Immune-related Signaling Pathways Research Articles

IGF2BP1 in Mesenchymal GBM Immune Signalling Regulation via c-Myc

Glioblastoma multiforme (GBM) is a highly aggressive and lethal brain tumor, with poor patient prognosis and median overall survival of only 10 months despite the current Stupp protocol treatment, due to its high aggressiveness and recurrence rate. This study investigated the role of the IGF2BP1 gene in mesenchymal glioblastoma multiforme (GBM), revealing that IGF2BP1 is upregulated in tumor tissues compared to adjacent normal tissues and positively correlates with MYC gene expression and poor patient prognosis. Immune infiltration analysis showed that IGF2BP1 is associated with specific immune cell populations, and GSVA analysis confirmed its positive correlation with the immune functions of most B cells and macrophages. The mechanism of IGF2BP1 regulating c-Myc expression in mesenchymal GBM and its subsequent impact on immune-related signalling pathways, thereby affecting the immune microenvironment of tumors and patient prognosis, provides new targets and ideas for future immunotherapy of mesenchymal GBM.

Polysaccharides isolated from Ampelopsis grossedentata and their immunomodulatory activity.

To explore the immunomodulatory activity of polysaccharides from Ampelopsis grossedentata, two polysaccharides named AGP1 and AGP2 were isolated and purified by DEAE-cellulose 52 column and Sephacryl S-300HR chromatography. AGP1 and AGP2 were composed of fucose, arabinose, rhamnose, galactose, glucose, mannose, galacturonic acid, and glucuronic acid, with a ratio of 0.5: 10.2: 0.9: 31.8: 7.4: 3.4: 21.6: 24.2 and 0.4: 6.0: 0.5: 23.3: 3.3: 6.2: 33.5: 26.8, respectively. The average molecular weights of AGP1 and AGP2 were found to be 6.60×105Da and 7.24×105Da, respectively. AGP1 contained →4,6)-Galp-(1→glycosidic linkages, while AGP2 contained →2)-Galp-(1→and →2,3,4)-Glcp-(1→glycosidic linkages. The structures of AGPs were characterized by Fourier transform infrared spectroscopy, nuclear magnetic resonance, and scanning electron microscope. The immunomodulatory activity of AGPs was investigated in RAW264.7 cells, and the results indicated that AGPs significantly activated macrophages, promoted cells differentiation and NO secretion, increased the expression of IL-6 and TNF-α, and induced macrophage M1 polarization. Transcriptomic analysis indicated that AGP1 and AGP2 regulated a total of 1043 and 970 differentially expressed genes respectively, which were identified in different immune related signaling pathways. Moreover, the immunoblot demonstrated that AGPs exerted immune-promoting effects through the TLR4, MAPK and NF-κB signaling pathways in macrophages. Consequently, AGPs have potent immunomodulatory activity and can be considered as immunomodulators in medical and food industries.

KLRD1 (CD94): A Prognostic Biomarker and Therapeutic Candidate in Head and Neck Squamous Cell Carcinoma.

Background: Killer Cell Lectin Like Receptor D1 (KLRD1) plays a crucial role in antitumor immunity. However, its expression patterns across various cancers, its relationship with patient prognosis, and its potential as an immunotherapy target remain inadequately understood. Methods: We analyzed KLRD1 expression across various cancer types using multi-omics data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases, correlating it with patient prognosis. Single-cell RNA sequencing data were employed to further explore KLRD1 expression in natural killer (NK) cells and exhausted CD8+ T cells (CD8Tex). Functional enrichment analyses using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) identified the biological processes and pathways associated with KLRD1. Immune infiltration analysis, conducted via CIBERSORT, assessed the relationship between KLRD1 expression and immune cell infiltration within the tumor microenvironment. Furthermore, the Tracking Tumor Immunophenotype (TIP) meta-server and Easier tool were employed to assess the role of KLRD1 in the cancer immunity cycle and to predict immunotherapy responses. Drug sensitivity was predicted using tools like CellMiner and the Genomics of Drug Sensitivity in Cancer (GDSC) database to explore the link between KLRD1 expression and responsiveness to various anticancer drugs. Results: KLRD1 exhibits significant differential expression and strong prognostic value across cancers, particularly as an independent prognostic factor in head and neck squamous cell carcinoma (HNSC). Single-cell analysis revealed high expression of KLRD1 in NK and CD8Tex cells, indicating its critical role in antitumor immune responses. Functional enrichment analyses showed that KLRD1 is involved in several immune-related signaling pathways, including NK cell-mediated cytotoxicity and T cell receptor pathways. Immune infiltration analysis further confirmed a positive correlation between KLRD1 expression and the infiltration of various immune cells. Moreover, higher KLRD1 expression in HNSC is associated with enhanced immune pathway activity, increased sensitivity to cell division inhibitors, and the identification of arachidonyltrifluoromethane as a potential compound to counteract its oncogenic effects. Conclusion: In HNSC, KLRD1 is a key prognostic marker and potential target for personalized immunotherapy.

Integrating Single-Cell RNA-Seq and ATAC-Seq Analysis Reveals Uterine Cell Heterogeneity and Regulatory Networks Linked to Pimpled Eggs in Chickens.

Pimpled eggs have defective shells, which severely impacts hatching rates and transportation safety. In this study, we constructed single-cell resolution transcriptomic and chromatin accessibility maps from uterine tissues of chickens using single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq). We identified 11 major cell types and characterized their marker genes, along with specific transcription factors (TFs) that determine cell fate. CellChat analysis showed that fibroblasts had the most extensive intercellular communication network and that the chickens laying pimpled eggs had amplified immune-related signaling pathways. Differential expression and enrichment analyses indicated that inflammation in pimpled egg-laying chickens may lead to disruptions in their circadian rhythm and changes in the expression of ion transport-related genes, which negatively impacts eggshell quality. We then integrated TF analysis to construct a regulatory network involving TF-target gene-Gene Ontology associations related to pimpled eggs. We found that the transcription factors ATF3, ATF4, JUN, and FOS regulate uterine activities upstream, while the downregulation of ion pumps and genes associated with metal ion binding directly promotes the formation of pimpled eggs. Finally, by integrating the results of scRNA-seq and scATAC-seq, we identified a rare cell type-ionocytes. Our study constructed single-cell resolution transcriptomic and chromatin accessibility maps of chicken uterine tissue and explored the molecular regulatory mechanisms underlying pimpled egg formation. Our findings provide deeper insights into the structure and function of the chicken uterus, as well as the molecular mechanisms of eggshell formation.

Surgery-induced neuroinflammatory transcriptional programs in medial prefrontal cortex of mice during early phase of perioperative neurocognitive disorders.

Patients receiving anesthesia and surgery may experience cognitive dysfunction, memory deficits, and mental disturbances, which are referred to as perioperative neurocognitive disorders (PND). The function of the medial prefrontal cortex (mPFC) is disrupted during early phase of PND. To gain insight into the mechanisms of PND, we collected mouse mPFC tissues 6 h post-surgery and performed RNA sequencing analysis. In total, 178 differentially expressed genes (DEGs) were identified, including 105 upregulated and 73 downregulated genes. Bioinformatic analysis highlighted the significant enrichment of these DEGs in several immune-related biological processes and signaling pathways, suggesting that pronounced neuroinflammatory transcriptional programming in the mPFC was evoked during early phase of PND. Interleukin-6 level increased in both serum and mPFC, while the mRNA levels of Il-6, Tnf-α, and Il-1β remained unchanged. Taken together, our findings suggest that a distinct and acute neuroinflammatory response in the mPFC is evoked after peripheral surgery, which might play a key role in the development of PND.

Multi-omics reveals the mechanism of Sparassis latifolia polysaccharides to relieve cyclophosphamide-induced immune injury in liver of mice.

The present study aimed to investigate the impact of Sparassis latifolia polysaccharides (SLPs) on hepatic immune function in cyclophosphamide (CTX)-induced immunocompromised mice. Our findings demonstrated that SLPs effectively suppressed the production of alanine aminotransferase (ALT), aspartate aminotransferase (AST), inflammatory factors, and acute phase proteins, while improving the hepatic oxidative stress state. Additionally, SLPs exerted inhibitory effects on inflammatory cell infiltration within hepatic tissue. Transcriptomic results revealed that 246 differentially-expressed genes (DEGs) were identified. Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis showed that the more DEGs in SLPs group were mainly related to immune signal transduction and metabolism pathways. And more DEGs were mainly related to MAPK signaling pathway and JAK/STAT signaling pathway. Metabolome analysis demonstrated that SLPs significantly modulated specific metabolites in the liver, including lipids and lipid-like molecules, organic acids and their derivatives, organic heterocyclic compounds, phenylpropanoids and polyketones, organic oxygenates, and benzene. The comprehensive analysis of transcriptome and metabonomics revealed the activation of immune-related signal pathways in mice liver stimulated by CTX. Notably, the involvement of diverse genes and metabolites was observed in the metabolism of arachidonic acid (AA) and JAK/STAT pathway. Correlation analysis also showed that there was a certain correlation between metabolites and differential genes. The present findings offer novel insights into the regulatory mechanism of liver immune injury by SLPs, which exhibits potential application value in improving immunocompromised populations.

Effect of Selenium Nanoparticles on Alternative Splicing of Rainbow Trout Head Kidney under Heat Stress.

Alternative splicing (AS) is an important post-transcriptional regulation, which can expand the functional diversity of gene products and is a mechanism for eukaryotes to cope with abiotic stress. However, there are few studies on AS events in rainbow trout under heat stress. In this study, RNA-Seq data were used to clarify the effect of selenium nanoparticles (SeNPs) on the AS events of rainbow trout head kidney under heat stress. The results showed that a total of 45,398 AS events were identified from 9804 genes, of which Skipped Exon (SE) was the most common type of AS event. Through the analysis of the differentially expressed genes (DEGs) in each group, we learned that DEGs were enriched in the spliceosome, and the relevant genes were significantly changed, which promoted the occurrence of AS. We found that lysine degradation, ubiquitin mediated proteolysis, RNA degradation, protein processing in endoplasmic reticulum processing and other pathways were significantly enriched after addition of SeNPs. In addition, some immune related signaling pathways, such as the mTOR signaling pathway, interact with each other to enhance the resistance of rainbow trout to heat stress. These results indicated that AS in head kidney of rainbow trout changed under heat stress and SeNPs played a key role in alleviating heat stress for rainbow trout.

New direction: identification of immunoinflammatory subtypes and potential therapeutic targets for cholangiocarcinoma

BackgroundCholangiocarcinoma (CHOL) is a rare cancer with low survival rates. Despite advances in precision medicine targeting molecular subtypes, the immune subtypes of CHOL remain poorly understood. This study aimed to identify immune subtypes of CHOL and investigate their implications in the metabolic regulation of macrophage functions in inflammation.MethodsWe conducted a comprehensive analysis of transcriptome and single-cell sequencing data from multiple databases to classify the immune subtypes of CHOL. Immune cell infiltration within the tumor microenvironment (TME) and the metabolic pathways involved in macrophage activation and polarization were also analyzed.ResultsTwo distinct immune subtypes, immune-infiltrated CS1 and immune-depleted CS2, were identified in CHOL. CS1 exhibited a highly active TME with substantial immune cell infiltration, including macrophages, and activation of immune-related signaling pathways, such as inflammatory and interferon pathways. In contrast, CS2 was characterized by a deficiency in immune components and poorer prognosis. Metabolic regulation of macrophages, particularly the downregulation of oxidative phosphorylation in CS1, suggested a shift towards glycolysis as an energy source for activated macrophages, contributing to the immune-responsive phenotype observed in CS1. Additionally, the oncogenic role of DLX5 in CHOL was revealed, with potential impacts on macrophage functions in inflammation.ConclusionThis study provides insights into immune subtype classification, novel biomarker identification, and the metabolic regulation of macrophage functions in CHOL. Understanding macrophage metabolic reprogramming within immune subtypes may contribute to the development of targeted immunotherapies for CHOL.

Therapeutic effects and mechanisms of berberine on enteritis caused by Salmonella in poultry.

The present study aimed to investigate the therapeutic effects of berberine (BBR) on Salmonella enteritis in broiler chickens and to elucidate its mechanisms of action preliminarily. Blood samples were collected from 21- to 35-day-old Sanhuang male chicks to measure immune and biochemical indicators and to calculate the organ coefficients for the liver, spleen, bursa of Fabricius, and thymus. The caecal microbiota was analysed through 16S ribosomal RNA (rRNA) gene sequencing, and transcriptome sequencing was conducted. Compared with the positive control group (S), the berberine-treated group (BS) presented increased serum immunoglobulin M (IgM) levels, serum IgG levels, and total antioxidant capacity; berberine ameliorated the increase in the thymus index caused by Salmonella administration. The addition of berberine to the diet increased the abundance of beneficial bacterial genera, including Bacteroides and Lactobacillus. It also decreased the abundance of harmful bacterial genera, including Faecalibacterium and Streptococcus. Transcriptome analysis revealed that gene expression in the S and BS groups was associated with T cell selection and B cell receptor signalling pathways, which are enriched primarily in multiple immune-related signalling pathways, including the B cell receptor signalling pathway, NF-κ B signalling pathway, intestinal immune network for IgA production, asthma, and African trypanosomiasis. The significantly expressed genes included ATAD5, ERP29, MGST2, PIK3CA, and HSP90AA1. The present study demonstrated that berberine has a good therapeutic effect on Salmonella infection in chicks, as it inhibits the occurrence and development of Salmonella-induced intestinal inflammation by regulating the balance of the gut microbiota and the expression of related genes, including ATAD5, ERP29, MGST2, PIK3CA, and HSP90AA1.

Proteomic Analysis of Vibrio parahaemolyticus-Stimulated Pinctada martensii Proteins for Antimicrobial Activity, Potential Mechanisms, and Key Components.

Background: Bacterial infections are a major challenge in food processing and public health, and there is an urgent need to develop novel antimicrobial agents. Objectives: The purpose of this study is to investigate the potential mechanism and key components of Pinctada martensii antimicrobial proteins (Pm-Aps) to provide a theoretical basis for the development of novel antimicrobial agents. Methods: The researchers used Vibrio parahaemolyticus (VP) to stimulate Pinctada martensii, extracted the antimicrobial proteins, and analyzed their antimicrobial activities, potential mechanisms of action, and key components using proteomics. Results: The results showed that the antimicrobial activity of Pm-Aps, with broad-spectrum antimicrobial effects, was significantly enhanced after VP stimulation. This was associated with the upregulation of LAAO, CHDH, TLR2, ATG16L1, BAK, CLCA4, and CASP8 and the downregulation of MCM3, MCM5, DTYMK, PLK1, FBXO6, LPCAT3, GST, LAMTOR5, CYP17A, CTSA, and RRM1. It is hypothesized that these proteins may inhibit bacterial growth and multiplication by activating immune-related signaling pathways, inhibiting DNA replication and repair, and inducing apoptosis and autophagy. Furthermore, it was found that LAAO may be a key component of the antimicrobial action of Pm-Aps, killing bacteria by catalyzing the oxidation of amino acids to produce hydrogen peroxide (H2O2). Conclusions: These results strongly suggest that Pm-Aps is an effective antimicrobial protein, and it is expected that new LAAO can be obtained from Pm-Aps.

RBIO-06. STEREOTACTIC RADIOSURGERY ENHANCES T-CELL RECEPTOR REPERTOIRES AND INDUCES IMMUNOGENICITY IN BRAIN METASTASIS

Abstract BACKGROUND Brain metastasis is a frequent and deadly complication of systemic malignancy. The incidence rate is increasing and the prognosis remains poor, in contrast to recent advances in the management of systemic malignancy. Our previous work revealed an immunosuppressive microenvironment in brain metastasis and correlation between T-cell status and patient outcomes, shared across the primary tumor histologies. Therefore, we hypothesize that induction of immunogenicity has potential to improve brain metastasis patient outcome. METHODS Pre-operative stereotactic radiosurgery (SRS) (n = 44) and post-operative SRS (n = 47) brain metastasis specimens were collected from an ongoing clinical trial (MDACC protocol 2018-0552) designed to determine optimal timing of SRS for the treatment of brain metastasis. The patient materials were extracted DNA and RNA, and subjected to T-cell receptor (TCR) repertoire sequencing and mRNA-seq to interrogate radiation-induced immunogenicity. RESULTS In a preliminary analysis of the first 21 specimens, Gene Set Enrichment Analysis revealed that SRS significantly enhanced multiple immune-related signaling pathways including interferon response, along with apoptotic pathways, in brain metastasis. We also found that TCR signaling and PD-1 signaling was upregulated by radiotherapy. TCR repertoire analysis further identified increased density and diversity of TCRs induced by SRS treatment. Profiling of the remaining sample set is currently ongoing. CONCLUSIONS In light of our previous finding regarding the correlation between immune status and outcomes of patients with brain metastases, reversing immunosuppression in brain metastasis could be a key factor on patient prognosis and treatment. Our TCR repertoire and mRNA sequencing analyses with pre-operative and post-operative SRS brain metastasis cohorts support a role for radiation-induced immunogenicity, pointing to a prospective therapeutic approach for brain metastasis management.

Immune Response and Transcriptome Analysis of the Head Kidney to Different Concentrations of Aeromonas veronii in Common Carp (Cyprinus carpio).

The common carp (Cyprinus carpio), a major economic freshwater fish, is suffering from a variety of bacterial infectious diseases because of its high-density, factory and intensive farming patterns. Aeromonas veronii is the causative agent of high mortality in common carp, causing severe economic losses in aquaculture. However, the regulatory mechanisms involved in the response of common carp to this bacterial infection remain poorly understood. In this study, we compared mortality, blood serum LZM (Lysozyme) and IgM (Immunoglobulin M) levels and transcriptome patterns of head kidney tissues after infection with different concentrations of Aeromonas veronii. We observed that mortality increased progressively with an increasing pathogen concentration. The concentrations of blood serum LZM and IgM significantly increased after infection. A total of 13 and 925 differentially expressed genes (DEGs) were identified after infection with low (T4) and high (T9) concentrations of bacterial suspension, respectively. KEGG and GO analyses of the DEGs highlighted multiple immune-related signaling pathways. Weighted gene co-expression network analysis (WGCNA) revealed that 136 and 83 hub genes were related to blood serum LZM and IgM, respectively. Finally, the gene expression in the head kidney was validated via RT-qPCR to be consistent with the transcriptome. These results provide insights into the mechanisms of the immune response to infection with different concentrations of Aeromonas veronii and offer useful information for further studies on immune defense mechanisms in common carp.

Mesenchymal stem cells: a novel therapeutic approach for feline inflammatory bowel disease

BackgroundInflammatory bowel disease (IBD) poses a significant and growing global health challenge, affecting both humans and domestic cats. Research on feline IBD has not kept pace with its widespread prevalence in human populations. This study aimed to develop a model of feline IBD by incorporating dextran sulfate sodium (DSS) to evaluate the therapeutic potential of MSCs and to elucidate the mechanisms that enhance their action.MethodsWe conducted a comprehensive clinical assessment, including magnetic resonance imaging (MRI), endoscopy, and histopathological examination. Additionally, alterations in intestinal microbiota were characterized by 16 S rDNA sequencing, and the influence of MSCs on IBD-related gene expression was investigated through transcriptome analysis.ResultsAccording to our findings, MSC treatment significantly mitigated DSS-induced clinical manifestations, reduced inflammatory cell infiltration, decreased the production of inflammatory mediators, and promoted mucosal repair. Regarding the intestinal microbiota, MSC intervention effectively corrected the DSS-induced dysbiosis, increasing the presence of beneficial bacteria and suppressing the proliferation of harmful bacteria. Transcriptome analysis revealed the ability of MSCs to modulate various inflammatory and immune-related signaling pathways, including cytokine-cytokine receptor interactions, TLR signaling pathways, and NF-κB pathways.ConclusionThe collective findings indicate that MSCs exert multifaceted therapeutic effects on IBD, including the regulation of intestinal microbiota balance, suppression of inflammatory responses, enhancement of intestinal barrier repair, and modulation of immune responses. These insights provide a solid scientific foundation for employing MSCs as an innovative therapeutic strategy for IBD and pave the way for future clinical explorations.

Identification of Cellular Senescence-Related Critical Genes and Molecular Classification and Revealing the Drug-Resistant Therapeutic Effect of IGFBP2 in Chronic Myeloid Leukemia.

The occurrence and development of hematologic tumors are closely linked to cellular senescence. However, the molecular characteristics associated with this phenomenon in chronic myeloid leukemia (CML) have not been thoroughly investigated. The cellular senescence score was calculated using gene set variation analysis. Consensus clustering algorithm was used to identify the molecular subtypes associated with cellular senescence. Clinical samples were collected for sequencing analysis to verify the expression of critical cellular senescence-related genes (CSRG). The effect of targeted inhibition of IGFBP2 on the malignant phenotype of CML-resistant cells was studied by cell experiments. The cellular senescence score in CML samples was significantly lower compared to normal samples. Higher expression of immune checkpoint markers correlated with increased cellular senescence scores. We identified two distinct molecular subtypes (C1 and C2) related to cellular senescence. The C1 subtype exhibited enhanced metabolic function and DNA damage repair capacity, while the C2 subtype showed higher infiltration of immune effector cells and activity in immune-related signaling pathways. We also discovered a group of drugs that displayed significant sensitivity differences between these two molecular subtypes, with the C2 subtype showing greater responsiveness to immunotherapy. Four critical cellular senescence-related genes (CSRGs), namely IGFBP2, IL7R, PLAU, and SUN1 demonstrated high diagnostic value for CML. We validated the expression levels of these four genes using clinical samples and confirmed through cell experiments that targeted inhibition of IGFBP2 effectively suppressed proliferation of resistant CML cells, promoted apoptosis, and enhanced therapeutic sensitivity to imatinib. Our study conducted a comprehensive analysis on CSRG expression characteristics in CML and explored potential correlations between cellular senescence and immune function. The identification of molecular subtypes provides valuable insights into assessing individual patients' biological characteristics for guiding clinical treatment decisions. Additionally, IGFBP2has emerged as a promising therapeutic target for therapy-resistant cases of CML.

Co-mutation of TP53 and TTN is Correlated with the Efficacy of Immunotherapy in Lung Squamous Cell Carcinoma.

Immunotherapy has been a promising treatment in advanced lung cancer. However, only a few patients could benefit from it. Herein, we aimed to explore mutationrelated predictive biomarkers in lung squamous cell carcinoma (LUSC), which could help develop clinical immunotherapy strategies and screen beneficial populations. Co-occurrence and mutually exclusive analysis was conducted on the TCGA-LUSC cohort. Correlations between the gene mutation status and tumor mutation burden (TMB) levels, and neo-antigen levels were analyzed by Wilcoxon test. Kaplan-Meier method was employed to analyze the progression-free survival (PFS) of lung cancer patients with immunotherapy. Gene set enrichment analysis (GSEA) was used to investigate the functional changes affected by TP53mut/TTNmut. The immune cell infiltration landscape in co-mutation subgroups was analyzed using CIBERSORT. 1) TP53, TTN, CSMD3, MUC16, RYR2, LRP1B, USH2A, SYNE1, ZFHX4, FAM135B, KMT2D, and NAV3 were frequently mutated in LUSC patients. 2) TMB levels in highly mutated groups were higher than that in wild type groups. 3) There were higher neoantigen levels in mutation group compared to the wild-type group, and LUSC patients in mutation group had longer PFS. 4) TP53mut/TTNmut co-mutation group exhibited higher TMB levels and better response to immunotherapy. 5) A host of immune-related signaling pathways was inhibited in TP53mut/TTNmut subgroup. 6) There were more T follicular helper cells and NK cells were in TP53mut/TTNmut subgroup than in the WT subgroup. The LUSC patients with TP53 and TTN co-mutation had higher TMB levels and better response to immunotherapy. The TP53 and TTN co-mutation is a promising novel biomarker to assist LUSC immunotherapy evaluation.

Comprehensive analysis of a necroptosis-associated diagnostic signature for myelodysplastic syndromes based on single-cell RNA-seq and bulk RNA-seq

BackgroundMyelodysplastic syndromes (MDS) are heterogeneous and clonal hematological disorders. The role and mechanism of necroptosis in MDS remain poorly understood.MethodsmRNA expression profiles and single-cell RNA-sequencing (scRNA-seq) data were sourced from the GEO database. ScRNA-seq data were processed using the “Seurat” package. After cell annotation, necroptosis-related scores (NRscores) for each cell were calculated using the “UCell” package. Differentially expressed genes (DEGs) and their associated biological functions in NRscore-related cell populations were identified. Additionally, DEGs and necroptosis-related genes (DE-NRGs) between MDS patients and healthy controls were identified. Consensus clustering was employed to classify MDS patients into distinct subclusters based on DE-NRGs. The biological functions and immune characteristics of these classifications were analyzed. Prognostic gene signatures were determined using LASSO and SVM-RFE analyses, and a nomogram was constructed based on the prognostic gene signature.ResultsA total of 12 cell types were identified in MDS and healthy controls. NRscore was found to be elevated in monocytes and common lymphoid precursors (CLPs). Enrichment analysis revealed that monocytes and CLPs with high NRscore were associated with mitochondria-related and immune-related pathways. Eleven DEGs in monocytes and CLPs between MDS patients and healthy controls were identified. Additionally, 13 DE-NRGs were identified from 951 DEGs between MDS and healthy controls. MDS patients were classified into two distinct subclusters based on these 13 DE-NRGs, revealing several immune-related processes and signaling pathways. Differences in immune subpopulations between the two subclusters were observed. A necroptosis-related diagnostic gene signature (IRF9, PLA2G4A, MLKL, BAX, JAK2, and STAT3) was identified as predictive of MDS prevalence.ConclusionNecroptosis plays a role in MDS progression by inducing inflammation. A novel necroptotic gene signature has been developed to distinguish and diagnose MDS at early stages of the disease.

Effect of Moniezia Benedeni infection on ileal transcriptome profile characteristics of sheep

BackgroundThe intestinal mucosal immune system, renowned for its precise and sensitive regulation, can provide comprehensive and effective protection for the body, among which the ileum is a critical induction site for regulating mucosal immune homeostasis. Moniezia benedeni parasitizes the small intestine of sheep and can cause serious pathological damage or even death to the host when the infection is severe. In this study, 5 sheep infected with Moniezia benedeni were selected as the infected group, and 5 uninfected sheep were selected as the control group. The ileal transcriptome profile characteristics of Moniezia benedeni infection were analyzed based on RNA-seq sequencing technology, aiming to lay a foundation for further exploring the perception mechanism of sheep intestines to Moniezia benedeni infection and formulating effective prevention and control strategies.ResultsThe results showed that a total of 3,891 differentially expressed genes (DEGs) were detected in the ileum tissues of sheep between the infected and control groups with 2,429 up-regulated genes and 1,462 down-regulated genes. GO and KEGG pathway enrichment analysis of differential genes, as well as Clue GO analysis showed that differential genes were significantly enriched in immune and metabolic-related biological processes and signaling pathways. Particularly, in immune-related signaling pathways, the B cell receptor signaling pathway was significantly down-regulated, while in metabolic regulation related signaling pathways, Bile secretion, Fat digestion and absorption and Vitamin digestion and absorption were notably up-regulated. On this basis, the differential core genes related to immune metabolism were verified by qRT-PCR method. The results showed that OVAR, CD3E, CD8A, CD4 and CD28 were significantly up-regulated (P < 0.05), while CIITA, BLNK, BCL6 and CD79A were significantly down-regulated (P < 0.05), which were consistent with transcriptome sequencing data.ConclusionsThe results demonstrated that Moniezia benedeni infection significantly affected the immune and metabolic processes in sheep ileum, particularly, it significantly inhibited the activation process of host B cells, and also led to an overactive function of bile acid metabolism. This finding provides a solid foundation for further elucidating the response mechanism of Peyer's patches in sheep ileum to Moniezia tapeworm infection.

Overexpression of TPD52L2 in HNSCC: prognostic significance and correlation with immune infiltrates.

Evidence has been presented that the tumor protein D52 (TPD52) family plays a critical role in tumor development and progression. As a member of the TPD52 family, the changes in TPD52L2 gene status are instrumental in kinds of cancer development. However, its effects on patient prognosis and immune infiltration in Head and Neck Squamous Carcinoma (HNSCC) are still poorly understood. The Tumor Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and c-BioPortal database was used to explore the expression pattern, prognostic value, and variation of gene status in HNSCC. The LinkedOmics database was used to obtain the co-expression genes of TPD52L2 and identify the diagnostic value of TPD52L2 in HNSCC. The correlations between TPD52L2 expression and six main types of immune cell infiltrations and immune signatures were explored using Tumor Immune Estimation Resource (TIMER). The correlation between TPD52L2 expression and immune checkpoint genes (ICGs) was analyzed by TCGA database. Immunohistochemistry (IHC) was performed to validate the expression of three ICGs (PDL1, PDL2, EGFR) and TPD52L2 using 5 paired HNSCC and normal head and neck tissues. Polymerase Chain Reaction (PCR) and Western Blot (WB) of HNSCC and normal head and neck cell lines were performed to verify the high level of TPD52L2 mRNA and protein expression. protein expression of TPD52L2 in pan-cancer was also validated using UALCAN. TPD52L2 was overexpressed in tumor tissues, and it predicted worse survival status in HNSCC. ROC analysis suggested that TPD52L2 had a diagnostic value. Multivariate Cox analysis identified TPD52L2 as an independent negative prognostic marker of overall survival. Functional network analysis suggested that TPD52L2 was associated with immune-related signaling pathways, cell migration pathways, and cancer-related pathways. High expression of TPD52L2 was associated with a more mutant frequency of TP53. Notably, we found that the expression of TPD52L2 was closely negatively correlated with the infiltration levels of 15 types of immune cells and positively correlated with several immune markers. PCR, WB experiments, and UALCAN database verified the high level of TPD52L2 mRNA and protein expression. TPD52L2 is upregulated in HNSCC, which is an independent factor for adverse prognosis prediction. It probably plays a role in the negative regulation of immune cell infiltration. TPD52L2 might be a promising prognostic biomarker and therapeutic target in HNSCC.

202 Longitudinal comparative transcriptomics of dairy cattle at different altitudes reveals unique mechanisms underlying plateau hypoxia adaptation

Abstract The adaptation of livestock to high altitude hypoxic environment (plateau hypoxia adaptation) is important as they have a key role in the socio-economic conditions of the local residents. However, the underlying molecular mechanisms of plateau hypoxia adaptation of livestock are poorly understood. This study was objective to 1) construct the longitudinal transcriptional profiles of dairy cattle across five development stages; 2) reveal the transcriptomic changes of peripheral blood under different altitudes environment; and 3) identify key genes involved in plateau hypoxia adaptation in bovine. In this study, 109 peripheral blood samples from 70 Holstein cattle were performed whole transcriptome sequencing, including 56 at high altitude (&amp;gt; 3600 m) at five development stages (1, 2, 6, 12 and 18 mo) from 56 individuals, and 53 at low altitude (~1000 m) at three development stages (1, 2 and 6 mo) from 14 individuals. The peripheral transcriptional profile was obtained for high altitude cattle at five development stages, and for low altitude cattle for three development stages. By the transcriptome profile analysis in plateau cattle across five development stages, it was found that there were significant differences on mRNA transcriptome at different stages, and a noticeable shift occurred between 2 mo and 6 mo. By a comparative analysis of the transcription levels between high and low altitude cattle, 795, 900 and 880 differentially expressed genes (DEGs) were identified at the age of 1, 2 and 6 mo, respectively. The DEGs at three stages were enriched in several cellular communication, hypoxia response, and regulation of blood pressure, and immune-related signaling pathways. Furthermore, there were 64 DEGs shared across three comparative analyses at the three stages. By functional annotation analysis, we observed the shared DEGs of the three stages were enriched in the Notch signaling involved in heart development, regulation of phosphorylation, and positive regulation of MAP kinase activity. In summary, this study revealed the development-related transcriptomic shifts from birth to 18 mo of age in dairy cattle, and preliminarily elucidated the important signaling pathways involved in bovine plateau hypoxia adaptation by comparative analysis between high and low altitude cattle. The results of the current study will drive a better understanding of plateau hypoxia adaptation and can provide molecular targets for future breeding of plateau-adapted dairy cattle.

Pentachlorophenol impairs the antimicrobic capability of blood clam via undermining humoral immunity and disrupting humoral-cellular crosstalk

Due to past massive usage and persistent nature, pentachlorophenol (PCP) residues are prevalent in environments, posing a potential threat to various organisms such as sessile filter-feeding bivalves. Although humoral immunity and its crosstalk with cellular one are crucial for the maintaining of robust antimicrobic capability, little is known about the impacts of PCP on these critical processes in bivalve mollusks. In this study, pathogenic bacterial challenge and plasma antimicrobic capability assays were carried out to assess the toxic effects of PCP on the immunity of a common bivalve species, blood clam (Tegillarca granosa). Moreover, the impacts of PCP-exposure on the capabilities of pathogen recognition, hemocyte recruitment, and pathogen degradation were analyzed as well. Furthermore, the activation status of downstream immune-related signalling pathways upon PCP exposure was also assessed. Data obtained illustrated that 28-day treatment with environmentally realistic levels of PCP resulted in evident declines in the survival rates of blood clam upon Vibrio challenge along with markedly weakened plasma antimicrobic capability. Additionally, the levels of lectin and peptidoglycan-recognition proteins (PGRPs) in plasma as well as the expression of pattern recognition receptors (PRRs) in hemocytes were found to be significantly inhibited by PCP-exposure. Moreover, along with the downregulation of immune-related signalling pathway, markedly fewer chemokines (interleukin 8 (IL-8), IL-17, and tumor necrosis factor α (TNF-α)) in plasma and significantly suppressed chemotactic activity of hemocytes were also observed in PCP-exposed blood clams. Furthermore, compared to that of the control, blood clams treated with PCP had markedly lower levels of antimicrobic active substances, lysozyme (LZM) and antimicrobial peptides (AMP), in their plasma. In general, the results of this study suggest that PCP exposure could significantly impair the antimicrobic capability of blood clam via undermining humoral immunity and disrupting humoral-cellular crosstalk.