Search

Background: The management of gastric cancer (GC) still lacks tumor markers with high specificity and sensitivity. The goal of current research is to find effective diagnostic and prognostic markers and to clarify their related mechanisms.Methods: In this study, we integrated GC DNA methylation data from publicly available datasets obtained from TCGA and GEO databases, and applied random forest and LASSO analysis methods to screen reliable differential methylation sites (DMSs) for GC diagnosis. We constructed a diagnostic model of GC by logistic analysis and conducted verification and clinical correlation analysis. We screened credible prognostic DMSs through univariate Cox and LASSO analyses and verified a prognostic model of GC by multivariate Cox analysis. Independent prognostic and biological function analyses were performed for the prognostic risk score. We performed TP53 correlation analysis, mutation and prognosis analysis on eleven-DNA methylation driver gene (DMG), and constructed a multifactor regulatory network of key genes.Results: The five-DMS diagnostic model distinguished GC from normal samples, and diagnostic risk value was significantly correlated with grade and tumor location. The prediction accuracy of the eleven-DMS prognostic model was verified in both the training and validation datasets, indicating its certain potential for GC survival prediction. The survival rate of the high-risk group was significantly lower than that of the low-risk group. The prognostic risk score was an independent risk factor for the prognosis of GC, which was significantly correlated with N stage and tumor location, positively correlated with the VIM gene, and negatively correlated with the CDH1 gene. The expression of CHRNB2 decreased significantly in the TP53 mutation group of gastric cancer patients, and there were significant differences in CCDC69, RASSF2, CHRNB2, ARMC9, and RPN1 between the TP53 mutation group and the TP53 non-mutation group of gastric cancer patients. In addition, CEP290, UBXN8, KDM4A, RPN1 had high frequency mutations and the function of eleven-DMG mutation related genes in GC patients is widely enriched in multiple pathways.Conclusion: Combined, the five-DMS diagnostic and eleven-DMS prognostic GC models are important tools for accurate and individualized treatment. The study provides direction for exploring potential markers of GC.

BackgroundThe SET and MYND domain-containing (SMYD) gene family comprises a set of genes encoding lysine methyltransferases. This study aimed to clarify the relationship between the expression levels of SMYD family members and the prognosis and immune infiltration of malignant tumors of the digestive system.MethodsThe Oncomine, Ualcan, Kaplan–Meier Plotter, cBioPortal, Metascape, and TIMER databases and tools were used to analyze the correlation of SMYD family mRNA expression, clinical stage, TP53 mutation status, prognostic value, gene mutation, and immune infiltration in patients with esophageal carcinoma (ESCA), liver hepatocellular carcinoma (LIHC), and stomach adenocarcinoma (STAD).ResultsIn ESCA, the mRNA expression of SMYD2/3/4/5 was significantly correlated with the incidence rate, that of SMYD2/3 with the clinical stage, that of SMYD2/3/4/5 with TP53 mutation status, that of SMYD2/4/5 with overall survival (OS), and that of SMYD1/2/3/4 with relapse-free survival (RFS). In LIHC, the mRNA expression of SMYD1/2/3/4/5 was significantly correlated with the incidence rate, that of SMYD2/4/5 with the clinical stage, that of SMYD3/5 with TP53 mutation status, that of SMYD2/3/4/5 with OS, and that of SMYD3/5 with RFS. In STAD, the mRNA expression of SMYD2/3/4/5 was significantly correlated with the incidence rate, that of SMYD1/4 with the clinical stage, that of SMYD1/2/3/5 with TP53 mutation status, that of SMYD1/3/4 with OS, and that of SMYD1/3 with RFS. Furthermore, the function of SMYD family mutation-related genes in ESCA, LIHC, and STAD patients was mainly related to pathways, such as mitochondrial gene expression, mitochondrial matrix, and mitochondrial translation. The expression of SMYD family genes was significantly correlated with the infiltration of six immune cell types and eight types of immune check sites.ConclusionSMYD family genes are differentially expressed and frequently mutated in malignant tumors of the digestive system (ESCA, LIHC, and gastric cancer). They are potential markers for prognostic prediction and have important significance in immunity and targeted therapy.

Dear Editors, Enclosed please find the description of the colon cancer prognostic predictive model entitled “Accurate prediction of hierarchy prognosis integrated clinical and molecular characteristic in colon cancer”, wrote by Wang et al. To highlight the importance of the results, we are submitting it to Frontiers in Cell and Developmental Biology.The difference of prognosis for colon cancer is associated with complicated factors. This increases the difficulty of accurate prognosic assessment and treatment decision in clinical practice.In the study, a series of prediction models were exploited to screen potential factors for stratified survival probability in colon cancer,based on SEER database and TCGA database by machine learning and statistical model. The 9 clinical characteristics of 161,694 postoperative patients with adenocarcinoma were obtained in colon cancer, based on SEER. We also collected clinical and four types molecular datasets from the TCGA. To better assess the prognosis of colon cancer using clinical features, we redefined the ratio of positive lymph nodes(LNR) by information gain method. LNR thresholds for one and three years survival time were 0, 0.2 and 0.6, for five years were 0, 0.3 and 0.7. . For the survival of one, three and five years, We obtained 8, 9 and 4 features consisting of combination clinical factors and a group of molecular features to predict the difference between high and low risk. In all feature sets, molecular risk score was the best factor for survival assessment, the top one of molecular features was DNA methylation.T4&poorly differentiated or undifferentiated was the most important clinical factor for one year, and M0 was for three and five years overall lifetime. According to the combination of clinical factors and molecular features, the classier AUC, survivalROC, nomogram, C-index and Kaplan-Meier survival curves were displayed the results of different follow-up time. Our study is original, unpublished and is not being considered for publication elsewhere. All authors have contributed to this study and approved to submit to the journal. We would be grateful if the study could be reviewed and published in Frontiers in Cell and Developmental Biology Best regards, Yan Zhang

Background Cerebral small vessel disease (CSVD) is a common age-related vascular disease of the brain associated with slowly accumulating tissue damage. At present, total CSVD burden score is a commonly used method to evaluate the severity of the disease. Purpose To observe whether global and regional cerebral perfusion is related to total CSVD score and to explore global and regional cerebral blood flow (CBF) changes in patients with different degrees of CSVD. Methods We collected 130 subjects with different total burden score of CSVD (0 point: 33 subjects, 1 point: 39 subjects, 2 points: 24 subjects, 3 points: 24 subjects, 4 points: 10 subjects). Total CSVD burden score was evaluated by clinically routine sequences (T2WI, T2-FLAIR, T1WI, DWI, and SWAN sequence). Global and regional CBF were calculated and correlation analysis was used to investigate the relationship between total CSVD score and CBF of the whole brain and several brain regions. Results The analysis results showed that there was a negative correlation between total CSVD burden score and global CBF (r = -0.33, p = 0.001). Total CSVD burden score also had moderately negative correlations with CBF of almost all the brain regions. Conclusion CSVD is a disease that affects the whole brain. With the increase of total CSVD burden score, the global and regional CBF decreased. The CSVD total burden score could be used to evaluate the overall condition of brain perfusion.

Changes of regulatory T (Treg) cells and Th17 cells, and related cytokines in peripheral blood of patients with chronic hepatitis B combined with thrombocytopenia were investigated to explore the relationship with treatment outcomes. A total of 45 chronic hepatitis B patients combined with thrombocytopenia were selected in Heilongjiang Provincial Hospital from June 2015 to December 2016. All patients were treated with prednisolone acetate + γ globulins for 60 days. Treg cells and Th17 cells in peripheral blood were detected by flow cytometry, and IL-10, TGF-β, IL-17, IL-21 and IL-22 in peripheral blood were detected by ELISA before and after treatment. No significant differences in the percentages of Treg and Th17, and levels of IL-10, TGF-β, IL-17, IL-21 and IL-22 were found in non-responders (n=17, platelets 0.05). After treatment, percentage of Treg was significantly increased (higher than that of non-responders) and percentage of Th17 was significantly decreased (lower than that of non-responders) in responders (P

Treatment of acute myeloid leukemia (AML) remains challenging. Enhancement of anti-tumor responses by blocking negative immune regulators is a promising strategy for novel effective leukemia therapeutics. V-domain Ig suppressor of T-cell activation (VISTA) is a recently defined negative regulator mediating immune evasion in cancer. To investigate the effect of VISTA on anti-leukemia immune response in AML, we initiated a study using clinical samples collected from AML patients. Here we report that VISTA is highly expressed on myeloid-derived suppressor cells (MDSCs) in the peripheral blood of AML patients. Both the frequency and intensity of VISTA expression on MDSCs are significantly higher in newly diagnosed AML than in healthy controls. Importantly knockdown of VISTA by specific siRNA potently reduced the MDSCs-mediated inhibition of CD8 T cell activity in AML, suggesting a suppressive effect of VISTA on anti-leukemia T cell response. Furthermore, we observed a strong positive association between MDSC expression of VISTA and T cell expression of PD-1 in AML. These results support the strategy of VISTA-targeted treatment for AML and underscore the strong potential for combined blockade of VISTA and PD-1 pathways in effective leukemia control.

Treatment for elderly AML patients who are unfit for intensive chemotherapy remains challenging. Induction with hypomethylating agents (HMA) are the most commonly used approach, however the rate of complete remission (CR) is only around 20% and median survival of 7-12 months. Clearly how to improve the clinical outcome in this patient population is an unmet need. Immunotherapy is promising in cancer treatment. A recent study demonstrated that HMA enhanced PD-1 pathway in MDS and AML patients (Yang et al., Leukemia 2014), suggesting a role of combining HMA and immunotherapy in leukemia therapeutics. To optimize this strategy, it is crucial to understand the interaction between HMA and immune response in AML. Here we performed both phenotypic and functional analysis on clinical samples collected from AML patients undergoing treatment of decitabine (DAC), a broadly used HMA. We aim to determine 1) how DAC influences the immune system; and 2) whether the immune status in AML patients predict the response to DAC treatment. Total of 22 peripheral blood samples from 11 AML patients receiving DAC were examined. Samples were collected at the time of prior to and 1-month post DAC treatment. We conducted a comprehensive phenotypic analysis of immune markers characterizing each immune component (T cells, B cells, NK, NKT, monocytes, myeloid-derived suppressor cells, and dendritic cells) and expression patterns of co-stimulatory or inhibitory molecules. In addition, perforin, granzyme B and cytokine release in response to anti-CD3/CD28 stimulation were examined to determine the functional status of T cells. A total of 45 markers separated in 8 overlapped staining panels were tested by flow cytometry. We first assessed the impact of DAC on the immune response in AML. Comparing the paired samples prior to vs. post treatment from the same patients, we observed an increase of the percentage of NK cells, as well as their expression of granzyme B and perforin upon DAC treatment. In contrast, DAC appears to cause CD8 T cell suppression as CD8 T cells from post-DAC samples showed higher PD-1 expression whereas lower IFN-γ production. We next investigated the predictive value of immune status for the response to DAC treatment. Among the 18 evaluable samples, we defined 10 responders (CR/Cri/PR) vs. 8 non-responders (treatment failure) based on the ELN 2017 recommendations. The correlation of immune characteristics to the clinical response was carefully examined. We started with an unsupervised principal component analysis (PCA), which revealed a distinguished pattern between the responders and non-responders (Fig. 1A). This encouraging observation suggests an association of immune signature to clinical outcome. Subsequent analysis demonstrated a major contribution of CD8 T cells to the association. We then focused on the phenotypic and functional analysis of CD8 T cells in responders vs. non-responders. We found a significantly higher percentage of terminal differentiated cells in non-responders compared with that of responders. Importantly, in the perspective of phenotypes, hierarchical clustering on markers of CD8 T cells divided samples into two major clades, 7 of 8 samples (87.5%) were responders on one branch and 7 of 10 samples (70%) were non-responders on the other. Most responders expressed lower frequency of inhibitory receptors and higher frequency of stimulatory receptors, whereas non-responders showed the opposite trend (Fig. 1B). The significant difference of these receptors was validated in paired t test analysis. Functional studies also showed more IFN-γ production in responders. Interestingly the intracellular staining of perforin and granzyme B was higher in non-responders, likely due to exhausted T cells that are unable to release these particles extracellularly. Collectively, our study discovered the vital role of the immune signature in predicting clinical outcome in AML. High functional CD8 T cell status, manifested by more capability of IFN-γ production, enhanced stimulatory molecule and low inhibitory receptor expression, associated with effective clinical response to DAC treatment. In addition, CD8 T cell function was down-regulated upon DAC treatment. Our results provide a strong rationale for integrating immunotherapy into HMA treatment in AML, also highlight the importance of immune signature analysis in the future trial design for this clinical setting. Disclosures No relevant conflicts of interest to declare.

Eight additional genes, jadX, O, P, Q, S, T, U and V, in the jad cluster of Streptomyces venezuelae ISP5230, were located immediately downstream of jadN by chromosome walking. Sequence analyses and comparisons implicated them in biosynthesis of the 2,6-dideoxysugar in jadomycin B. The genes were cloned in Escherichia coli, inactivated by inserting an apramycin resistance cassette with a promoter driving transcription of downstream genes, and transferred into Streptomyces venezuelae by intergeneric conjugation. Analysis by HPLC and NMR of intermediates accumulated by cultures of the insertionally inactivated Streptomyces venezuelae mutants indicated that jadO, P, Q, S, T, U and V mediate formation of the dideoxysugar moiety of jadomycin B and its attachment to the aglycone. Based on these results and sequence similarities to genes described in other species producing deoxysugar derivatives, a biosynthetic pathway is proposed in which the jadQ product (glucose-1-phosphate nucleotidyltransferase) activates glucose to its nucleotide diphosphate (NDP) derivative, and the jadT product (a 4,6-dehydratase) converts this to NDP-4-keto-6-deoxy-D-glucose. An NDP-hexose 2,3-dehydratase and an oxidoreductase, encoded by jadO and jadP, respectively, catalyse ensuing reactions that produce an NDP-2,6-dideoxy-D-threo-4-hexulose. The product of jadU (NDP-4-keto-2,6-dideoxy-5-epimerase) converts this intermediate to its L-erythro form and the jadV product (NDP-4-keto-2,6-dideoxyhexose 4-ketoreductase) reduces the keto group of the NDP-4-hexulose to give an activated form of the L-digitoxose moiety in jadomycin B. Finally, a glycosyltransferase encoded by jadS transfers the activated sugar to jadomycin aglycone. The function of jadX is unclear; the gene is not essential for jadomycin B biosynthesis, but its presence ensures complete conversion of the aglycone to the glycoside. The deduced amino acid sequence of a 612 bp ORF (jadR*) downstream of the dideoxysugar biosynthesis genes resembles many TetR-family transcriptional regulator sequences.

Microcin J25 (MccJ25) is a plasmid-encoded, ribosomally synthesized antibacterial peptide with a unique lasso structure. The lasso structure, produced with the aid of two processing enzymes, provides exceptional stability to MccJ25. We report the synthesis of six peptides ( 1 – 6 ), derived from the MccJ25 sequence, that are designed to form folded conformation by disulfide bond formation and electrostatic or hydrophobic interactions. Two peptides ( 1 and 6 ) display good activity against Salmonella newport , and are the first synthetic derivatives of MccJ25 that are bactericidal. Peptide 1 displays potent activity against several Salmonella strains including two MccJ25 resistant strains. The solution conformation and the stability studies of the active peptides suggest that they do not fold into a lasso conformation and peptide 1 displays antimicrobial activity by inhibition of target cell respiration. Like MccJ25, the synthetic MccJ25 derivatives display minimal toxicity to mammalian cells suggesting that these peptides act specifically on bacterial cells.