Unveiling the oncogenic role of CLDN11-secreting fibroblasts in gastric cancer peritoneal metastasis through single-cell sequencing and experimental approaches.

BACKGROUND: Fibroblasts are necessary to the progression of cancer. However, the role of fibroblasts in peritoneal metastasis (PM) of gastric cancer (GC) remains elusive. In this study, we would explore the role of fibroblasts mediated cell interaction in PM of GC. METHODS: Single-cell sequencing data from public database GSE183904 was used to explore the specific fibroblast cluster. Fibroblasts were extracted from PM and GC tissues. The expression level of CXCR7 was verified by western blot, immunohistochemistry. The role of CLDN11 was investigate through in vitro and in vivo study. Multiple immunohistochemistry was used to characterize the tumor microenvironment. RESULTS: CXCR7-positive fibroblasts were significantly enriched in PM of GC. CXCR7 could promote the expression of CLDN11 through activation of the AKT pathway in fibroblasts. Fibroblasts promote the GC proliferation and peritoneal metastasis by secreting CLDN11 in vitro and in vivo. Furthermore, it was revealed that CXCR7-positive fibroblasts were significantly associated with M2-type macrophages infiltration in tissues. CONCLUSION: CXCR7-positive fibroblasts play an essential role in PM of GC via CLDN11. Therapy targeting CXCR7-positive fibroblasts or CLDN11 may be helpful in the treatment of GC with PM.

N6-methyladenosine-modified MIB1 promotes stemness properties and peritoneal metastasis of gastric cancer cells by ubiquitinating DDX3X.

BACKGROUND: Peritoneal metastasis (PM), one of the most typical forms of metastasis in advanced gastric cancer (GC), indicates a poor prognosis. Exploring the potential molecular mechanism of PM is urgently necessary, as it has not been well studied. E3 ubiquitin ligase has been widely established to exert a biological function in various cancers, but its mechanism of action in GC with PM remains unknown. METHODS: The effect of MIB1 on PM of GC was confirmed in vitro and in vivo. Co-immunoprecipitation (Co-IP) and mass spectrometry demonstrated the association between MIB1 and DDX3X. Western blot, flow cytometry and immunofluorescence determined that DDX3X was ubiquitylated by MIB1 and promoted stemness. We further confirmed that METTL3 promoted the up-regulation of MIB1 by RNA immunoprecipitation (RIP), luciferase reporter assay and other experiments. RESULTS: We observed that the E3 ubiquitin ligase Mind bomb 1 (MIB1) was highly expressed in PMs, and patients with PM with high MIB1 expression showed a worse prognosis than those with low MIB1 expression. Mechanistically, our study demonstrated that the E3 ubiquitin ligase MIB1 promoted epithelial-mesenchymal transition (EMT) progression and stemness in GC cells by degrading DDX3X. In addition, METTL3 mediated m6A modification to stabilize MIB1, which required the m6A reader IGF2BP2. CONCLUSIONS: Our study elucidated the specific molecular mechanism by which MIB1 promotes PM of GC, and suggested that targeting the METTL3-MIB1-DDX3X axis may be a promising therapeutic strategy for GC with PM.

Integrative analysis of metabolome and transcriptome reveals the improvements of seed quality in vegetable soybean (Glycine max (L.) Merr.).

Vegetable soybean is derived from grain soybean. Seeds of vegetable soybean are bigger, sweeter, and have smoother texture and better flavor than those of grain soybean. To better understand the improvements of seed quality in vegetable soybean, comparative metabolome and transcriptome analyses were performed in the developing seeds between grain (Williams 82) and vegetable (Jiaoda 133) soybeans. A total of 299 differential metabolites were identified between two genotypes, with an increase in free amino acids, carbohydrates, sterols, and flavonoids and a decrease in fatty acid in vegetable soybean. Thousands of differentially expressed genes (DEGs) were identified by transcriptome analysis. DEGs were used for weighted gene co-expression network analysis (WGCNA), yielding 16 co-expression modules. The expression patterns of DEGs within these modules were distinct between two genotypes. Functional enrichment analysis revealed that metabolic pathways, including alanine, aspartate and glutamate metabolism, fatty acid degradation, starch and sucrose metabolism, sucrose transport, and flavonoid biosynthesis, were up-regulated, whereas photosynthesis, arginine biosynthesis, arginine and proline metabolism, glycolysis/gluconeogenesis, and fatty acid biosynthesis were down-regulated in vegetable soybean. Reasonably, the alterations of metabolic pathways corresponding to DEGs partly explained the formation of differential metabolites. These findings provide a better understanding of seed development and breeding improvements of vegetable soybean.

TMT-based quantitative proteomics analyses of sterile/fertile anthers from a genic male-sterile line and its maintainer in cotton (Gossypium hirsutum L.).

Genetic male sterility (GMS) in cotton is important for utilization of heterosis. However, the molecular mechanism of GMS is poorly known. In this study, cytological and proteomics analyses of anthers were conducted in three stages (stage 3 to 5) between GMS line (GA18) and its maintainer (GA18M). The cross-section observation revealed that the tapetal layer in stage 3 was thinner in GA18 compared to GA18M, and the tapetum cells did not degrade in stage 4 in GA18, thus providing no material for microspore development. A total of 1952 differentially expressed proteins (DEPs) were identified between GA18 and GA18M anthers. They were annotated to 52 gene ontology (GO) terms and enriched in 115 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which formed several complex regulator networks, and dozens of important nodes were identified. Moreover, DEPs were also identified between two consecutive stages of GA18 and GA18M, with functional analyses indicating that numerous developmental differences existed between fertile and sterile anthers. The metabolic pathways were significantly altered, including decreased carbohydrate metabolism, ribosome defects, disturbed protein synthesis, disrupted flavonoids synthesis, etc., that may be involved in male sterility. Overall, these results provide genetic resources that help decipher the molecular mechanisms behind GMS. SIGNIFICANCE: Male sterility is a common phenomenon in flowering plant species, and plays a role in the application of heterosis. However, the molecular mechanism of it remains to be elucidated. Using cytological and proteomics approaches, we found that the tapetal layer development retardation may be the reason of male sterility, which was different from the delayed degradation described in previous studies. More than one thousand differentially expressed proteins were identified between male sterile line and its maintainer, forming a complex regulatory network, and the key nodes were remarked that could be used as candidate proteins related to male sterility in future study. Dozens of metabolic pathways were significantly altered, among them, ribosome defects was a novel pathway that may be involved in male sterility. These results enhance our understanding of the molecular mechanism governing male sterility and lay a foundation for clone of genes association with male sterility.

[EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences].

Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding.

Mitochondrial genomes of the hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Syrphidae), with a phylogenetic analysis of Muscomorpha.

The hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Muscomorpha: Syrphidae) are important natural aphid predators. We obtained mitochondrial genome sequences from these two species using methods of PCR amplification and sequencing. The complete Episyrphus mitochondrial genome is 16,175 bp long while the incomplete one of Eupeodes is 15,326 bp long. All 37 typical mitochondrial genes are present in both species and arranged in ancestral positions and directions. The two mitochondrial genomes showed a biased A/T usage versus G/C. The cox1, cox2, cox3, cob and nad1 showed relatively low level of nucleotide diversity among protein-coding genes, while the trnM was the most conserved one without any nucleotide variation in stem regions within Muscomorpha. Phylogenetic relationships among the major lineages of Muscomorpha were reconstructed using a complete set of mitochondrial genes. Bayesian and maximum likelihood analyses generated congruent topologies. Our results supported the monophyly of five species within the Syrphidae (Syrphoidea). The Platypezoidea was sister to all other species of Muscomorpha in our phylogeny. Our study demonstrated the power of the complete mitochondrial gene set for phylogenetic analysis in Muscomorpha.

The complete chloroplast genome sequence and phylogenetic analysis of Chuanminshen (Chuanminshenviolaceum Sheh et Shan).

Chloroplast genome sequences are very useful for species identification and phylogenetics. Chuanminshen (Chuanminshen violaceum Sheh et Shan) is an important traditional Chinese medicinal plant, for which the phylogenetic position is still controversial. In this study, the complete chloroplast genome of Chuanminshen violaceum Sheh et Shan was determined. The total size of Chuanminshen chloroplast genome was 154,529 bp with 37.8% GC content. It has the typical quadripartite structure, a large single copy (17,800 bp) and a small single copy (84,171 bp) and a pair of inverted repeats (26,279 bp). The whole genome harbors 132 genes, which includes 85 protein coding genes, 37 tRNA genes, eight rRNA genes, and two pseudogenes. Thirty-nine SSR loci, 32 tandem repeats and 49 dispersed repeats were found. Phylogenetic analyses results with the help of MEGA showed a new insight for the Chuanminshen phylogenetic relationship with the reported chloroplast genomes in Apiales plants.