Immune Genes Research Articles

Bioinformatics insights into mitochondrial and immune gene regulation in Alzheimer's disease

BackgroundThere is growing evidence that the pathogenesis of Alzheimer's disease is closely linked to the resident innate immune cells of the central nervous system, including microglia and astrocytes. Mitochondrial dysfunction in microglia has also been reported to play an essential role in the pathogenesis of AD and other neurological diseases. Therefore, finding the mitochondrial and immune-related gene (MIRG) signatures in AD can be significant in diagnosing and treating AD.MethodsIn this study, the intersection of the differentially expressed genes (DEGs) from the GSE109887 cohort, immune-related genes (IRGs) obtained from WGCNA analysis, and mitochondria-related genes (MRGs) was taken to identify mitochondria–immune-related genes (MIRGs). Then, using machine learning algorithms, biomarkers with good diagnostic value were selected, and a nomogram was constructed. Subsequently, we further analyzed the signaling pathways and potential biological mechanisms of the biomarkers through gene set enrichment analysis, prediction of transcription factors (TFs), miRNAs, and drug prediction.ResultsUsing machine learning algorithms, five biomarkers (TSPO, HIGD1A, NDUFAB1, NT5DC3, and MRPS30) were successfully identified, and a nomogram model with strong diagnostic ability and accuracy (AUC > 0.9) was constructed. In addition, single-gene enrichment analysis revealed that NDUFAB1 was significantly enriched in pathways associated with diseases, such as Alzheimer's and Parkinson's, providing valuable insights for future clinical research on Alzheimer's in the context of mitochondrial–immune interactions. Interestingly, brain tissue pathology showed neuronal atrophy and demyelination in AD mice, along with a reduction in Nissl bodies. Furthermore, the escape latency of AD mice was significantly longer than that of the control group. After platform removal, there was a notable increase in the path complexity and time required to reach the target quadrant, suggesting a reduction in spatial memory capacity in AD mice. Moreover, qRT-PCR validation confirmed that the mRNA expression of the five biomarkers was consistent with bioinformatics results. In AD mice, TSPO expression was increased, while HIGD1A, NDUFAB1, NT5DC3, and MRPS30 expressions were decreased. However, peripheral blood samples did not show expression of HIGD1A or MRPS30. These findings provide new insights for research on Alzheimer's disease in the context of mitochondrial–immune interactions, further exploring the pathogenesis of Alzheimer's disease and offering new perspectives for the clinical development of novel drugs.ConclusionsFive mitochondrial and immune biomarkers, i.e., TSPO, HIGD1A, NDUFAB1, NT5DC3, and MRPS30, with diagnostic value in Alzheimer's disease, were screened by machine-learning algorithmic models, which will be a guide for future clinical research of Alzheimer's disease in the mitochondria–immunity-related direction.

Immune gene features and prognosis in colorectal cancer: insights from ssGSEA typing

BackgroundColorectal cancer (CRC) is a molecularly heterogeneous disease, and its treatment and prognosis vary greatly among subgroups. Therefore, it is necessary to identify prognostic factors associated with the biological heterogeneity of CRC in order to improve patients' survival expectations.MethodsWe obtained and merged RNA-Seq data along with clinical details for colorectal cancer (CRC) from The Cancer Genome Atlas (TCGA) repository, and then performed immunocluster typing on all CRC specimens. We conducted differential expression gene (DEG) analysis, gene set enrichment analysis (GSEA), and tumor microenvironment (TME) analysis on CRC samples that were divided into high and low Immunity categories. Moreover, we pinpointed prognostic genes from immune-related gene (IRGs) sets, developed a prognostic risk model, and executed survival analysis, receiver operating characteristic (ROC) curve analysis, and independent prognostic analysis. Additionally, we assessed the risk for patients categorized into high- and low-risk groups based on the model. Lastly, we created a Nomogram to customize the prediction of survival outcomes in CRC patients.ResultsCRC samples were divided into high and low Immunity groups based on the median value of the immunity score. Between the two groups, a total of 1550 DEGs were identified and 395 differentially expressed immune-related genes (DE-IRGs) were identified by intersection with 2483 IRGs. The DE-IRGs of the high Immunity group were dominated by Cytokine receptor interactions, chemokine signaling pathways and immune cell-mediated cytotoxicity, and molecule function of immune effector process. TME analysis showed that most of the 27 immune cells and functions were highly enriched in high Immunity group, whose Immune Score, Stromal Score and ESTIMATE Score were significantly higher. Subsequently, a prognostic risk model of CRC was constructed based on 12 prognostic genes, and the accuracy and reliability of the model prediction were verified. Finally, Nomogram enabled accurate individual prediction of the survival prognosis of CRC patients.ConclusionsOur study develops an immune-related prognostic model and Nomogram that reliably predicts survival outcomes in CRC patients and enhances understanding of the tumor immunity and molecular mechanisms of CRC.

Anopheles gambiae phagocytic hemocytes promote Plasmodium falciparum infection by regulating midgut epithelial integrity

For successful transmission, the malaria parasite must traverse tissue epithelia and survive attack from the insect’s innate immune system. Hemocytes play a multitude of roles in mosquitoes, including defense against invading pathogens. Here, we show that hemocytes of the major malaria vector Anopheles gambiae promote Plasmodium falciparum infection by maintaining midgut epithelial integrity by controlling cell proliferation upon blood feeding. The mosquito’s hemocytes also control the midgut microbiota and immune gene expression. Our study unveils novel hemocyte functions that are exploited by the human malaria parasite to evade the mosquito’s immune system.

Identification of Interleukin-Related Genes Signature for Prognosis Prediction in Head and Neck Squamous Cell Carcinoma Patients.

This study focused on identifying the interleukin (IL)-related genes that influence the head and neck squamous cell carcinoma (HNSCC) patients' prognosis and response to anticancer therapy in patients with HNSCC. We developed a risk model that included three gene signatures, IL Enhancer Binding Factor 2 (ILF2), IL 36 alpha (IL36A), and IL10, based on differential expression analysis, survival analysis, Least Absolute Shrinkage and Selection Operator (LASSO) analysis, and Cox regression analysis. We found that the low-risk group was scored with higher immune cell infiltration, higher expression of human leukocyte antigen (HLA) family genes and immune checkpoint genes, higher cytolytic activity (CYT), tertiary lymphoid structures (TLS), and CD8A/PD-L1 ratio. In contrast, the high-risk group was scored with higher tumor immune dysfunction and exclusion (TIDE), which implied worse response to immunotherapy and worse prognosis. The results above indicated that the low-risk group had stronger antitumor immunity and better responsiveness to immunotherapy. We also observed a significantly enriched pattern of cancer-related pathways and immune pathways in the comparison of the high-risk and low-risk groups. Furthermore, the high-risk group had higher sensitivity to chemotherapy drugs, which suggested that they might benefit from chemotherapy treatment. Following the results above, we confirmed in HNSCC cell lines and clinical specimens that the level of ILF2 in tumors was significantly higher than that in adjacent tumor tissues. Besides, in vivo and in vitro results both showed that silencing ILF2 might depress tumor growth, invasion, and migration. This study not only provided novel perspectives into the immunological and molecular mechanisms of HNSCC and uncovered IL-related gene signatures for predicting HNSCC patients' prognosis and response to chemotherapy and immunotherapy, but also preliminarily suggested that ILF2 might be an important target in the treatment of HNSCC.

Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancer

We aimed to create a NK cell marker genes-based signature to predict immunotherapy response and prognosis in colorectal cancer. We integrated scRNA-seq data from four Gene Expression Omnibus (GEO) samples and performed Weighted gene correlation network analysis (WGCNA) based on 587 the Cancer Genome Atlas (TCGA) colorectal cancer samples to uncover NK cell-related genes. We identified 1080 NK cell-related core genes and 276 NK cell-related feature genes based on WGCNA and clustering and annotation of scRNA-seq data, respectively. Six key NK cell-related prognostic signature genes were obtained by univariate and LASSO regression analyses, including ADAM8, CTSD, CCL4, IL2RB, TTC38, and PLEK. Two validation cohorts from the GEO dataset, comprising 124 and 201 samples respectively, were used. The signature was significantly associated with overall survival and correlated with immune cell infiltration, immune and stromal scores, and immune checkpoint genes. Furthermore, the signature was associated with the homologous recombination deficiency (HRD) and T-cell receptor (TCR) scores. In conclusion, our study proposes a new prognostic signature based on NK cell marker genes, which may serve as a potential tool to predict overall survival and immunotherapy response for CRC patients.

Unveiling prognostic value of JAK/STAT signaling pathway related genes in colorectal cancer: a study of Mendelian randomization analysis

BackgroundColorectal cancer (CRC) ranks among the frequently occurring malignant neoplasms affecting the gastrointestinal tract. This study aimed to explore JAK-STAT signaling pathway related genes in CRC and establish a new prognostic model.MethodsThe data set used in this study is from a public database. JAK-STAT-differentially expressed genes (DEGs) were identified through differential expression analysis and weighted gene co-expression network analysis (WGCNA). Prognostic genes were selected from JAK-STAT-DEGs through Mendelian randomization (MR), univariate Cox regression, and least absolute shrinkage and selection operator (LASSO) analyses. The expressions of prognostic genes were verified by RT-qPCR. Then, a risk model was built and validated by the GSE39582. Independent prognostic factors were screened underlying risk scores and different clinical indicators, resulting in the construction of a nomogram. Additionally, immune infiltration, immune scores and immune checkpoint inhibitors analyses and gene set enrichment analysis (GSEA) were carried out.ResultsThe 3,668 JAK-STAT-DEGs were obtained by intersection of 5826 CRC-DEGs and 9766 JAK-STAT key module genes. Five prognostic genes were selected (ANK3, F5, FAM50B, KLHL35, MPP2), and their expressions were significantly different between CRC and control groups. A risk model was constructed according to prognostic genes and verified by GSE39582. In addition, the nomogram exhibited superior predictive accuracy for CRC. Furthermore, immune analysis results indicated a notable positive correlation between risk score and the scores of immune (R = 0.486), stromal (R = 0.309), and ESTIMATE (R = 0.422). Immune checkpoint inhibitor ADORA2A (Cor = 0.483263) exhibited the strongest positive correlation with risk score. And MPP2 exhibited the most potent activating influence on the cell cycle pathway, whereas ANK3 demonstrated the most significant inhibitory effect within the apoptosis pathway.ConclusionsA new JAK-STAT related CRC prognostic model was constructed and validated, which possessed an underlying predictive potential for CRC patients’ prognosis and could potentially enhance tailored guidance for immunotherapy.

Identification of the immune infiltration and biomarkers in ulcerative colitis based on liquid–liquid phase separation-related genes

Liquid–liquid phase separation (LLPS) associates with immune infiltration in multiple diseases. Nonetheless, the role of LLPS-related genes (LLPS-RGs) in immune infiltration of ulcerative colitis (UC) is still elusive. We identified the hub LLPS-RGs (DE-LLPS-RGs) (HSPB3, SLC16A1, TRIM22, SRI, PLEKHG6, GBP1, PADI2) by machine learning algorithms. Hub genes were screened that displayed high prediction accuracy of UC patients. Both the microarray and scRNA-seq datasets showed a strong correlation with immune cell infiltration and cytokines, especially GBP1, TRIM22, SRI. And qRT-PCR analysis showed that GBP1 play a pro-inflammatory role in UC. Two distinct clusters were identified, in which cluster A displayed higher immune infiltration level compared with the cluster B. The top targeted biological pathways of two clusters were distinct, glutamate receptor antagonist ranked top for cluster A while HDAC inhibitor ranked top in cluster B. External cohort and UC cell model validation indicated the similar immune infiltration levels, gene expression and cytokine expression patterns. We determined the seven high accuracy diagnostic genes of UC patients and provide a new perspective on immunoregulation in UC pathogenesis. And suggest patient stratification and candidate targets for precision treatment based on hub genes screened.

A new signature associated with anoikis predicts the outcome and immune infiltration in nasopharyngeal carcinoma

BackgroundPrevious studies have confirmed the phenomenon of anoikis resistance in nasopharyngeal carcinoma (NPC). Nevertheless, the prognostic significance of anoikis-related genes (ARGs) in NPC remains incompletely understood. This study aimed to create a predictive risk score using an ARGs signature for NPC patients and to investigate how this score relates to clinicopathologic features and immune infiltration in the tumor microenvironment.MethodsBy using data from the Gene Expression Omnibus (GEO) database, we employed machine learning methods to discover prognostic ARGs and create a risk score. Key gene expression levels were validated through real-time PCR and immunohistochemical staining.ResultsThree differentially expressed ARGs (CDC25C, E2F1 and RBL2) with prognostic value were identified by the intersection of multiple machine learning algorithms. A risk score based on t 3-ARG feature was developed to stratify NPC patients into two distinct risk groups using the optimal model, Random Survival Forest. NPC patients with high-risk scores experienced notably shorter progression-free survival in comparison to those with low-risk scores. Multivariate Cox regression analysis indicated that the risk score served as an independent prognostic factor. The time-dependent ROC and decision curve analyses demonstrated the risk model's strong predictive accuracy and clinical utility. The low-risk score group exhibited features indicative of early clinical stage, immune activation, high immune checkpoint gene's expression, and low Epstein-Barr virus gene's expression. Functional analysis revealed enrichment of immune-related pathways in the low-risk group. Patients with high-risk scores were discovered to be unlikely to benefit from immune checkpoint inhibitor treatment. Moreover, the expression of RBL2, E2F1, and CDC25C were significantly correlated with the expression of caspase family genes. Finally, the lower mRNA and protein expression of RBL2 were validated in NPC cell lines and tissues.ConclusionsOur ARGs-based signature model shows promising results in predicting the prognosis of NPC patients and might be associated with immune cell infiltration.

Memory B cells and their transcriptomic profiles associated with belimumab resistance in systemic lupus erythematosus in the maintenance phase

The factors contributing to the treatment efficacy of belimumab in patients with systemic lupus erythematosus (SLE) in the maintenance phase are unknown. Here, we collected blood samples from patients with SLE (n=44) treated with belimumab before and three and six months after treatment. RNA-Seq of whole blood was performed, and gene expression was quantified. Immune cell type enrichment analysis estimated immune cell subtype proportions and gene expression in each subtype. The Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2K) < 4 at six months was set as the primary efficacy criterion. Non-responders exhibited upregulated B cell proliferation signals before treatment, associated with an increased number of memory B cells. A higher proportion of memory B cells before treatment predicted poor response (p=5.1×10-4). This was also associated with changes in disease activity and glucocorticoid dose at six months compared with baseline. Belimumab did not affect memory B cell proportion during the treatment time course, in contrast to naïve B cells. Higher memory B cell proportion was associated with higher type-I interferon (IFN) scores and lower white blood cell and complement C4 levels. Transcriptomic analysis of memory B cells in non-responders revealed significant upregulation of immunoglobulin genes (Ig). Memory B cells and high Ig expression in them were identified as a treatment-resistant factor of belimumab in SLE patients. Lower C4 and white blood cell counts may serve as clinical markers of higher memory B cells.

IRG1/itaconate enhances efferocytosis by activating Nrf2-TIM4 signaling pathway to alleviate con A induced autoimmune liver injury

Immune response gene 1 (IRG1) is highly expressed in mitochondria of macrophages in a pro-inflammatory state. IRG1 and its metabolites play important roles in infection, immune-related diseases and tumor progression by exerting resistance of pathogens, attenuating inflammation and producing antioxidant substances through various pathways and mechanisms. IRG1 deficiency aggravates liver injury. Efferocytosis is a vital mechanism for preventing the progression of inflammatory tissue damage. However, the mechanism by how IRG1/itaconate regulates efferocytosis in autoimmune hepatitis has yet to be fully understood. Therefore, we explored the influence of IRG1-/- on efferocytosis and its effects on regulating the nuclear factor erythroid 2-associated factor 2 (Nrf2)-T-cell immunoglobulin domain and mucin domain 4 (TIM4) pathway and autoimmune liver injury. An autoimmune hepatitis model was established by injecting Con A into wild-type and IRG1-/- mice via the tail vein. Liver injury and inflammatory response were assessed. The efferocytosis role of IRG1-/- macrophages and its potential regulatory mechanisms were also analysed. Exogenous 4-octyl itaconate (OI) supplementation promoted the expression of Nrf2 and TIM4 and restored IRG1-/- bone marrow-derived macrophage (BMDM) efferocytosis, whereas inhibition of Nrf2 mediated by ML385 led to impaired efferocytosis of BMDMs, decreased expression of TIM4, and aggravated liver inflammation injury. Additionally, after supplementing Nrf2-/- BMDMs with exogenous OI, we evaluated the changes in its efferocytosis effect, efferocytosis did not change, and the protective effect of OI disappeared. However, when TIM4 was blocked, the efferocytotic effect of BMDMs was attenuated, inflammatory liver injury and oxidative stress were aggravated. OI promoted the transformation of macrophages into M2 macrophages, and this was inhibited when TIM4 was blocked. To our best understanding, this is the initial exploration to show that TIM4, a downstream molecule of the IRG1/itaconate-Nrf2 pathway, regulates macrophage efferocytosis. These findings suggest a new mechanism and potential treatment for promoting the resolution of inflammation and efferocytosis in autoimmune hepatitis.

Treatment with the CCR5 antagonist OB-002 reduces lung pathology, but does not prevent disease in a Syrian hamster model of SARS-CoV-2 infection.

Since the emergence of SARS-CoV-2 and the COVID-19 pandemic, a wide range of treatment options have been evaluated in preclinical studies and clinical trials, with several being approved for use in humans. Immunomodulatory drugs have shown success in dampening the deleterious inflammatory response seen in severe COVID-19 patients, but there remains an urgent need for development of additional therapeutic options for COVID-19 treatment. A potential drug target is the CCR5-CCL5 axis, and blocking this pathway may protect against severe disease. Here we evaluated whether OB-002, an analog of human CCL5 and a potent antagonist of CCR5, provides therapeutic benefit in SARS-CoV-2 infected Syrian hamsters. Daily treatment with OB-002 altered immune gene transcription in the lungs, and reduced pathology following infection, but did not prevent weight loss or viral replication in the lungs of infected animals, even in combination with the antiviral drug remdesivir. Our data suggest that targeting the CCR5-CCL5 pathway in SARS-CoV-2 infection in hamsters is insufficient to significantly impact disease development in this model.

EDF1 accelerates ganglioside GD3 accumulation to boost CD52-mediated CD8+ T cell dysfunction in neuroblastoma

BackgroundHeterogeneous clinical features and prognosis in neuroblastoma (NB) children are frequently dominated by immune elements. Dysfunction and apoptosis in immune cells result from the exposure to continuous tumor-related antigen stimulation and coinhibitory signals. To date, key factors pointing to the restriction of NB-specific CD8+ T cells remain elusive.MethodsWe performed bulk-RNA sequencing and lipidomic analyses of children with mediastinal NB. Bioinformatics analysis and biological validation were applied to uncover the underlying mechanism.ResultsThree subtypes were identified using nonnegative matrix factorization (NMF), among which we highlighted an apoptotic status of infiltrated CD8+ T cells, along with the highest CD52 and EDF1 expression in Cluster3 (C3) subtypes. It was verified that high EDF1 expression in NB cells led to Lactosylceramide (LacCer) accumulation, as well as downstream ganglioside-GD3, which subsequently increased the expression of CD52 and immune checkpoint genes, chemotaxis, and apoptosis-related events in activated CD8+T cells. Mechanistically, EDF1 was recruited as a coactivator to form the NF-κB/RelA/EDF1 complex, which further prevented the promoter region methylation of ST8SIA1, to elevate its transcription.ConclusionThese findings characterize abundant GD3 in NB cells, which regulated by the EDF1/RelA/ST8SIA1 axis, is responsible for CD8+ T cell dysfunction. Inhibition of EDF1 may reduce suppressive factors and prevent immune escape of NB cells. Modulating NB-associated GD3 levels through metabolic intervention is beneficial for tuning the depth and duration of responses to current NB therapies. The integration of transcriptomic and lipidomic data offers a more comprehensive understanding of the interaction between LacCer metabolites and the immune status in NB.Graphical

Overexpression of miR-155 Modulates Interferon Response and Inhibits Viral Replication of IHNV and IPNV in EPC Cells.

Infections caused by RNA viruses, including infectious haematopoietic necrosis virus (IHNV) and infectious pancreatic necrosis virus (IPNV), result in substantial economic losses in the aquaculture industry. MicroRNAs (miRNAs), particularly miR-155, play crucial roles in regulating host immune responses and viral infections. In this study, we investigated the overexpression effect of miR-155 in Epithelioma papulosum cyprini (EPC) cells infected with IHNV and IPNV and analysed the mechanisms underlying these antiviral activities. EPC cells were transfected with miR-155 at 40 pmol and then infected with IHNV or IPNV at an MOI of 0.01. The cytopathogenic effect (CPE) was observed for 5 days post-infection. The cells transfected with miR-155 did not show any signs of CPE or exhibit any viral growth over time after infection with both viruses. Additionally, real-time qPCR of type I interferon-related immune genes (ISG15 and Mx1) showed upregulation at 0, 24, and 48 h.p.i in cells transfected with miR-155. At 48 h post-infection, the cells transfected with miR-155 did not show any bands of viral protein by western blot. Furthermore, the overexpression of miR-155 in EPC cells significantly enhanced the expression of interferon response genes by targeting BCL2 and CYLD and suppressed the viral replication through directly targeting viral genes, including the L gene of IHNV and the VP2 gene of IPNV. These findings elucidate the dual mechanism of miR-155's antiviral effect through immune modulation and direct viral gene targeting, offering insights for developing novel antiviral strategies in aquaculture.

Single-cell landscape of dynamic changes in CD8+ T cells, CD4+ T cells and exhausted T cells in hepatocellular carcinoma

Hepatocellular carcinoma has a high incidence and poor prognosis. In this study, we investigated the value of T-cell-related genes in prognosis by single-cell sequencing data in hepatocellular carcinoma. Twelve cases of hepatocellular carcinoma single-cell sequencing were included in the study. The high dimensional weighted gene co-expression network analysis (hdWGCNA) was used to identify gene modules associated with CD4+ T cells, CD8+ T cells and exhausted T cells. Altered signaling pathway activity in exhausted T cells was uncovered by the AUCell algorithm. xCELL, TIMER, QUANTISEQ, CIBERSORT and CIBERSORT-abs were performed to explore immune cell infiltration. Immune checkpoint inhibitor genes and TIDE methods were used to predict immunotherapy response. Finally, immunohistochemistry and real-time PCR were used to verify gene expression. The hdWGCNA algorithm identified 40 genes strongly associated with CD4+ T cells, CD8+ T cells and exhausted T cells. Seven genes were finally selected for transcriptome data modeling. The results of the three independent datasets suggested that the model had strong prognostic value. Model genes were critical factors influencing CD4+ T cell and CD8+ T cell infiltration in patients. The efficacy of PD-1 immunotherapy was higher in patients belonging to the low-risk group. Alterations in signaling pathways’ activity within exhausted T cells were crucial factors contributing to the decline in immune function. Differential expression of seven genes in CD8+ T cells, CD4+ T cells and exhausted T cells were key targets for improving immunotherapy response in HCC.

Chinese sacbrood virus mediates m6A modification to target and suppress the expression of hemolymph maintenance gene AF9, exacerbating bee infections.

The Chinese sacbrood virus (CSBV) poses a serious threat to the health of Apis cerana colonies, yet its specific pathogenic mechanism remains unclear. This study shows that infection with CSBV can enhance overall m6A modification levels in Apis cerana larvae and suppress the expression of AF9 by promoting targeting of AcMETTL3, thereby inhibiting the innate immune response and exacerbating CSBV infection. Further analyses indicated that AF9 functions similarly as the mammalian homologous gene MLLT3 by maintaining normal functions of hemolymph. Moreover, AF9 can also significantly inhibit infections by common Apis mellifera viruses. In summary, a new mechanism is detailed here by which CSBV escapes the host's innate immune response by enhancing m6A modification to target and suppress the immune response gene AF9. This study also provides new insights into the mechanisms by which bee viruses inhibit host immune responses and suggests that AF9 may serve as a potential new broad-spectrum antiviral target in bees.

Characterization and functional analysis of Spodoptera litura galectins.

Insects rely on their effective innate immune system to defend against pathogen infection, and pattern recognition receptors (PRRs) play a crucial role in insect immunity. Galectins, a family of animal β-galactoside-binding lectins, may serve as PRRs. Mammalian galectins are involved in diverse physiological processes; however, less is known about functions of insect galectins. In this study, we focused on an agricultural pest Spodoptera litura and identified a total of 13 Slgalectins, and a functional study of Slgalectin-4 and Slgalectin-7 was conducted. Both recombinant Slgalectin-4 and Slgalectin-7 proteins directly bound to Bacillus thuringiensis and an entomopathogenic fungus Metarhizium rileyi. Importantly, supplementing recombinant Slgalectin-4 to S. litura larvae significantly increased larval survival after M. rileyi infection but accelerated larvae death after B. thuringiensis infection, whereas supplementing Slgalectin-7 increased larval survival after B. thuringiensis infection but did not influence larval survival after M. rileyi infection. Supplementing both Slgalectin-4 and Slgalectin-7 altered the expression of some antimicrobial peptide genes in larval hemocytes after microbial infection, which may partly account for the roles of Slgalectin-4 and -7 in larval survival. Our findings revealed that Slgalectin-4 and -7 may serve as PRRs to bind different pathogens and alter expression of immune effector genes such as antimicrobial peptide genes, eventually modulating immune responses of S. litura larvae to pathogens such as B. thuringiensis and M. rileyi. © 2025 Society of Chemical Industry.

Evaluation of mucosal adjuvants to chitosan-nanoparticle-based oral subunit vaccine for controlling salmonellosis in broilers

Salmonellosis, a gastrointestinal disease, continues to be one of the major public health concerns worldwide. Poultry meat and eggs are recognized as the major source of Salmonella food poisoning in humans. Our study evaluated the protective efficacy of mannose-conjugated chitosan-nanoparticle (mChitosan-NP)-based subunit vaccine, consisting of immunogenic outer membrane proteins and flagella of Salmonella Enteritidis [mChitosan (OMP+FLA)/FLA-NP], coadministered orally with potent mucosal adjuvants to reduce the colonization of S. Enteritidis in the intestines of broiler chickens. We evaluated the adjuvant effects of three different doses of two well-known mucosal adjuvants, c-di-GMP (stimulator of interferon gene agonist) and whole cell lysate (WCL) of Mycobacterium smegmatis, to improve the efficacy of mChitosan (OMP+FLA)/FLA-NP vaccine. Our data reaffirmed the potent adjuvanticity of both of these adjuvants and identified their optimal dose when entrapped in mChitosan-NP to potentiate the immunogenicity and efficacy of orally delivered mChitosan (OMP+FLA)/FLA-NP vaccine. The physical characteristics of mChitosan (OMP+FLA)/FLA-NP, mChitosan-GMP/FLA-NP, and mChitosan-WCL/FLA-NP formulations revealed a high positive charge (Zeta potential +20–25 mV), size 235–260 nm, and polydispersity index 0.35–0.52, which are conducive for oral delivery. The efficacy in chickens that received oral administration with a combination of the vaccine-adjuvant formulations was evaluated by challenging with Salmonella Enteritidis. Our data showed that mChitosan (OMP+FLA)/FLA-NP WCL at 10 µg/dose formulation consistently reduced the S. Enteritidis load by over 0.5 log10 comparable to a commercial live vaccine at post-challenge days 4 and 10. Immunologically, we observed enhanced systemic and mucosal antibody and cellular (B cells and T-helper cells) immune responses as well as upregulation of expression of immune cytokine genes IFN-γ, TGF-β, and IL-17 in the cecal tonsils of adjuvanted mChitosan-NP Salmonella-subunit-vaccinated birds. Overall, particularly the mucosal adjuvant WCL consistently enhanced the efficacy of mChitosan (OMP+FLA)/FLA-NP vaccine by inducing effective immune responses.

Integrative bioinformatics and experimental analyses identify U2SURP as a novel lactylation-related prognostic signature in esophageal carcinoma.

The lactylation modification has been implicated in several cancer types; however, the role of lactylation modification-related genes in esophageal carcinoma (EC) remains underexplored. Utilizing a set of 16 lactylation modification-related genes, cohorts of patients with EC were stratified into two distinct clusters, characterized by significant disparities in both survival outcomes and the immune microenvironment. An extensive bioinformatics analysis unveiled 382 differentially expressed genes (DEGs) between these two clusters. A subsequent univariate Cox regression analysis identified 24 DEGs specifically associated with lactylation, forming the basis of a constructed lactylation-related score. The resultant lactylation-related score exhibited notable predictive efficacy for survival and other clinicopathological traits, which was validated through calibration curves, Kaplan-Meier survival curves and the Wilcoxon test. Moreover, the lactylation-related score displayed a close correlation with immune cell infiltration in EC. Notable differential expressions of immune checkpoints and regulators were observed between groups stratified by low and high lactylation scores, with the latter exhibiting a more favorable response to anti-PD-1/PD-L1 therapy. Furthermore, the expression profile of U2 snRNP associated SURP domain containing (U2SURP), a constituent of the lactylation-related score, underwent both ex vivo and in vitro validation. The expression of U2SURP was significantly associated with lactylation levels, histological grade and tumor stage. Notably, knockdown of U2SURP expression inhibited the lactylation levels, immune genes IL-1A and IL-1B, proliferation, migration and invasion of EC cells. In conclusion, the lactylation-related score developed in the present study showed promise in predicting the prognosis and immunotherapeutic responses among patients with EC. Moreover, the identification of U2SUPR as a novel oncogene in EC suggests its potential as a prospective therapeutic target for EC treatment.

The Chromosome-level Genome of the Ctenophore Mnemiopsis leidyi A. Agassiz, 1865 Reveals a Unique Immune Gene Repertoire.

Ctenophora are basal marine metazoans, the sister group of all other animals. Mnemiopsis leidyi is one of the most successful invasive species worldwide with intense ecological and evolutionary research interest. Here, we generated a chromosome-level genome assembly of M. leidyi with a focus on its immune gene repertoire. The genome was 247.97 Mb, with N50 16.84 Mb, and 84.7% completeness. Its karyotype was 13 chromosomes. In this genome and that of two other ctenophores, Bolinopsis microptera and Hormiphora californensis, we detected a high number of protein domains related to potential immune receptors. Among those, proteins containing Toll/interleukin-1 (TIR2) domain, NACHT domain, Scavenger Receptor Cystein-Rich (SRCR) domain, or C-type Lectin domain (CTLD) were abundant and presented unique domain architectures in M. leidyi. M. leidyi seems to lack bona fide Toll-like Receptors, but it does possess a repertoire of 15 TIR2 domain-containing genes. Besides, we detected a bona fide NOD-like receptor and 38 NACHT domain-containing genes. In order to verify the function of those domain-containing genes, we exposed M. leidyi to the pathogen Vibrio coralliilyticus. Among the differentially expressed genes, we identified potential immune receptors, including four TIR2 domain-containing genes, all of which were upregulated in response to pathogen exposure. To conclude, many common immune receptor domains, highly conserved across metazoans, are already present in Ctenophora. These domains have large expansions and unique architectures in M. leidyi, findings consistent with the basal evolutionary position of this group, but still might have conserved functions in immunity and host-microbe interaction.

Skeletal muscle stem cells modulate niche function in Duchenne muscular dystrophy mouse through YY1-CCL5 axis

Adult skeletal muscle stem cells (MuSCs) are indispensable for muscle regeneration and tightly regulated by macrophages (MPs) and fibro-adipogenic progenitors (FAPs) in their niche. Deregulated MuSC/MP/FAP interactions and the ensuing inflammation and fibrosis are hallmarks of dystrophic muscle. Here we demonstrate intrinsic deletion of transcription factor Yin Yang 1 (YY1) in MuSCs exacerbates dystrophic pathologies by altering composition and heterogeneity of MPs and FAPs. Further analysis reveals YY1 loss induces expression of immune genes in MuSCs, including C-C motif chemokine ligand 5 (Ccl5). Augmented CCL5 secretion promotes MP recruitment via CCL5/C-C chemokine receptor 5 (CCR5) crosstalk, which subsequently hinders FAP clearance through elevated Transforming growth factor-β1 (TGFβ1). Maraviroc-mediated pharmacological blockade of the CCL5/CCR5 axis effectively mitigates muscle dystrophy and improves muscle performance. Lastly, we demonstrate YY1 represses Ccl5 transcription by binding to its enhancer thus facilitating promoter-enhancer looping. Altogether, our study demonstrates the critical role of MuSCs in actively shaping their niche and provides novel insight into the therapeutic intervention of muscle dystrophy.