAP-25 was constructed and expressed in BL21, yielding the recombinant protein. Then, the rabbit anti-sheep SNAP-25 polyclonal antibody was prepared and immunofluorescence staining was performed with it. The expression levels of SNAP-25 in the intestines of normal and M. benedeni-infected sheep were detected by ELISA.ResultsThe results showed that the SNAP-25 recombinant protein was 29.3 KDa, the titer of the prepared immune serum reached 1:128,000. It was demonstrated that the rabbit anti-sheep SNAP-25 polyclonal antibody could bind to the natural protein of sheep SNAP-25 specifically. The expression levels of SNAP-25 in the sheep's small intestine revealed its primary presence in the muscular layer and lamina propria, particularly around nerve fibers surrounding the intestinal glands. Average expression levels in the duodenum, jejunum, and ileum were 130.32 pg/mg, 185.71 pg/mg, and 172.68 pg/mg, respectively. Under conditions of M. benedeni infection, the spatial distribution of SNAP-25-expressing nerve fibers remained consistent, but its expression level in each intestine segment was increased significantly (P < 0.05), up to 262.02 pg/mg, 276.84 pg/mg, and 326.65 pg/mg in the duodenum, jejunum, and ileum, and it was increased by 101.06%, 49.07%, and 89.16% respectively.ConclusionsThese findings suggest that M. benedeni could induce the SNAP-25 expression levels in sheep's intestinal nerves significantly. The results lay a foundation for further exploration of the molecular mechanism by which the gastrointestinal nerve-mucosal immune network perceives parasites in sheep.

The function of OforOrco in the allogrooming behavior of Odontotermes formosanus (Shiraki) induced by Serratia marcescens Bizio (SM1)

Termites are consistently confronted with a complex microbial environment. In addition to the role of their innate immune system in resisting pathogen infection, social immune behavior also plays a significant role in helping termites withstand the stress caused by pathogenic microorganisms. The allogrooming behavior among different individuals is commonly observed in termites, and it plays a crucial role in the social immune interaction network. In the case of Odontotermes formosanus (Shiraki), Orco is specifically involved in detecting pheromones and volatile chemicals released by termites to communicate with each other. Nonetheless, the function of Orco in the social immunity remains unreported in O. formosanus. Consequently, in this study, we recorded the allogrooming behavior of O. formosanus workers under SM1 stress. The results indicated a significant increase in allogrooming behavior due to SM1 infection. The allogrooming behavior of workers under SM1 stress was significantly increased after the addition of soldiers. Compared with pronotum group treated by SM1, SM1 treatment of workers' heads significantly reduced the allogrooming behavior among workers. In addition, we found that SM1 could greatly increase the expression of OforOrco. Furthermore, interfering with OforOrco could markedly reduce the allogrooming behavior among workers under SM1 stress, and increase the mortality of worker under SM1 stress. This study demonstrated the significant role of OforOrco in the social immunity of O. formosanus, which offers a theoretical foundation for the advancement of research on termite RNA biopesticides, and the integration of RNA interference (RNAi) with pathogens. This study is valuable for elucidating the social immune behavior and interaction network of termites.

The novel m6A writer methyltransferase 5 is a promising prognostic biomarker and associated with immune cell infiltration in oral squamous cell carcinoma.

Emerging research has identified the N6-methyladenosine (m6A) modification and its regulatory enzymes, including methyltransferase 5 (METTL5), as critical players in cancer biology. However, the role of METTL5 in oral squamous cell carcinoma (OSCC) remains poorly understood. We conducted a comprehensive study to investigate the expression and implications of METTL5 in OSCC. We recruited 76 OSCC patients to analyze METTL5 mRNA and protein expression using RT-qPCR and western blot. Additionally, we analyzed METTL5 expression and its correlation with clinical features, patient prognosis, immune cell infiltration, and biological pathways using the TCGA-HNSCC dataset, which primarily consists of OSCC samples. Our findings revealed significant overexpression of METTL5 in OSCC tissues compared to normal tissues. The high expression of METTL5 is associated with advanced cancer stages, higher tumor grades, nodal metastasis, and poorer patient outcomes, indicating its involvement in cancer progression. In silico functional analysis revealed that METTL5 plays a role in multiple biological pathways, highlighting its importance in cancer biology. Moreover, METTL5 has complex relationships with immune regulatory genes, suggesting its potential role in shaping the tumor immune microenvironment. METTL5 is a promising candidate for the prognosis and therapeutic intervention of OSCC. Its overexpression in cancer tissues, association with clinical features, and intricate links to immune regulatory networks underscore its significance in this malignancy. This study contributes to a deeper understanding of the complex factors influencing OSCC, and provides a foundation for future research and potential clinical applications.

Identification of a novel survival and immune microenvironment related ceRNA regulatory network for hepatocellular carcinoma based on circHECTD1

BackgroundCircHECTD1 (circ_0031450) is highly expressed in hepatocellular carcinoma (HCC) tissues and may act as an oncogene. Its specific competitive endogenous RNA (ceRNA) mechanism remains to be further elucidated. MethodsSeveral databases and online platforms, including pathway activity, immune checkpoint, and overall survival analyses, were used to predict targets, download datasets, and perform online analyses. The R software was used for differential gene expression analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), clinical relevance, receiver operator characteristic curve, and single-cell analysis. Cytoscape software was used to construct ceRNAs, protein-protein interactions (PPI), and pivotal networks. ResultsThe ceRNA, PPI, and pivotal networks were successfully constructed. Pathway enrichment analysis was mainly related to apoptosis, cell cycle, and epithelial-mesenchymal transition (EMT) pathways. Six pivotal targets related to survival, immune infiltration, immune checkpoints, clinical stage, and diagnosis of patients with HCC were identified. The recovery function and pathway enrichment results were consistent with previous results. Single-cell analysis suggested that the pivotal targets were highly expressed in T cells. ConclusionWe successfully constructed a prognosis and immune microenvironment-related ceRNA network based on circHECTD1, providing new insights for diagnosing and treating HCC.

NRC immune receptor networks show diversified hierarchical genetic architecture across plant lineages.

Plants' complex immune systems include nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins, which help recognize invading pathogens. In solanaceous plants, the NRC (NLR required for cell death) family includes helper NLRs that form a complex genetic network with multiple sensor NLRs to provide resistance against pathogens. However, the evolution and function of NRC networks outside solanaceous plants are currently unclear. Here, we conducted phylogenomic and macroevolutionary analyses comparing NLRs identified from different asterid lineages and found that NRC networks expanded significantly in most lamiids but not in Ericales and campanulids. Using transient expression assays in Nicotiana benthamiana, we showed that NRC networks are simple in Ericales and campanulids, but have high complexity in lamiids. Phylogenetic analyses grouped the NRC helper NLRs into three NRC0 subclades that are conserved, and several family-specific NRC subclades of lamiids that show signatures of diversifying selection. Functional analyses revealed that members of the NRC0 subclades are partially interchangeable, whereas family-specific NRC members in lamiids lack interchangeability. Our findings highlight the distinctive evolutionary patterns of the NRC networks in asterids and provide potential insights into transferring disease resistance across plant lineages.

Trematode Diplostomum pseudospathaceum inducing differential immune gene expression in sexual and gynogenetic gibel carp (Carassius gibelio): parasites facilitating the coexistence of two reproductive forms of the invasive species.

Parasite-mediated selection is considered one of the potential mechanisms contributing to the coexistence of asexual-sexual complexes. Gibel carp (Carassius gibelio), an invasive fish species in Europe, often forms populations composed of gynogenetic and sexual specimens. The experimental infection was induced in gynogenetic and sexual gibel carp using eye-fluke Diplostomum pseudospathaceum (Trematoda), and the transcriptome profile of the spleen as a major immune organ in fish was analyzed to reveal the differentially expressed immunity-associated genes related to D. pseudospathaceum infection differing between gynogenetic and sexual gibel carp. High parasite infection was found in gynogenetic fish when compared to genetically diverse sexuals. Although metacercariae of D. pseudospathaceum are situated in an immune-privileged organ, our results show that eye trematodes may induce a host immune response. We found differential gene expression induced by eye-fluke infection, with various impacts on gynogenetic and sexual hosts, documenting for the majority of DEGs upregulation in sexuals, and downregulation in asexuals. Differences in gene regulation between gynogenetic and sexual gibel carp were evidenced in many immunity-associated genes. GO analyses revealed the importance of genes assigned to the GO terms: immune function, the Notch signaling pathway, MAP kinase tyrosine/threonine/phosphatase activity, and chemokine receptor activity. KEGG analyses revealed the importance of the genes involved in 12 immunity-associated pathways - specifically, FoxO signaling, adipocytokine signaling, TGF-beta signaling, apoptosis, Notch signaling, C-type lectin receptor signaling, efferocytosis, intestinal immune network for IgA production, insulin signaling, virion - human immunodeficiency virus, Toll-like receptor signaling, and phosphatidylinositol signaling system. Our study indicates the limited potential of asexual fish to cope with higher parasite infection (likely a loss of capacity to induce an effective immune response) and highlights the important role of molecular mechanisms associated with immunity for the coexistence of gynogenetic and sexual gibel carp, potentially contributing to its invasiveness.

Transcriptome analysis of cynomolgus macaques throughout their lifespan reveals age-related immune patterns

Despite the different perspectives by diverse research sectors spanning several decades, aging research remains uncharted territory for human beings. Therefore, we investigated the transcriptomic characteristics of eight male healthy cynomolgus macaques, and the annual sampling was designed with two individuals in four age groups. As a laboratory animal, the macaques were meticulously shielded from all environmental factors except aging. The results showed recent findings of certain immune response and the age-associated network of primate immunity. Three important aging patterns were identified and each gene clusters represented a different immune response. The increased expression pattern was predominantly associated with innate immune cells, such as Neutrophils and NK cells, causing chronic inflammation with aging whereas the other two decreased patterns were associated with adaptive immunity, especially “B cell activation” affecting antibody diversity of aging. Furthermore, the hub gene network of the patterns reflected transcriptomic age and correlated with human illness status, aiding in future human disease prediction. Our macaque transcriptome profiling results offer systematic insights into the age-related immunological features of primates.

An emerging maestro of immune regulation: how DOT1L orchestrates the harmonies of the immune system.

The immune system comprises a complex yet tightly regulated network of cells and molecules that play a critical role in protecting the body from infection and disease. The activity and development of each immune cell is regulated in a myriad of ways including through the cytokine milieu, the availability of key receptors, via tailored intracellular signalling cascades, dedicated transcription factors and even by directly modulating gene accessibility and expression; the latter is more commonly known as epigenetic regulation. In recent years, epigenetic regulators have begun to emerge as key players involved in modulating the immune system. Among these, the lysine methyltransferase DOT1L has gained significant attention for its involvement in orchestrating immune cell formation and function. In this review we provide an overview of the role of DOT1L across the immune system and the implications of this role on health and disease. We begin by elucidating the general mechanisms of DOT1L-mediated histone methylation and its impact on gene expression within immune cells. Subsequently, we provide a detailed and comprehensive overview of recent studies that identify DOT1L as a crucial regulator of immune cell development, differentiation, and activation. Next, we discuss the potential mechanisms of DOT1L-mediated regulation of immune cell function and shed light on how DOT1L might be contributing to immune cell homeostasis and dysfunction. We then provide food for thought by highlighting some of the current obstacles and technical limitations precluding a more in-depth elucidation of DOT1L's role. Finally, we explore the potential therapeutic implications of targeting DOT1L in the context of immune-related diseases and discuss ongoing research efforts to this end. Overall, this review consolidates the current paradigm regarding DOT1L's role across the immune network and emphasises its critical role in governing the healthy immune system and its potential as a novel therapeutic target for immune-related diseases. A deeper understanding of DOT1L's immunomodulatory functions could pave the way for innovative therapeutic approaches which fine-tune the immune response to enhance or restore human health.

The SAMHD1-MX2 axis restricts HIV-1 infection at postviral DNA synthesis.

In contrast to most restriction factors that directly bind to viral components to exert their antiviral effects, SAMHD1, the only known deoxynucleotide triphosphate (dNTP) hydrolase in eukaryotes, indirectly inhibits viral replication in quiescent cells by reducing the pool of dNTP substrates available for viral cDNA synthesis. Our study provides a novel perspective on the antiviral functions of SAMHD1. In addition to its role in dNTP hydrolysis, SAMHD1 cooperates with MX2 to inhibit HIV-1 nuclear import. In this process, SAMHD1 acts as a sensor for incoming HIV-1 cores, detecting and binding to them, before subsequently delivering the complex to the molecular trap formed by MX2, thereby immobilizing the virus. This study not only reveals a new antiviral pathway for SAMHD1 but also identifies a unique collaboration and interaction between two distinct restriction factors, establishing a novel line of defense against HIV-1 infection, which challenges the traditional view of restriction factors acting independently. Overall, our findings further indicate the intricate complexity of the host immune defense network and provide potential targets for promoting host antiviral immune defense.

Transcriptome-based protein-protein interaction analysis reveals immune gene network elucidating white body immunity mechanisms in response to LPS stimulation in Amphioctopus fangsiao

One of the major challenges in the aquaculture of marine organisms is the susceptibility to pathogens. Immune cells defend bacterial invasion by recognizing pathogen-associated molecular patterns (PAMPs) such as Lipopolysaccharides (LPS) in Gram-negative bacteria. The white body are key organs for immune response and hematopoiesis, and play an important role in understanding the antimicrobial biological response in gold-ringed octopus (Amphioctopus fangsiao). In the present research, transcriptome sequencing and bioinformatics analysis were conducted on A. fangsiao white body tissue after 6 h and 24 h of LPS stimulation. The results showed 2,029 and 73 differentially expressed genes (DEGs) at the 6- and 24-hour time points, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were beneficial in determining immune-related terms and signaling pathways. Subsequently, a protein-protein interaction (PPI) network was constructed and 20 hub genes, such as AKT3, MAPK14, and PIK3CA, were identified. These genes are involved in a variety of signaling pathways, including the Hippo signaling pathway, chemokine signaling pathway, and leukocyte trans endothelial migration. Using qRT-PCR, the accuracy of the 20 hub genes was verified. The present study provides a substantial theoretical foundation for the research on A. fangsiao white body immunity, enhancing the current understanding of cephalopods' innate immunity.

Pleiotropy alleviates the fitness costs associated with resource allocation trade-offs in immune signalling networks.

Many genes and signalling pathways within plant and animal taxa drive the expression of multiple organismal traits. This form of genetic pleiotropy instigates trade-offs among life-history traits if a mutation in the pleiotropic gene improves the fitness contribution of one trait at the expense of another. Whether or not pleiotropy gives rise to conflict among traits, however, likely depends on the resource costs and timing of trait deployment during organismal development. To investigate factors that could influence the evolutionary maintenance of pleiotropy in gene networks, we developed an agent-based model of co-evolution between parasites and hosts. Hosts comprise signalling networks that must faithfully complete a developmental programme while also defending against parasites, and trait signalling networks could be independent or share a pleiotropic component as they evolved to improve host fitness. We found that hosts with independent developmental and immune networks were significantly more fit than hosts with pleiotropic networks when traits were deployed asynchronously during development. When host genotypes directly competed against each other, however, pleiotropic hosts were victorious regardless of trait synchrony because the pleiotropic networks were more robust to parasite manipulation, potentially explaining the abundance of pleiotropy in immune systems despite its contribution to life history trade-offs.

Enhancing the revelation of key genes and interaction networks in non-small cell lung cancer with major depressive disorder: A bioinformatics analysis.

Lung cancer is ranked as the second most prevalent form of cancer worldwide. Nonsmall cell lung cancer (NSCLC) represents the predominant histological subtype. Research suggests that one-third of lung cancer patients also experiencing depression. Antidepressants play an indispensable role in the management of NSCLC. Despite significant advancements in treatment, lung cancer patients still face a high mortality rate. Major depressive disorder (MDD) and related antidepressants involved in treatment efficacy and prognosis of NSCLC. However, there has been a lack of screening and analysis regarding genes and networks associated with both NSCLC and MDD. To investigate the correlation between MDD and NSCLC, our discovery and validation analysis included four datasets from the Gene Expression Omnibus database from NSCLC or MDD. Differential gene expression (DEGs) analysis, GO and KEGG Pathway, and protein-protein interaction network analyzes to identify hub genes, networks, and associated observations link between MDD and NSCLC. The analysis of two datasets yielded a total of 84 downregulated and 52 upregulated DEGs. Pathway enrichment analyzes indicated that co-upregulated genes were enriched in the regulation of positive regulation of cellular development, collagen-containing extracellular matrix (ECM), cytokine binding, and axon guidance. We identified 20 key genes, which were further analyzed using the MCODE plugin to identify two core subnetworks. The integration of functionally similar genes provided valuable insights into the potential involvement of these hub genes in diverse biological processes including angiogenesis humoral immune response regulation inflammatory response organization ECM network. We have identified a total of 136 DEGs that participate in multiple biological signaling pathways. A total of 20 hub genes have demonstrated robust associations, potentially indicating novel diagnostic and therapeutic targets for both diseases.

High-dimensional longitudinal immune profiling uncovers a dual role of the CXCL9/CXCR3, CXCL13/CXCR5, and CCL11/CCL3 axis in the coupling of immune-related adverse events to immune checkpoint inhibitor response.

2512 Background: Additional characterization is required to understand the immune network signatures and immunophenotypes that link immune-related adverse events (irAEs) to immune checkpoint inhibitor (ICI) therapy responses in cancer patients. Methods: A comprehensive immune profiling analysis was conducted on whole blood and peripheral blood mononuclear cells (PBMC) from 165 oncology patients with various irAEs, including colitis (n=64), myocarditis (n=19), pneumonitis (n=25), arthritis (n=24), and cytokine release syndrome CRS (n=33), and compared to a cohort of 219 cancer patients prior to ICI treatment. Results: Following ICI therapy on cycle 2 day 1 (C2D1), we observed significant increases in IL-6, CCL2, CXCL9, CXCL10, and CXCL13 levels preceding irAEs. CXCL9 was specifically upregulated during the development of colitis, arthritis, CRS, and myocarditis, while CXCL13 increased only in CRS, and CCL3 only in myocarditis and CRS, with no CCL11 upregulation in any irAE. High levels of CXCL9, high CCL11 and low CXCL13 strongly correlated with improved oncologic outcomes in different irAEs. Compared to other cluster, in the high CXCL9 cluster, 5-year overall survival (OS) was significantly improved (HR = 10.26 [95% CI, 1.27-82.82], p = 0.029) in colitis (n=20), in CRS (n=21) (HR = 6.45 [95% CI, 1.60-25.99], p = 0.009), and in arthritis. In the high CCL11 cluster, 5-year OS was significantly improved in pneumonitis (n=15), (HR = 4.04 [95% CI, 1.05-15.46]). Conversely, in myocarditis, the high CXCL13 cluster (n=9) was associated with decreased 2-year OS (HR = 6.05 [95% CI, 1.03-35.48], p = 0.046). It is important to note that the CXCL9-driven immunophenotypes were characterized by low IL-6. Notable observations include CD38 upregulation and large-scale activation of CD8 memory subsets during ICI therapy, concomitant with increased circulation of immature neutrophils at the onset of irAEs diagnosis. This event may increase the migration of TCRγδ, NK, DC, and CD8 cells to tumor sites through CXCR3/CXCL9 interactions. Conclusions: This study unravels intricate connections between immune activation and tumor response. CXCL9, CCL11, and CXCL13 emerge as pivotal biomarkers bridging the gap between ICI therapy effectiveness and distinct irAEs-associated immunophenotypes.

F.2 Comprehensively mapping transcriptionally relevant histone modifications in aggressive meningioma leads to novel biologic insights and therapeutic vulnerabilities

Background: We recently identified four molecular subgroups of meningioma with distinct biology and outcomes. While two (MG3/MG4) are associated with poor outcome, they display divergent transcriptional profiles (enriched in metabolic and cell cycling pathways, respectively) and therapeutic vulnerabilities (MG3 has no clear treatment target). We sought to understand drivers of these key differences at a chromatin level. Methods: We profiled MG3/MG4 meningiomas for common histone marks H3K27me3, H3K27Ac, H3K4me1, H3K4me3, H3K9me3, and H3K36me3. Multiple computational approaches were used to compare MG3 and MG4 tumours including superenhancer ranking, differential binding analysis, and unsupervised clustering. Results: Our cohort includes 11-20 meningiomas per histone mark. Clustering revealed striking separation of subgroups based on multiple histone marks, particularly H3K36me3. FOXC1, a known driver of the epithelial to mesenchymal transition, was identified as a recurrent superenhancer in both groups, whereas MG3-specific superenhancers mapped to immune regulatory networks. Integrated differential binding analysis confirmed an immune-rich microenvironment in MG3 tumours driven by multiple histone marks, suggesting a role for targeting novel immune checkpoint genes CD84 and CD48. Conclusions: This study is the first to apply integrated analysis of multiple histone modifications to aggressive meningioma. We further characterize MG3 tumours by identifying an epigenetically-driven immune phenotype and propose novel treatment targets.

Transcriptional Response of Wolfberry to Infestation with the Endophytic Fusarium nematophilum Strain NQ8GII4.

Fusarium nematophilum NQ8GII4 is an endophytic fungus isolated from the root of healthy wolfberry (Lycium barbarum). Previous studies have reported that NQ8GII4 could dwell in wolfberry roots and enhance the defense responses in wolfberry against root rot, which is caused by F. oxysporum. To further elucidate the molecular mechanism of wolfberry disease resistance induced by NQ8GII4, in the present study, we adopted RNA sequencing analysis to profile the transcriptome of wolfberry response to NQ8GII4 infestation over a time course of 3 and 7 days postinoculation. Gene ontology enrichment analysis revealed that differentially expressed genes (DEGs) were enriched in biological regulation, response to stimulus, signaling, detoxification, immune system process, transporter activity, electron carrier activity, transcription factor activity, nucleic acid binding transcription factor, and antioxidant activity. Through Kyoto Encyclopedia of Genes and Genomes analysis, it was found that many of these DEGs were enriched in pathways related to plant-pathogen interactions, hormone signal transduction, and the phenylpropanoid biosynthesis pathway in wolfberry. This result suggested that innate immunity, phytohormone signaling, and numerous phenylpropanoid compounds comprise a complex defense network in wolfberry. Chloroplast 50S ribosomal proteins were consistently located at the core position of the response in wolfberry following infestation with NQ8GII4 analyzed by the protein-protein interaction network. This study elucidated the molecular mechanism underlying the interaction between NQ8GII4 and wolfberry, clarified the wolfberry immune response network to endophytic fungi infestation, identified candidate resistance genes in wolfberry, and provided a fundamental date for subsequent work.

Abstract PO2-03-11: A novel peripheral CD4+ T cell immune network associated with response to PD-1 inhibitor in early-stage triple negative breast cancer

Abstract A novel peripheral CD4+ T cell immune network associated with response to PD-1 inhibitor in early-stage triple negative breast cancer Background: Immunotherapy has showed benefits in early-stage triple-negative breast cancer (eTNBC). However, there is an urgent need to identify novel biomarkers that can guide stratification for immunotherapy in eTNBC. Anti-tumor immunity is a systemic response that encompasses the mobilization of dendritic cells, lymphocytes, and myeloid cells involving the tumor, blood, and lymph nodes. The activation of anti-tumor immune responses via immunotherapy is expected to reflect in the subset change of circulation. Combined with advantage of dynamic monitoring by liquid biopsy, we detected peripheral blood in the eTNBC patients under immunotherapy to explore potential immune therapeutic predictive subsets. Methods: Single-cell (sc) RNA sequencing was utilized to determine the transcriptomics of immune cells in the peripheral blood. Meanwhile scTCR sequencing was used to trace the dynamic changes of clonetypes under multi-therapy. Nanostring analysis of primary tumor and in vivo models were used to validate the mechanism of immune crosstalk. Prediction index was built based on the proportion of immune subsets at each time point and change of tumor size in each patient. Results: 12 eTNBC patients who participated in neoadjuvant chemotherapy in combination with PD-1 inhibitor (Toripalimab) clinical trial were included in this study. The clinical trial consists of two stages. All eligible patients received four cycles of EC (cyclophosphamide plus epirubicin) regimen and followed four cycles of nab-paclitaxel plus PD-1 inhibitor. Among the 12 patients, 5 patients achieved pCR, while the remaining 7 patients were non-pCR. Peripheral blood samples were collected at baseline, after chemotherapy induction, and on PD-1 inhibitor treatment for scRNA- and scTCR-sequencing. Through prediction index, a novel predictive pattern based on ratio of memory T cells (central memory T and resident memory T) to effective T cells in the peripheral was vividly defined, by which the patients could be classified into C-type (memory T cells dominated) and E-type (effective T cells dominated). The C-type indicated better efficacy of immunotherapy combination therapy, while the E-type suggested better efficacy of chemotherapy alone. Meanwhile, a novel peripheral CD4+Trm (resident-memory-like) subset that possessed both strong differentiation potential and memory function was higher in pCR group at baseline. TCR-tracing analysis revealed that the new clones induced by chemotherapy mainly belong to the CD4+ Trm and CD8+ CD161+ Tcm (central memory) subsets, and the upregulation of CD8+ CD161+ Tcm during therapy was a dynamic predictor for immunotherapy benefits. Besides, most of CD4+Trm transitioned into CD4+Th1-like cells as an activated status, which considered CD4+Trm as a group of reservoirs with polyclonality and differentiation potential for tumor-killing. Meanwhile, the increase in CD5+ cDC2 (type 2 conventional dendritic cell) after chemotherapy was associated with enhanced antigen-presenting function and cell communication and co-stimulation with CD4+ Trm cells which helped the activated transition from CD4+Trm into CD4+Th1-like cells in lymph nodes. Moreover, CD4+Th1-like cells increased secretion of Th1 cytokines thus leading to promote CD8+CD161+ Tcm upregulation and tumor-infiltration after immunotherapy. Conclusions: A novel peripheral pattern based on subsets of T cells as C-type and E-type was established as potential predictors for immunotherapy stratification in eTNBC patients. Meanwhile, a novel peripheral CD4+Trm immune network was identified, in which CD5+cDC2 activated the transition of CD4+Trm into CD4+Th1-like subset leading to activation and tumor-infiltration of CD8+CD161+Tcm. All the above provided potential therapeutic targets for enhancing immunotherapy. Citation Format: Zehao Wang, Zhibo Shao, Bingqiu Xiu, Jiong Wu. A novel peripheral CD4+ T cell immune network associated with response to PD-1 inhibitor in early-stage triple negative breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-03-11.

Abstract PO4-28-09: Upregulation of the immune checkpoint protein B7-H3 is associated with an immune suppressive microenvironment in progression from in situ to invasive lobular breast cancer

Abstract Invasive lobular breast cancer (ILC) is an understudied subtype of breast cancer characterized by late recurrence, metastasis to serosal surfaces including the peritoneum, and poor long-term outcomes. Lobular carcinoma in situ (LCIS) is a non-obligate precursor to ILC but is associated with a 30% increased risk of developing ILC. Therefore, understanding the underlying changes that occur in the invasive lobular cells as well as their tumor microenvironment (TME) during the transition from LCIS to ILC is critical for the development of novel therapeutic targets that could be used in early disease. To address this, we used combined spatial whole genome transcriptomics and a 97-protein proteomics assay to examine the spatial molecular profiles of coexistent LCIS and ILC. PanCK-positive tumor cells and panCK-negative stromal cells were segmented and analyzed separately for both RNA and protein. Despite the close spatial proximity of LCIS and ILC, there were notable differences in gene and protein expression in the tumor cells as well as the tumor microenvironment (TME). RNA profiling revealed significant upregulation of genes encoding essential components of the extracellular matrix, including type I, 3 and 5 collagens, small leucine-rich proteoglycans byglycan (BGN) and lumican (LUM), periostin (POSTN) and secreted protein acidic and cysteine rich (SPARC). Metalloprotease genes MMP2 and MMP11 were also upregulated. Genes highly expressed in the LCIS tumor compartment were KRT5, KRT14 KRT17 and MYLK which are highly expressed in myoepithelial cells at the periphery of the LCIS. One of the most upregulated proteins in ILC cells was B7 homology 3 protein (B7-H3) or Cluster of Differentiation 276 (CD276). B7-H3 is a transmembrane immunoregulatory protein belonging to the B7 family (that also includes PD-L1 and PD-L2). This immune checkpoint protein is overexpressed in many tumors but is barely expressed in normal cells. B7-H3 has been associated with several aspects of cancer progression, such as evasion of tumor immune surveillance and metastasis, and is strongly linked to poor prognosis in cancer. Compared to the LCIS TME, B7-H3 was also the most upregulated protein in the ILC TME along with the tumor-promoting M1 macrophage marker CD68 and the regulatory T-cell marker FOXP3. The lymphocyte marker CD45 was downregulated as well as T-cell proteins CD3, CD40 and granzyme B. Moreover, CD27, a memory B-cell marker was most highly expressed in the TME surrounding LCIS compared to ILC. Overall, these molecular profiles support a transition to a toward a much more immunosuppressive environment for invasive tumor cells compared to LCIS. Based on these data, our working hypothesis is that upregulation of B7-H3 on lobular tumor cells promotes invasion allowing interaction with laminins, integrins and other ECM proteins in the basement membrane and the interstitial membrane as LCIS acquire invasive properties of ILC. Furthermore, upregulation of B7-H3 on CD3+ HLA-DR+ expressing antigen presenting cells also promotes a suppressive immune microenvironment by inhibiting T-cell proliferation and downregulating cytokine production. In sum, these strongly concurrent spatial transcriptome and protein data suggest that B7-H3 and the immune suppressive network of ILC may be a promising target for early stage lobular breast cancer. B7-H3 Inhibitors could be explored in the neoadjuvant setting to evaluate the efficacy of immunotherapy in primary ILC. Citation Format: Lynda Bennett, Sunati Sahoo, Cheryl Lewis, Indu Raman, Candace Frerich, Guanchun Chen, Min Xu, Suzanne Conzen. Upregulation of the immune checkpoint protein B7-H3 is associated with an immune suppressive microenvironment in progression from in situ to invasive lobular breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-28-09.