Identification and Validation of Three PDAC Subtypes and Individualized GSVA Immune Pathway-Related Prognostic Risk Score Formula in Pancreatic Ductal Adenocarcinoma Patients

Background. With the progress of precision medicine treatment in pancreatic ductal adenocarcinoma (PDAC), individualized cancer-related medical examination and prediction are of great importance in this high malignant tumor and tumor-immune microenvironment with changed pathways highly enrolled in the carcinogenesis of PDAC. Methods. High-throughput data of pancreatic ductal adenocarcinoma were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. After batch normalization, the enrichment pathway and relevant scores were identified by the enrichment of immune-related pathway signature using gene set variation analysis (GSVA). Then, cancerous subtype in TCGA and GEO samples was defined through the NMF methods by cancertypes packages in R software, respectively. Subsequently, the significance between the characteristics of each TCGA sample and cancer type and the significant prognosis-related pathway with risk score formula is calculated through t-test and univariate Cox analysis. Next, the prognostic value of gained risk score formula and each significant prognosis-related pathway were validated in TCGA and GEO samples by survival analysis. The pivotal hub genes in the enriched significant prognosis-related pathway are identified and validated, and the TIMER database was used to identify the potential role of hub genes in the PDAC immune environment. The potential role of hub genes is promoting the transdifferentiation of cancer-associated fibroblasts. Results. The enrichment pathway and relevant scores were identified by GSVA, and 3 subtypes of pancreatic ductal adenocarcinoma were defined in TCGA and GEO samples. The clinical stage, tumor node metastasis classification, and tumor grade are strongly relative to the subtype above in TCGA samples. A risk formula about GSVA significant pathway “GSE45365_WT_VS_IFNAR_KO_CD11B_DC_MCMV_INFECTION_DN ∗ 0.80 + HALLMARK_GLYCOLYSIS ∗ 16.8 + GSE19888_CTRL_VS_T_CELL_MEMBRANES_ACT_MAST_CELL_DN ∗ 14.4” was identified and validated in TCGA and GEO samples through survival analysis with significance. DCN, VCAN, B4GALT7, SDC1, SDC2, B3GALT6, B3GAT3, SDC3, GPC1, and XYLT2 were identified as hub genes in these GSVA significant pathways and validated in silico. Conclusions. Three pancreatic ductal adenocarcinoma subtypes are identified, and an individualized GSVA immune pathway score-related prognostic risk score formula with 10 hub genes is identified and validated. The predicted function of the 10 upregulated hub genes in tumor-immune microenvironment was promoting the infiltration of cancer-associated fibroblasts. These findings will contribute to the precision medicine of pancreatic ductal adenocarcinoma treatment and tumor immune-related basic research.

Deferasirox combination with eltrombopag shows anti-myelodysplastic syndrome effects by enhancing iron deprivation–related apoptosis

Iron overload (IO) affected the survival of patients with myelodysplastic syndrome (MDS). Deferasirox (DFX) is widely used in patients with MDS for iron chelation therapy, but is not suitable for MDS patients with severe thrombocytopenia. Eltrombopag (ELT) is a type of thrombopoietin receptor (TPOR) analog used in the treatment of thrombocytopenia. Therefore, we sought to explore the synergistic effects and possible mechanisms of DFX combination with ELT in MDS cells. In our study, the combination of DFX with ELT synergistically inhibited proliferation, induced apoptosis and arrested cell cycle of MDS cells. Through the RNA-sequence and gene set enrichment analysis (GSEA), iron metabolism–related pathway played important roles in apoptosis of SKM-1 cells treated with DFX plus ELT. Transferrin receptor (TFRC) was significantly highly expressed in combination group than that in single agent groups, without affecting TPOR. Furthermore, the apoptosis of the combination group MDS cells could be partially reversed by ferric ammonium citrate (FAC), accompanied with decreased expression of TFRC. These results suggested that the combination of DFX and ELT synergistically induced apoptosis of MDS cells by enhancing iron deprivation–related pathway.

Short chain fatty acids reduces OPCs loss by inhibiting activation of astrocytes via SGK1/IL-6 signaling pathway

Short chain fatty acids (SCFAs) are known to be actively involved in neurological disease, but their roles in hypoxic-ischemic brain injury (HIBI) is unclear. This study established a rat model of HIBI, then measured the changes in IL-6 and NLRP3, proliferation and apoptosis indicators of oligodendrocyte precursor cells (OPCs). The mechanism of SCFAs on astrocytes were also investigated. To further explore the mechanism, astrocytes were treated with hypoxia in vitro and OPCs were treated with IL-6. The results showed that SCFAs significantly alleviated the activation of astrocyte and loss of OPCs induced by HIBI. SCFAs pretreatment was associated with the following: (1) downregulation of NLRP3, IL-6, CCL2, and IP-10; (2) was no effect on proliferation of OPCs; (3) amelioration of the abnormal expression of Bax and Bcl-2; and (4) regulation of IL-6 expression via SGK1 related pathway in astrocytes. Our findings revealed that SCFAs alleviated loss of OPCs through regulating the astrocytes activation by SGK1/IL-6 signaling pathway.

The Role of Ferroptosis in Cardiovascular Disease and Its Therapeutic Significance

Cardiovascular diseases (CVDs) are the leading cause of deaths worldwide with regulated cell death playing an important role in cardiac pathophysiology. However, the classical mode of cell death cannot fully explain the occurrence and development of heart disease. In recent years, much research has been performed on ferroptosis, a new type of cell death that causes cell damage and contributes to the development of atherosclerosis, myocardial infarction, heart failure, and other diseases. In this review, we discuss the role of different organelles in ferroptosis and also focus on the relationship between autophagy and ferroptosis. Additionally, we describe the specific mechanism by which ferroptosis contributes to the development of CVD. Finally, we summarize the current research on ferroptosis-related pathway inhibitors and the applications of clinically beneficial cardiovascular drugs.

Transcriptomics and Metagenomics of Common Cutworm (Spodoptera Litura) and Fall Armyworm (Spodoptera Frugiperda) Reveal Their Differences on Detoxification and Development

BackgroundSpodoptera litura is an important polyphagous pest that causes great damage to agriculture. We performed RNA-seq from 15 individuals of S. litura, including different larval (fifth and sixth instar larvae), chrysalis, and adult developmental stages. We also sequenced the Spodoptera frugiperda to compared with the S. litura. ResultsA total of 101,885 differentially expressed transcripts (DETs) were identified in the S. litura. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that the S. litura may undergo active development and basic metabolism, such as xenobiotic and detoxifying metabolism, during its larvae and adult stages, which explains the difficulty to control it. We also found that DETs of single-copy orthologous genes between S. litura and S. frugiperda were involved in basic metabolism and developmental, but S. litura were highly enriched in energy and metabolic processes, whereas S. frugiperda had stronger nervous and olfactory functions. Metagenomics analysis in larval S. litura and S. frugiperda revealed that microbiota can both participate in the detoxification and metabolism processes in them, but the relative abundance of detoxification-related microbiota was more abundant in S. frugiperda. Transcriptome results also confirmed the detoxification-related pathway of S. frugiperda was more abundant than that of S. litura. ConclusionsTherefore, we can conclude that the detoxification ability of S. frugiperda is stronger than that of in S. litura, which is related to the wide adaptation and strong resistance of S. frugiperda. Our study might provide clues to the development of novel pest control strategies.

Engineering Escherichia coli for highly efficient production of lacto-N-triose II from N-acetylglucosamine, the monomer of chitin

Background Lacto-N-triose II (LNT II), an important backbone for the synthesis of different human milk oligosaccharides, such as lacto-N-neotetraose and lacto-N-tetraose, has recently received significant attention. The production of LNT II from renewable carbon sources has attracted worldwide attention from the perspective of sustainable development and green environmental protection. Results In this study, we first constructed an engineered E. coli cell factory for producing LNT II from N-acetylglucosamine (GlcNAc) feedstock, a monomer of chitin, by introducing heterologous β-1,3-acetylglucosaminyltransferase, resulting in a LNT II titer of 0.12 g L−1. Then, lacZ (lactose hydrolysis) and nanE (GlcNAc-6-P epimerization to ManNAc-6-P) were inactivated to further strengthen the synthesis of LNT II, and the titer of LNT II was increased to 0.41 g L−1. To increase the supply of UDP-GlcNAc, a precursor of LNT II, related pathway enzymes including GlcNAc-6-P deacetylase, glucosamine synthase, and UDP-N-acetylglucosamine pyrophosphorylase, were overexpressed in combination, optimized, and modulated. Finally, a maximum titer of 15.8 g L−1 of LNT II was obtained in a 3-L bioreactor with optimal enzyme expression levels and β-lactose and GlcNAc feeding strategy. Conclusions Metabolic engineering of E. coli is an effective strategy for LNT II production from GlcNAc feedstock. The titer of LNT II could be significantly increased by modulating the gene expression strength and blocking the bypass pathway, providing a new utilization for GlcNAc to produce high value-added products.

Genetic Variants of CLEC4E and BIRC3 in Damage-Associated Molecular Patterns-Related Pathway Genes Predict Non-Small Cell Lung Cancer Survival

Accumulating evidence supports a role of various damage-associated molecular patterns (DAMPs) in progression of lung cancer, but roles of genetic variants of the DAMPs-related pathway genes in lung cancer survival remain unknown. We investigated associations of 18,588 single-nucleotide polymorphisms (SNPs) in 195 DAMPs-related pathway genes with non-small cell lung cancer (NSCLC) survival in a subset of genotyping data for 1,185 patients from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial and validated the findings in another independent subset of genotyping data for 984 patients from Harvard Lung Cancer Susceptibility Study. We performed multivariate Cox proportional hazards regression analysis, followed by expression quantitative trait loci (eQTL) analysis, Kaplan-Meier survival analysis and bioinformatics functional prediction. We identified that two SNPs (i.e., CLEC4E rs10841847 G>A and BIRC3 rs11225211 G>A) were independently associated with NSCLC overall survival, with adjusted allelic hazards ratios of 0.89 (95% confidence interval=0.82-0.95 and P=0.001) and 0.82 (0.73-0.91 and P=0.0003), respectively; so were their combined predictive alleles from discovery and replication datasets (Ptrend=0.0002 for overall survival). We also found that the CLEC4E rs10841847 A allele was associated with elevated mRNA expression levels in normal lymphoblastoid cells and whole blood cells, while the BIRC3 rs11225211 A allele was associated with increased mRNA expression levels in normal lung tissues. Collectively, these findings indicated that genetic variants of CLEC4E and BIRC3 in the DAMPs-related pathway genes were associated with NSCLC survival, likely by regulating the mRNA expression of the corresponding genes.

Metformin ameliorates neuronal necroptosis after intracerebral hemorrhage by activating AMPK

Background: Intracerebral hemorrhage (ICH) is a major cause of death and disability globally. As a type of secondary injury after ICH, treatment for cell death can promote the recovery of neurological function. Methods: Among all the cell death, neuronal necroptosis has recently been demonstrated of significance in the pathogenesis of ICH. However, the administration of drugs against necroptosis has many limitations. Results: In the present study, we found that metformin, a first-line medication for the treatment of type 2 diabetes, can effectively inhibit neuronal necroptosis after ICH through activating AMPK related pathway, thereby significantly improving neurological function scores and reducing brain edema. Conclusion: These results will provide a new perspective for future research in necroptosis.