Interactions between immunity,proliferation and molecular subtype in breast cancer prognosis

Background

Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified.

Results

To investigate the relationship between proliferation and immune gene signatures, we analyzed an integrated dataset of 1,954 clinically annotated breast tumor expression profiles randomized into training and test sets to allow two-way discovery and validation of gene-survival associations. Hierarchical clustering revealed a large cluster of distant metastasis-free survival-associated genes with known immunological functions that further partitioned into three distinct immune metagenes likely reflecting B cells and/or plasma cells; T cells and natural killer cells; and monocytes and/or dendritic cells. A proliferation metagene allowed stratification of cases into proliferation tertiles. The prognostic strength of these metagenes was largely restricted to tumors within the highest proliferation tertile, though intrinsic subtype-specific differences were observed in the intermediate and low proliferation tertiles. In highly proliferative tumors, high tertile immune metagene expression equated with markedly reduced risk of metastasis whereas tumors with low tertile expression of any one of the three immune metagenes were associated with poor outcome despite higher expression of the other two metagenes.

Conclusions

These findings suggest that a productive interplay among multiple immune cell types at the tumor site promotes long-term anti-metastatic immunity in a proliferation-dependent manner. The emergence of a subset of effective immune responders among highly proliferative tumors has novel prognostic ramifications.     

Oral delivery of bioencapsulated exendin‐4 expressed in chloroplasts lowers blood glucose level in mice and stimulates insulin secretion in beta‐TC6 cells

Glucagon‐like peptide (GLP‐1) increases insulin secretion but is rapidly degraded (half‐life: 2 min in circulation). GLP‐1 analogue, exenatide (Byetta) has a longer half‐life (3.3–4 h) with potent insulinotropic effects but requires cold storage, daily abdominal injections with short shelf life. Because patients with diabetes take >60 000 injections in their life time, alternative delivery methods are highly desired. Exenatide is ideal for oral delivery because insulinotropism is glucose dependent, with reduced risk of hypoglycaemia even at higher doses. Therefore, exendin‐4 (EX4) was expressed as a cholera toxin B subunit (CTB)–fusion protein in tobacco chloroplasts to facilitate bioencapsulation within plant cells and transmucosal delivery in the gut via GM1 receptors present in the intestinal epithelium. The transgene integration was confirmed by PCR and Southern blot analysis. Expression level of CTB‐EX4 reached up to 14.3% of total leaf protein (TLP). Lyophilization of leaf material increased therapeutic protein concentration by 12‐ to 24‐fold, extended their shelf life up to 15 months when stored at room temperature and eliminated microbes present in fresh leaves. The pentameric structure, disulphide bonds and functionality of CTB‐EX4 were well preserved in lyophilized materials. Chloroplast‐derived CTB‐EX4 showed increased insulin secretion similar to the commercial EX4 in beta‐TC6, a mouse pancreatic cell line. Even when 5000‐fold excess dose of CTB‐EX4 was orally delivered, it stimulated insulin secretion similar to the intraperitoneal injection of commercial EX4 but did not cause hypoglycaemia in mice. Oral delivery of the bioencapsulated EX4 should eliminate injections, increase patient compliance/convenience and significantly lower their cost.     

Identification of PSMD7 as a prognostic factor correlated with immune infiltration in head and neck squamous cell carcinoma

Background: Recurrent locally advanced or metastatic head and neck squamous cell carcinoma (HNSCC) is associated with dismal prognosis because of its highly invasive behavior and resistance to conventional intensive chemotherapy. The identification of effective markers for early diagnosis and prognosis is important for reducing mortality and ensuring that therapy for HNSCC is effective. Proteasome 26S subunit, non-ATPase 7 (PSMD7) is an ATP-independent component of the 19S regulatory subunit. The prognostic value of PSMD7 and the association with immune infiltration in HNSCC remains unclear.Methods: The Sangerbox, Oncomine, UALCAN and Human Protein Atlas (HPA) databases were used to examine PSMD7 expression profiles in HNSCC. The CVCDAP was used to analysis the association of PSMD7 with the prognosis of patients with HNSCC. The mechanism was investigated with gene set enrichment analysis (GSEA). The association between expression of PSMD7 and immune infiltration in HNSCC was investigated using the Tumor Immune Estimation Resource (TIMER), TISIDB database and CIBERSORT algorithm.Results: PSMD7 expression was significantly up-regulated in HNSCC compared with relative normal tissues. In addition, up-regulated PSMD7 expression was associated with various clinicopathological parameters. High expression of PSMD7 suggested inferior survival of HNSCC patients. GSEA and CERES score indicated that PSMD7 was closely correlated with tumor-related signaling pathways and cell survival. Functional analyses revealed that PSMD7 was positively correlated with various infiltration levels. Moreover, PSMD7 influenced the prognosis of HNSCC patients partially via immune infiltration.Conclusion: Our findings suggest that PSMD7 is associated poor prognosis in patients with HNSCC and plays an important role in tumor-related immune infiltration.     

Correlation of zinc finger protein 2, a prognostic biomarker,with immune infiltrates in liver cancer

Purpose: The expression and clinical value of zinc finger protein 2 gene (ZIC2) in hepatocellular carcinoma (HCC) were analyzed by mining gene information from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases.Methods: Gene chip data sets were retrieved from GEO and TCGA and screened for differentially expressed genes in HCC. Gene expression profile interaction analysis (GEPIA) and Kaplan–Meier curves were used to analyze the relationship between differentially expressed genes (DEGs) and survival and prognosis in patients with HCC. Moreover, the Genecards database was used to extract ZIC2-related proteins and to analyze the physiological process of protein enrichment. Furthermore, the relationships between ZIC2 gene and tumor cell immune invasion and that between immune cell infiltration and the 5-year survival rate were studied using the tumor immune evaluation resource (TIMER) database.Results: Datasets from GEO and TCGA revealed that ZIC2 was differentially expressed in HCC tissues and normal tissues (P<0.05). High ZIC2 expression was associated with overall survival (OS) and progress-free survival in HCC patients. Overall, 25 ZIC2 related proteins, including Gli3, PRKDC, and rnf180 were identified and protein enrichment analysis indicated these were associated with four types of cell components, six types of cell functions, and eight types of biological processes. ZIC2 was positively correlated with immune infiltration cells in patients with HCC, and higher expression of ZIC2 mRNA CD4+T cells is associated with a better 5-year survival.Conclusion: ZIC2 gene may be used as an immune response marker in liver cancer to predict the prognosis of HCC.     

A dual immune signature of CD8+ T cells and MMP9 improves the survival of patients with hepatocellular carcinoma

The 5-year survival of hepatocellular carcinoma (HCC) is difficult due to the high recurrence rate and metastasis. Tumor infiltrating immune cells (TICs) and immune-related genes (IRGs) bring hope to improve survival and treatment of HCC patients. However, there are problems in predicting immune signatures and identifying novel therapeutic targets. In the study, the CIBERSORT algorithm was used to evaluate 22 immune cell infiltration patterns in gene expression omnibus (GEO) and the cancer genome atlas (TCGA) data. Eight immune cells were found to have significant infiltration differences between the tumor and normal groups. The CD8+ T cells immune signature was constructed by least absolute shrinkage and selection operator (LASSO) algorithm. The high infiltration level of CD8+ T cells could significantly improve survival of patients. The weighted gene co-expression network analysis (WGCNA) algorithm identified MMP9 was closely related to the overall survival of HCC patients. K-M survival and tROC analysis confirmed that MMP9 had an excellent prognostic prediction. Cox regression showed that a dual immune signature of CD8+ T cells and MMP9 was independent survival factor in HCC. Therefore, a dual prognostic immune signature could improve the survival of patient and may provide a new strategy for the immunotherapy of HCC.     

Comprehensive analysis reveals a prognostic and therapeutic biomarker CD3D in the breast carcinoma microenvironment

Breast carcinoma (BRCA) is the most common carcinoma among women worldwide. Despite the great progress achieved in early detection and treatment, morbidity and mortality rates remain high. In the present study, we make a systematic analysis of BRCA using TCGA database by applying CIBERSORT and ESTIMATE computational methods, uncovered CD3D as a prognostic biomarker by intersection analysis of univariate COX and protein–protein interaction (PPI). It revealed that high CD3D expression was strongly associated with poor survival of BRCA, based on The Cancer Genome Atlas (TCGA) database and online websites. Gene Set Enrichment Analysis (GSEA) revealed that the high CD3D expression group was mainly enriched for the immune-related pathways and the low CD3D expression group was mainly enriched for metabolic-related activities. Based on CIBERSORT analysis, the difference test and correlation test suggested that CD3D had a strong correlation with T cells, particularly CD8 + T cells, which indicated that CD3D up-regulation may increase T cell immune infiltration in the TME and induce antitumor immunity by activating T lymphocytes. Furthermore, the correlation analysis showed that CD3D expression had a strongly positive correlation with immune checkpoints, which indicating that the underlying mechanism involves CD3D mediated regulation of T cell functions in BRCA, and single cell RNA-seq analysis revealed that CD3D correlate with CD8 + T cells and it is itself highly expressed in CD8 + T cells. In summary, we identified a prognostic biomarker CD3D in BRCA, which was associated with lymphocyte infiltration, immune checkpoints and could be developed for innovative therapeutics of BRCA.     

Effect of dietary replacement of fish meal protein with crawfish shell meal (Procambarus clarkii) on the growth performance,digestive enzyme activity and anti-oxidative capacity of Oujiang color common carp (Cyprinus carpio var. color)

This study was designed to evaluate the effects of dietary crawfish shell meal (CSM) on the growth performance, digestive enzyme activity and anti-oxidative capacity of Oujiang color common carp. 180 juvenile fish (initial weight 3.0 ± 0.5 g) were assigned to the control group and the CSM25 group (fed with 25% substitution of fish meal by CSM) for 8 weeks. Results showed that significant improvement in the weight gain rate (WGR) in CSM25 group than the control (p < .05), whereas no significant change in feed conversion ratio, specific growth rate and feeding intake between the groups (p > .05). Also, no significant difference was obsevered between the groups in terms of serum biochemical index and muscle composition (p > .05). And liver superoxide dismutase, catalase, glutathione peroxidase (GPx), lysozyme (LYZ) and protease activities in CSM25 group were significantly higher (p < .05). Moreover, histological analysis indicated that width of mucosa and thickness of muscular coat in mid-intestine were significantly changed (p < .05). In conclusion, dietary supplement with CSM25 induced high oxidative stress, promote protease activities and had no negative effects on the growth performance of Oujiang color common carp. Hence, CSM may be a viable alternative protein source to reduce the demand for fish meal.     

肠炎沙门氏菌基因工程减毒株的免疫效果及安全性评价

[背景] 相较于灭活疫苗和弱毒疫苗,沙门氏菌（Salmonella）基因工程减毒活疫苗具有的优越性逐渐显现,研究也不断深入。[目的] 探究肠炎沙门氏菌G9菌株的4株基因缺失株G9（ΔhilA）、G9（ΔhilD）、G9（ΔssrABhilA）和G9（ΔssrABhilAhilD）的免疫效果及生物安全性。[方法] 以肠炎沙门氏菌基因缺失菌株G9（ΔhilA）、G9（ΔhilD）、G9（ΔssrABhilA）、G9（ΔssrABhilAhilD）及其亲本菌株G9的最佳免疫剂量接种小鼠后,利用间接ELISA法、流式细胞术、MTT法、小鼠攻毒试验及倾注平板法等对各缺失株的免疫效果和安全性进行评价。[结果] G9（ΔhilD）诱导血清IgG抗体效价最高,G9（ΔhilD）和G9（ΔssrABhilAhilD）产生肠黏膜IgA抗体效价最高,4株缺失菌诱导IL-4、IL-10、IFN-γ、TNF-β、MCP-1细胞因子的能力与亲本株G9差异不显著（P>0.05）,产生的CD4⁺/CD3⁺、CD8⁺/CD3⁺ T细胞比率呈上升趋势,而且G9（ΔssrABhilA）和G9（ΔssrABhilAhilD）最高;G9（ΔssrABhilAhilD）诱发的脾淋巴细胞增殖指数最高;免疫小鼠后4株缺失株对G9攻毒提供的保护率为80%-100%,而且小鼠肝脏、脾脏及小肠绒毛无明显病理变化,对鼠伤寒沙门氏菌攻毒提供的保护率为50%-80%;接种后12 d,小鼠肝脏、脾脏及小肠中定殖的菌株能基本清除,而且在体外能连续稳定传代30代。[结论] G9（ΔhilA）、G9（ΔhilD）、G9（ΔssrABhilA）和G9（ΔssrABhilAhilD）对小鼠的免疫效果和生物安全性均良好,有成为肠炎沙门氏菌基因工程减毒活疫苗的可能。     

The novel pathogen-responsive glycosyltransferase UGT73C7 mediates the redirection of phenylpropanoid metabolism and promotes SNC1-dependent Arabidopsis immunity

Recent studies have shown that global metabolic reprogramming is a common event in plant innate immunity; however, the relevant molecular mechanisms remain largely unknown. Here, we identified a pathogen-induced glycosyltransferase, UGT73C7, that plays a critical role in Arabidopsis disease resistance through mediating redirection of the phenylpropanoid pathway. Loss of UGT73C7 function resulted in significantly decreased resistance to Pseudomonas syringae pv. tomato DC3000, whereas constitutive overexpression of UGT73C7 led to an enhanced defense response. UGT73C7-activated immunity was demonstrated to be dependent on the upregulated expression of SNC1, a Toll/interleukin 1 receptor-type NLR gene. Furthermore, in vitro and in vivo assays indicated that UGT73C7 could glycosylate p-coumaric acid and ferulic acid, the upstream metabolites in the phenylpropanoid pathway. Mutations that lead to the loss of UGT73C7 enzyme activities resulted in the failure to induce SNC1 expression. Moreover, glycosylation activity of UGT73C7 resulted in the redirection of phenylpropanoid metabolic flux to biosynthesis of hydroxycinnamic acids and coumarins. The disruption of the phenylpropanoid pathway suppressed UGT73C7-promoted SNC1 expression and the immune response. This study not only identified UGT73C7 as an important regulator that adjusts phenylpropanoid metabolism upon pathogen challenge, but also provided a link between phenylpropanoid metabolism and an NLR gene.