Identification of proteolytic bacteria from Yunnan fermented foods and their use to reduce the allergenicity of ß-lactoglobulin.

Beta-lactoglobulin (ß-LG) is considered to be the major allergenic protein in milk. Lactic acid bacteria (LAB) possess a protein hydrolysis system that holds great promise for hydrolyzing ß-LG and reducing its allergenicity. Therefore, this study aimed to screen LAB with ß-LG hydrolysis activity from Yunnan traditional fermented foods. The results showed that Pediococcus pentosaceus C1001, Pediococcus acidilactici E1601-1, and Lactobacillus paracasei E1601-2, could effectively hydrolyze ß-LG and further reduce its sensitization (more than 40%). All 3 lactic acid bacteria hydrolyzed ß-LG allergenic fragments V41-K60 and L149-I162. Moreover, they encode a variety of genes related to proteolysis, such as aminopeptidase pepC and pepN, proline peptidase pepIP and endopeptidase pepO, and L. paracasei E1601-2 contains extracellular protease coding gene prtP. And they encode a variety of genes associated with hydrolyzed proteins. The 3 strains screened in this study can be used to develop hypoallergenic dairy products.

A Novel Tumor-Associated Neutrophil-Related Risk Signature Based on Single-Cell and Bulk RNA-Sequencing Analyses Predicts the Prognosis and Immune Landscape of Breast Cancer.

Tumor-associated neutrophils (TANs) are increasingly recognized as contributors to cancer prognosis and therapeutics. However, TAN-related targets of breast cancer (BRCA) remain scarce. This study aimed to develop a novel TAN-associated risk signature (TANRS) of BRCA using single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing data. Eighty-six TAN-related genes (TANRGs) were derived from the intersection of TAN marker genes identified from scRNA-seq with modular genes identified by weighted gene co-expression network analysis (WGCNA). The TANRS consisting of nine TANRGs (TAGLN2, IGF2R, LAMP2, TBL1X, ASAP1, DENND5A, SNRK, BCL3, and CEBPD) was constructed using Cox regression and the least absolute shrinkage and selection operator (LASSO) regression. The TANRS efficiently predicted the survival prognosis and clinicopathological progression of patients across multiple cohorts. Significant differences in immune infiltration landscapes between TANRS groups were observed. Additionally, patients with high TANRS exhibited tumor immunosuppression, enhanced cancer hallmarks, and unfavorable therapeutic effects. Four promising compounds for treating high-TANRS BRCA were also presented. SNRK was identified as a key prognostic TANRG, and its expression profile and correlation with TANs were validated using immunohistochemical assays of BRCA samples and spatial transcriptomic sections. This novel TAN-based signature exhibited promising predictive capabilities, with the potential to contribute to personalized medicine for BRCA patients.

Risk stratification based on DNA damage-repair-related signature reflects the microenvironmental feature, metabolic status and therapeutic response of breast cancer.

DNA damage-repair machinery participates in maintaining genomic integrity and affects tumorigenesis. Molecular signatures based on DNA damage-repair-related genes (DRGs) capable of comprehensively indicating the prognosis, tumor immunometabolic profile and therapeutic responsiveness of breast cancer (BRCA) patients are still lacking. Integrating public datasets and bioinformatics algorithms, we developed a robust prognostic signature based on 27 DRGs. Multiple patient cohorts identified significant differences in various types of survival between high- and low-risk patients stratified by the signature. The signature correlated well with clinicopathological factors and could serve as an independent prognostic indicator for BRCA patients. Furthermore, low-risk tumors were characterized by more infiltrated CD8+ T cells, follicular helper T cells, M1 macrophages, activated NK cells and resting dendritic cells, and fewer M0 and M2 macrophages. The favorable immune infiltration patterns of low-risk tumors were also accompanied by specific metabolic profiles, decreased DNA replication, and enhanced antitumor immunity. Low-risk patients may respond better to immunotherapy, and experience improved outcomes with conventional chemotherapy or targeted medicine. Real-world immunotherapy and chemotherapy cohorts verified the predictive results. Additionally, four small molecule compounds promising to target high-risk tumors were predicted. In vitro experiments confirmed the high expression of GNPNAT1 and MORF4L2 in BRCA tissues and their association with immune cells, and the knockdown of these two DRGs suppressed the proliferation of human BRCA cells. In summary, this DNA damage-repair-related signature performed well in predicting patient prognosis, immunometabolic profiles and therapeutic sensitivity, hopefully contributing to precision medicine and new target discovery of BRCA.

UFL1 promotes antiviral immune response by maintaining STING stability independent of UFMylation.

The precise regulation of STING homeostasis is essential for its antiviral function. Post-translational modification, especially ubiquitination, is important for the regulation of STING homeostasis. Previous studies have focused on how STING is degraded, but little is known about its maintenance. Here, we show that UFM1 specific ligase UFL1 promotes innate immune response by maintaining STING expression independent of UFMylation. Mechanistically, UFL1 inhibits TRIM29 to interact with STING, thereby reducing its ubiquitination at K338/K347/K370 and subsequent proteasomal degradation. DNA virus infection reduces the UFL1 expression, which may promote STING degradation and facilitate viral expansion. Our study identifies UFL1 as a crucial regulator for the maintenance of STING stability and antiviral function, and provides novel insights into the mechanistic explanation for the immunological escape of DNA virus.

Development of a metabolism-related signature for predicting prognosis, immune infiltration and immunotherapy response in breast cancer.

Breast cancer (BRCA) is the most commonly diagnosed cancer and among the top causes of cancer deaths globally. The abnormality of the metabolic process is an important characteristic that distinguishes cancer cells from normal cells. Currently, there are few metabolic molecular models to evaluate the prognosis and treatment response of BRCA patients. By analyzing RNA-seq data of BRCA samples from public databases via bioinformatic approaches, we developed a prognostic signature based on seven metabolic genes (PLA2G2D, GNPNAT1, QPRT, SHMT2, PAICS, NT5E and PLPP2). Low-risk patients showed better overall survival in all five cohorts (TCGA cohort, two external validation cohorts and two internal validation cohorts). There was a higher proportion of tumor-infiltrating CD8+ T cells, CD4+ memory resting T cells, gamma delta T cells and resting dendritic cells and a lower proportion of M0 and M2 macrophages in the low-risk group. Low-risk patients also showed higher ESTIMATE scores, higher immune function scores, higher Immunophenoscores (IPS) and checkpoint expression, lower stemness scores, lower TIDE (Tumor Immune Dysfunction and Exclusion) scores and IC50 values for several chemotherapeutic agents, suggesting that low-risk patients could respond more favorably to immunotherapy and chemotherapy. Two real-world patient cohorts receiving anti-PD-1 therapy were applied for validating the predictive results. Molecular subtypes identified based on these seven genes also showed different immune characteristics. Immunohistochemical data obtained from the human protein atlas database demonstrated the protein expression of signature genes. This research may contribute to the identification of metabolic targets for BRCA and the optimization of risk stratification and personalized treatment for BRCA patients.

mKLRL1 regulates the maturation of dendritic cells and plays important roles in immune tolerance.

KLRL1 is a member of C-type lectin-like receptors (CLEC) and preferentially expressed on the surface of immune cells. We have previously illustrated its inhibitory role in Natural killer (NK) cells. Though cloned from dendritic cells (DCs), its role in DCs has not been fully identified. Here, we found that mKLRL1 markedly decreased during DC maturation; mKLRL1-modifed DCs showed enhanced phagocytic capability and reduced ability to induce T cell proliferation, which mimics immature DCs. Further investigation revealed that IL-10 was indispensable for mKLRL1 to suppress DC maturation. And p38 activation was responsible for preferential IL-10 production. Pretreatment with mKLRL1-modified DCs protected mice from subsequently EAE induction, indicating a role in immune tolerance. Taken together, our results have revealed an inhibitory role of KLRL1 in mouse DCs.

The transcription factor Foxp1 regulates the differentiation and function of dendritic cells.

Dendritic cells (DCs) are the sentinels of the immune system and play a critical role in initiating adaptive immune responses against pathogens. As the most powerful antigen presenting cells, DCs are also important in maintaining immune homeostasis and participating in the development of autoimmune diseases. How the maturation and function of DCs is regulated in these conditions and what is the function of various transcription factors is still unclear. In this study, we found that the expression of the transcription factor Foxp1 gradually increased during the maturation of DCs. Then, we constructed a recombinant adenovirus carrying Foxp1-interfering RNA (Ad-simFoxp1) and transfected murine bone marrow-derived DCs in vitro. DCs transfected with Ad-simFoxp1 exhibited markedly lower costimulatory molecules, and decreased cytokines. And Ad-simFoxp1 greatly inhibited mature DC-induced T cell responses. Moreover, in vivo infusion with Ad-simFoxp1-modified DCs significantly delayed the onset of experimental autoimmune encephalomyelitis (EAE). Therefore, adoptive transfection of Ad-simFoxp1 in DCs may be a potential treatment strategy against autoimmune diseases.

CD24 aggravates acute liver injury in autoimmune hepatitis by promoting IFN-γ production by CD4+ T cells.

The T-cell-mediated immune response is implicated in many clinical hepatic injuries, such as autoimmune hepatitis and acute virus hepatitis. CD24 is widely expressed by different immune cells and plays an important role in the pathogenesis of many autoimmune diseases. However, the role of CD24 in T-cell-mediated liver injury has not been elucidated until now. Here we showed that CD24 deficiency protects mice from concanavalin A (ConA)-induced fulminant liver injury by reducing serum interferon-γ (IFN-γ) levels. CD24 expression by hepatic T cells was markedly increased following ConA challenge. Moreover, decreased IFN-γ production by hepatic CD4+ T cells in CD24-deficient mice was detected, which was correlated with downregulated phosphorylation of STAT1 in hepatic tissue. In vitro experiments also supported the conclusion that CD24 deficiency impaired IFN-γ production by CD4+ T cells following ConA, CD3/CD28 and phorbol myristate acetate/ionomycin stimulation. Our study suggests that CD24 deficiency confers hepatoprotection by decreasing CD4+ T-cell-dependent IFN-γ production in vivo, which suggests that CD24 might be a potential target molecule for reducing clinical hepatitis.

Ephedrine hydrochloride protects mice from staphylococcus aureus-induced peritonitis.

Staphylococcus aureus is a Gram-positive (G+) bacterium that causes a wide range of diseases in humans and livestock. Therefore, the development of innovative and effective therapies is essential for the treatment of S. aureus-induced severe infections. Ephedrine hydrochloride (EH) is a compound derived from ephedrine and is widely used for the management of cardiovascular diseases and hypotension. The results of our previous studies demonstrated that EH has anti-inflammatory activity in macrophages and protects against endotoxic shock. However, whether EH regulates the function of dendritic cells (DCs) and the immune response in S. aureus-induced infection is unknown. In this study, the anti-inflammatory and regulatory activity of EH on DCs was evaluated. EH increased the production of anti-inflammatory cytokine IL-10 and decreased the production of proinflammatory cytokines TNF-α and IL-12 in DCs stimulated with peptidoglycan (PGN), the main cell wall component in G+ bacteria. The PI3K/Akt and p38 MAPK signaling pathways controlled EH-induced IL-10 expression and EH-inhibited TNF-α expression, respectively. The PGN-induced expression of co-stimulatory molecules CD40, CD80, CD86, and MHC class II molecule Iab was down-regulated in DCs by EH. Furthermore, EH protected the liver and kidney and increased the survival rate of mice with S. aureus-induced peritonitis. In conclusion, EH helps to keep immune homeostasis and alleviate organ damage during S. aureus-induced peritonitis. Therefore, EH may be a promising drug candidate in the treatment of S. aureus-induced severe infections and other invasive G+ bacterial infections.