Identification of novel molecular subtypes to improve the classification framework of nasopharyngeal carcinoma.

BACKGROUND: Nasopharyngeal carcinoma (NPC) treatment is largely based on a 'one-drug-fits-all' strategy in patients with similar pathological characteristics. However, given its biological heterogeneity, patients at the same clinical stage or similar therapies exhibit significant clinical differences. Thus, novel molecular subgroups based on these characteristics may better therapeutic outcomes. METHODS: Herein, 192 treatment-naïve NPC samples with corresponding clinicopathological information were obtained from Fujian Cancer Hospital between January 2015 and January 2018. The gene expression profiles of the samples were obtained by RNA sequencing. Molecular subtypes were identified by consensus clustering. External NPC cohorts were used as the validation sets. RESULTS: Patients with NPC were classified into immune, metabolic, and proliferative molecular subtypes with distinct clinical features. Additionally, this classification was repeatable and predictable as validated by the external NPC cohorts. Metabolomics has shown that arachidonic acid metabolites were associated with NPC malignancy. We also identified several key genes in each subtype using a weighted correlation network analysis. Furthermore, a prognostic risk model based on these key genes was developed and was significantly associated with disease-free survival (hazard ratio, 1.11; 95% CI, 1.07-1.16; P < 0.0001), which was further validated by an external NPC cohort (hazard ratio, 7.71; 95% CI, 1.39-42.73; P < 0.0001). Moreover, the 1-, 3-, and 5-year areas under the curve were 0.84 (95% CI, 0.74-0.94), 0.81 (95% CI, 0.73-0.89), and 0.82 (95% CI, 0.73-0.90), respectively, demonstrating a high predictive value. CONCLUSIONS: Overall, we defined a novel classification of nasopharyngeal carcinoma (immune, metabolism, and proliferation subtypes). Among these subtypes, metabolism and proliferation subtypes were associated with advanced stage and poor prognosis of NPC patients, whereas the immune subtype was linked to early stage and favorable prognosis.

Characterization of Highbush Blueberry (Vaccinium corymbosum L.) Anthocyanin Biosynthesis Related MYBs and Functional Analysis of VcMYB Gene.

As one of the most important transcription factors regulating plant anthocyanin biosynthesis, MYB has attracted great attentions. In this study, we identified fifteen candidate anthocyanin biosynthesis related MYB (ABRM) proteins, including twelve R2R3-MYBs and three 1R-MYBs, from highbush blueberry. The subcellular localization prediction results showed that, with the exception of VcRVE8 (localized in chloroplast and nucleus), all of the blueberry ABRMs were nucleus-localized. The gene structure analysis revealed that the exon numbers of the blueberry ABRM genes varied greatly, ranging between one and eight. There are many light-responsive, phytohormone-responsive, abiotic stress-responsive and plant growth and development related cis-acting elements in the promoters of the blueberry ABRM genes. It is noteworthy that almost all of their promoters contain light-, ABA- and MeJA-responsive elements, which is consistent with the well-established results that anthocyanin accumulation and the expression of MYBs are influenced significantly by many factors, such as light, ABA and JA. The gene expression analysis revealed that VcMYB, VcMYB6, VcMYB23, VcMYBL2 and VcPH4 are expressed abundantly in blueberry fruits, and VcMYB is expressed the highest in the red, purple and blue fruits among all blueberry ABRMs. VcMYB shared high similarity with functionally proven ABRMs from many other plant species. The gene cloning results showed that VcMYB had three variable transcripts, but only the transient overexpression of VcMYB-1 promoted anthocyanin accumulation in the green fruits. Our study can provide a basis for future research on the anthocyanin biosynthesis related MYBs in blueberry.

Identification and Characterization of PRE Genes in Moso Bamboo (Phyllostachys edulis).

Basic helix-loop-helix (bHLH)/HLH transcription factors are involved in various aspects of the growth and development of plants. Here, we identified four HLH genes, PePRE1-4, in moso bamboo plants that are homologous to Arabidopsis PRE genes. In bamboo seedlings, PePRE1/3 were found to be highly expressed in the internode and lamina joint by using quantitative RT-PCR analysis. In the elongating internode of bamboo shoots, PePRE genes are expressed at higher levels in the basal segment than in the mature top segment. Overexpression of PePREs (PePREs-OX) in Arabidopsis showed longer petioles and hypocotyls, as well as earlier flowering. PePRE1 overexpression restored the phenotype due to the deficiency of AtPRE genes caused by artificial micro-RNA. PePRE1-OX plants showed hypersensitivity to propiconazole treatment compared with the wild type. In addition, PePRE1/3 but not PePRE2/4 proteins accumulated as punctate structures in the cytosol, which was disrupted by the vesicle recycling inhibitor brefeldin A (BFA). PePRE genes have a positive function in the internode elongation of moso bamboo shoots, and overexpression of PePREs genes promotes flowering and growth in Arabidopsis. Our findings provided new insights about the fast-growing mechanism of bamboo shoots and the application of PRE genes from bamboo.

KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma.

KDM2A is a histone demethylase, which primarily catalyzes the demethylation of H3K36me2. Abnormal expression of KDM2A is observed in many types of cancers; however, the molecular events connected to KDM2A expression remain unclear. We report that KDM2A performs an oncogenic function in esophageal squamous cell carcinoma (ESCC) and is robustly expressed in ESCC cells. ShRNA-mediated knockdown of KDM2A resulted in a significant inhibition of the malignant phenotype of ESCC cell lines, whereas ectopic expression of KDM2A showed the opposite effect. We also analyzed the function of KDM2A using a CRISPR-CAS9 depletion system and subsequent rescue experiment, which also indicated a cancerous role of KDM2A. Interestingly, analysis of the gene expression network controlled by KDM2A using RNA-seq revealed an unexpected feature: KDM2A could induce expression of a set of well-documented oncogenic genes, including IL6 and LAT2, while simultaneously suppressing another set of oncogenes, including MAT2A and HMGCS1. Targeted inhibition of the upregulated oncogene in the KDM2A-depleted cells led to a synergistic suppressive effect on the malignant phenotype of ESCC cells. Our results revealed the dual role of KDM2A in ESCC cells, which may have therapeutic implications.

Oral administration of Lactobacillus brevis 23017 combined with ellagic acid attenuates intestinal inflammatory injury caused by Eimeria infection by activating the Nrf2/HO-1 antioxidant pathway.

The aim of this study was to investigate whether oral administration of Lactobacillus brevis 23017 (LB) alone and in combination with ellagic acid inhibits ChTLR15/ChNLRP3/ChIL-1ß by activating the Nrf2/HO-1 pathway to attenuate intestinal inflammatory injury. Two animal experiments were performed. In Experiment 1, chickens were allocated into 7 groups: PBS, and low, medium and high dosages of live and heat-killed LB, named L/LB(+), M/LB(+) and H/LB(+), and L/LB(-), M/LB(-) and H/LB(-), respectively. In Experiment 2, chickens were divided into 5 groups: PBS, challenge control, and low, medium and high dosages of ellagic acid combined with LB(+), named L/EA + L/LB(+), M/EA + M/LB(+) and H/EA + H/LB(+), respectively. Chickens were gavaged with LB with or without ellagic acid once a day. Then, the mRNA and protein levels of the components of the Nrf2/HO-1 pathway found in the caecal tissues were quantified. On Day 7 post-infection with E. tenella, the levels of the components of the ChTLR15/NLRP3/IL-1ß pathway in the caeca were again quantified, and the anticoccidial effects were assessed. The results showed that the levels of the genes in the Nrf2/HO-1 pathway in the chickens in the LB(+) groups were higher than those in the LB(-) groups (p < 0.001); those in the H/LB(+) group were higher than those in the M/LB(+) and L/LB(+) groups (p < 0.001); and those in the H/EA + H/LB(+) group showed the highest expression levels compared with the other groups (p < 0.001). After challenge, the chickens in the H/LB(+) group displayed less inflammatory injury than those in the M/LB(+) and L/LB(+) groups (p < 0.05), and the chickens in the H/EA + H/LB(+) group showed stronger anti-inflammatory effects than the other groups (p < 0.05). Thus, these protective effects against infection were consistent with the above results. Overall, significant anti-inflammatory effects were observed in chickens orally gavaged with high dosages of live L. brevis 23017 and ellagic acid, which occurred by regulation of the ChTLR15/NLRP3/IL-1ß pathway.

Biochemical, transcriptomic, gut microbiome responses and defense mechanisms of the earthworm Eisenia fetida to salt stress.

The accumulation of sodium chloride (NaCl) in soil is a worldwide problem with detrimental effects on the survival of soil animals. The effects of NaCl on earthworms remain unclear. Here, we show that the growth rate, cocoon production rate, annetocin precursor (ANN) mRNA level, and superoxide dismutase and catalase activities in earthworms were reduced under NaCl stress, whereas the mortality rate, reactive oxygen species (ROS) and malondialdehyde activity level increased. Histological damage to the earthworm body wall and intestine were observed under NaCl stress. NaCl stress increased DNA damage in the seminal vesicle and coelomocytes. The mRNA level of lumbrokinase, 1,3-beta-glucanse, coelomic cytolytic factor (CCF1), and alpha-amylase was significantly down-regulated, whereas that of earthworm excitatory peptides2 (EEP2) was up-regulated. From 16 S rRNA sequencing, the earthworm gut microbiota diversity decreased under NaCl stress. However, Verminephrobacter, Kluyvera, Lactobacillus, and Ochrobactrum increased under NaCl stress. These findings contribute to the risk assessment of the salt stress on soil organisms.

Activation of ChTLR15/ChNF-κB-ChNLRP3/ChIL-1ß signaling transduction pathway mediated inflammatory responses to E. tenella infection.

Avian coccidiosis caused by Eimeria leads to severe economic losses in the global poultry industry. Although chicken Toll-like receptor 15 (ChTLR15) was reported to be involved in Eimeria infection, the detailed mechanism underlying its role in the inflammatory response remains to be discovered. The present study demonstrated that the mRNA expression levels of ChTLR15, ChMyD88, ChNF-κB, ChNLRP3, ChCaspase-1, ChIL-18 and ChIL-1ß and the protein levels of ChTLR15 and ChNLRP3 in cecal tissues of Eimeria-infected chickens were significantly elevated at 4, 12, and 24 h compared with those in noninfected control chickens (p < 0.01). Moreover, the mRNA levels of molecules in the ChTLR15/ChNF-κB and ChNLRP3/ChIL-1ß pathways and the protein levels of ChTLR15 and ChNLRP3 in chicken embryo fibroblast cells (DF-1) stimulated by E. tenella sporozoites were consistent with those in Eimeria-infected chickens. Furthermore, overexpression of ChTLR15 in DF1 cells augmented activation of the ChTLR15/ChNF-κB and ChNLRP3/ChIL-1ß pathways when stimulated with E. tenella sporozoites, while knockdown of ChTLR15 in DF1 cells showed inverse effects. Taken together, the present study provides evidence that E. tenella sporozoites specifically activate ChTLR15 and then trigger activation of the ChNLRP3/ChIL-1ß pathway, which partially mediates inflammatory responses to Eimeria infection.

Specific EtMIC3-binding peptides inhibit Eimeria tenella sporozoites entry into host cells.

Avian coccidiosis caused by Eimeria leads to huge economic losses on the global poultry industry. In this study, microneme adhesive repeat regions (MARR) bc1 of E. tenella microneme protein 3 (EtMIC3-bc1) was used as ligand, and peptides binding to EtMIC3 were screened from a phage display peptide library. The positive phage clones were checked by enzyme-linked immunosorbent assay (ELISA). Competitive ELISA was applied to further verify the binding capability between the positive phages and recombinant EtMIC3-bc1 protein or sporozoites protein. The inhibitory effects of target peptides on sporozoites invasion of MDBK cells were measured in vitro. Chickens were orally administrated with target positive phages and the protective effects against homologous challenge were evaluated. The model of three-dimensional (3D) structure for EtMIC3-bc1 was conducted, and molecular docking between target peptides and EtMIC3-bc1 model was analyzed. The results demonstrated that three selected positive phages specifically bind to EtMIC3-bc1 protein. The three peptides A, D and W effectively inhibited invasion of MDBK cells by sporozoites, showing inhibited ratio of 71.8%, 54.6% and 20.8%, respectively. Chickens in the group orally inoculated with phages A displayed more protective efficacies against homologous challenge than other groups. Molecular docking showed that amino acids in three peptides, especially in peptide A, insert into the hydrophobic groove of EtMIC3-bc1 protein, and bind to EtMIC3-bc1 through intermolecular hydrogen bonds. Taken together, the results suggest EtMIC3-binding peptides inhibit sporozoites entry into host cells. This study provides new idea for exploring novel strategies against coccidiosis.

Upregulation of circ-FBL promotes myogenic proliferation in myasthenia gravis by regulation of miR-133/PAX7.

Myasthenia gravis (MG) is a disease involving neuromuscular transmission that causes fatigue of skeletal muscles and fluctuating weakness. It has been shown that impairment of myogenic differentiation and myofiber maturation may be the underlying cause of MG. In this study, we detected the abnormal expression of circular RNA (circRNA) using next-generation sequencing in patients with MG. We then investigated the regulatory mechanism and the relationship among circRNA, microRNA, and messenger RNA using quantitative reverse-transcription polymerase chain reaction, bioinformatics analysis, and luciferase report analysis. The expression of inflammatory cytokines and regulatory T lymphocytes was shown to be increased. Circ-FBL was significantly increased in MG patients. Bioinformatics and luciferase report analyses confirmed that miR-133 and PAX7 were the downstream targets of circ-FBL. Overexpression of circ-FBL promoted myoblast proliferation by regulation of miR-133/PAX7. Taken together, our study showed that upregulation of circ-FBL promoted myogenic proliferation in patients with MG by regulating miR-133/PAX7.

A One-Dimensional Broadband Emissive Hybrid Lead Iodide with Face-Sharing PbI6 Octahedral Chains.

One-dimensional (1D) organic-inorganic hybrid lead halides with unique core-shell quantum wire structures and splendid photoluminescence properties have been considered one of the most promising high-efficiency broadband emitters. However, studies on the broadband emissions in 1D purely face-shared lead iodide hybrids are still rare so far. Herein, we report on a new 1D lead iodide hybrid, (2cepyH)PbI3 (2cepy = 1-(2-chloroethyl)pyrrolidine), characterized with face-sharing PbI6 octahedral chains. Upon UV photoexcitation, this material shows broadband yellow emissions originating from the self-trapped excitons associated with distorted Pb-I lattices on account of the strong exciton-phonon coupling, as proved by variable-temperature emission spectra. Moreover, experimental and calculated results reveal that (2cepyH)PbI3 is an indirect bandgap semiconductor, the band structures of which are governed by inorganic parts. Our work represents the first broadband emitter based on a 1D face-shared lead iodide hybrid and opens a new way to obtain the novel broadband emission materials.