Inhibition of OTUB2 suppresses colorectal cancer cell growth by regulating ß-Catenin signaling.

In the effort to identify deubiquitinating enzymes required for the growth of colorectal cancer (CRC) cells, we found that OTUB2 knockdown markedly inhibited the viability of these cancer cells in culture and in xenografted mice. It was also found that the level of OTUB2 was elevated in primary CRCs, and its high expression was a poor prognostic indicator for the patients. Interestingly, immunoprecipitation and LC-MS/MS analyses suggested that ß-Catenin was an OTUB2-interacting protein, and there was a positive correlation between OTUB2 and ß-Catenin expression in both CRC tissues and cell lines. We then performed reciprocal co-immunoprecipitations and demonstrated that OTUB2 and ß-Catenin bound to each other. Enforced expression of OTUB2 decreased ubiquitination of ß-Catenin and increased the half-life and intracellular level of ß-Catenin, whereas the catalytic inactive OTUB2 did not. OTUB2 also enhanced ß-Catenin-mediated transactivation as measured by TCF-luciferase and expression of endogenous CCND1 and MYC in CRC cells. These results indicated that OTUB2 was a potential target for therapeutic intervention for CRC.

TBK1 Facilitates GLUT1-Dependent Glucose Consumption by suppressing mTORC1 Signaling in Colorectal Cancer Progression.

Intestinal inflammation is a vital precipitating factor of colorectal cancer (CRC), but the underlying mechanisms are still elusive. TANK-binding kinase 1 (TBK1) is a core enzyme downstream of several inflammatory signals. Recent studies brought the impacts of TBK1 in malignant disease to the forefront, we found aberrant TBK1 expression in CRC is correlated with CRC progression. TBK1 inhibition impaired CRC cell proliferation, migration, drug resistance and tumor growth. Bioinformatic analysis and experiments in vitro showed overexpressed TBK1 inhibited mTORC1 signaling activation in CRC along with elevated GLUT1 expression without inducing GLUT1 translation. TBK1 mediated mTORC1 inhibition induces intracellular autophagy, which in turn decreasing GLUT1 degradation. As a rescue, blocking of autophagosome and retromer respectively via autophagy-related gene 7 (ATG7) or TBC1 Domain Family Member 5 (TBC1D5) silence diminished the regulation of TBK1 to GLUT1. GLUT1 staining presented that TBK1 facilitated GLUT1 membrane translocation which subsequently enhanced glucose consumption. Inhibitor of TBK1 also decreased GLUT1 expression which potentiated drug-sensitivity of CRC cell. Collectively, TBK1 facilitates glucose consumption for supporting CRC progression via initiating mTORC1 inhibition induced autophagy which decreases GLUT1 degradation and increases GLUT1 membrane location. The adaptive signaling cascade between TBK1 and GLUT1 proposes a new strategy for CRC therapy.

MiR-15a-3p regulates ferroptosis via targeting glutathione peroxidase GPX4 in colorectal cancer.

Colorectal cancer (CRC) is the second most common cancer-related deaths throughout the world. Ferroptosis is a recently regulated form of cell death, lately gains attention. MicroRNA-15a-3p (miR-15a-3p) plays a regulatory role in various kinds of cancers. However, the role of miR-15a-3p in cellular ferroptosis is still unclear. Here, we aimed to clarify whether miR-15a-3p could regulate the ferroptosis of CRC. Here we identified miR-15a-3p positively regulates ferroptosis via directly targeting glutathione peroxidase glutathione peroxidase 4 (GPX4) in CRC. Overexpression of miR-15a-3p repressed GPX4 through binding to the 3'-untranslated region of GPX4, resulting in increased reactive oxygen species level, intracellular Fe2+ level, and malondialdehyde accumulation in vitro and in vivo. Correspondingly, suppression of miR-15a-3p reduced the sensitivity of CRC cells to erastin and GPX4. Taken together, these data demonstrate that miR-15a-3p regulates ferroptosis through targeting GPX4 in CRC cells, illustrating the novel role of microRNA in ferroptosis.

TCGA database analysis of the tumor mutation burden and its clinical significance in colon cancer.

BACKGROUND: Colon cancer is one of the most common malignant tumors, with high rates of incidence and death. The tumor mutational burden (TMB), which is characterized by microsatellite instability, has been becoming a powerful predictor which can show tumor behavior and response to immunotherapy. METHODS: In this study, we analyzed 437 mutation data of colon cancer samples obtained from The Cancer Genome Atlas (TCGA) and divided patients into low- and high-TMB groups according to the TMB value. Then we identified differentially-expressed genes (DEGs), conducted immune cell infiltration and survival analyses between groups. RESULTS: The higher TMB of the patients with colon cancer predicts a poorer prognosis. Functional analysis was performed to assess the prognostic value of the top 30 core genes. The CIBER-SORT algorithm was used to investigate the correlation between the immune cells and TMB subtypes. An immune prognosis model was constructed to screen out immune genes related to prognosis, and the tumor immunity assessment resource (TIMER) was then used to determine the correlation between gene expression and the abundance of tumor-infiltrating immune cell subsets in colon cancer. We observed that APC, TP53, TTN, KRAS, MUC16, SYNE1, PIK3CA have higher somatic mutations. DEGs enrichment analysis showed that they are involved in the regulation of neuroactive ligand-receptor interaction, the Cyclic adenosine monophosphate (cAMP) signaling pathway, the calcium signaling pathway, and pantothenate and Coenzyme A (CoA) biosynthesis. The difference in the abundance of various white blood cell subtypes showed that Cluster of Differentiation 8 (CD8) T cells (P=0.008), activated CD4 memory T cells (P=0.019), M1 macrophages (P=0.002), follicular helper T cells (P=0.034), activated Natural killer (NK cell) cells (P=0.017) increased remarkably, while M0 macrophages significantly reduced (P=0.025). The two immune model genes showed that secretin (SCT) was negatively correlated with survival, while Guanylate cyclase activator 2A (GUCA2A) was positively correlated. CONCLUSIONS: This study conducted a systematically comprehensive analysis of the prediction and clinical significance of TMB in colon cancer in identification, monitoring, and prognosis of colon cancer, and providing reference information for immunotherapy.

DAB2IP decreases cell growth and migration and increases sensitivity to chemotherapeutic drugs in colorectal cancer.

BACKGROUND: Colorectal cancer (CRC) is one of the most common cancers worldwide with high rates of invasiveness and mortality. DAB2IP (DOC2/DAB2 interactive protein) is a member of the RAS-GTPase-activating protein (RAS-GAP) family that shows a suppressive effect on cancer progression, is downregulated in several cancers. However, the role of DAB2IP in CRC remains elusive. METHODS: Expression of DAB2IP was evaluated in human CRC tissues using immunohistochemistry (IHC), quantitative real-time reverse transcription PCR (qRT-PCR) and immunoblotting. Knockdown and overexpression of DAB2IP in CRC cells were achieved by transfecting siRNAs and DAB2IP expression vectors and assessed by qRT-PCR and immunoblotting. CCK-8, colony formation, wound-healing, and transwell assays were used to evaluate CRC cell growth, migration, and sensitivity to chemotherapeutic drugs. The cell cycle was analyzed by propidium iodide (PI) staining and flow cytometry. Cell apoptosis was evaluated by Annexin V-DAPI double staining and flow cytometry. The effect of DAB2IP overexpression on tumor formation was explored by an in vivo tumorigenesis assay. Finally, immunoblotting was performed to examine the molecules related to the action of DAB2IP in CRC. RESULTS: Compared with para-cancer tissues, there was a marked decrease of DAB2IP expression in surgically excised CRCs. In cultured CRC cells, enforced expression of DAB2IP inhibited cell growth and migration and sensitized the cells to DNA-acting cisplatin, oxaliplatin, and doxorubicin but not 5-fluorouracil (5-FU). In contrast, knockdown of DAB2IP produced the opposite effect. Moreover, DAB2IP overexpression hindered tumor growth in vivo. We further found that DAB2IP regulated the expression of cell growth, epithelial-mesenchymal transition (EMT), and apoptosis-related proteins in CRC cells and inhibited the phosphorylation of protein kinase B (AKT) and extracellular signal-regulated kinase (ERK). CONCLUSIONS: Expression of DAB2IP inhibited CRC cell growth and migration and sensitized CRC cells to chemotherapeutic drugs. Inhibition of the phosphorylation of AKT and ERK is associated with the effects of DAB2IP expression. Restoration of DAB2IP expression may be a novel target for treating CRC.

Genome variation in colorectal cancer patient with liver metastasis measured by whole-exome sequencing.

BACKGROUND: Liver metastasis of colorectal cancer (CRC) is an important cause of death from CRC, but its molecular mechanism is still unclear. In recent years, whole-exome sequencing has played an increasingly important role in the study of the occurrence and development of diseases, especially malignant tumors. Its high throughput and low cost advantages enable researchers to explore the pathogenic genes of diseases, and screen potential molecular markers and therapeutic targets from the level of genomics. METHODS: This study collected the primary tumor tissues, matched paracancerous, normal tissues, and liver metastases of 4 CRC patients admitted to the Department of General Surgery of the First Affiliated Hospital of Soochow University, and performed high-depth whole-exome sequencing, with the sequencing depth of each sample reaching 123× on average, then filtered the sequencing data, compared them, and analyzed the bioinformatics data. RESULTS: we found 8,565 single nucleotide variants (SNV) and 429 insertions/deletions (InDel) in the primary and hepatic lesion tissues, and the genes with the highest mutation frequency were titin (TTN), obscurin (OBSCN), and homeodomain-interacting protein kinase 2 (HIPK2). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the mutant genes was conducted, and it was found that the mutant genes were mainly concentrated in the cells, cell parts, and cellular process of GO. The results of KEGG pathway analysis showed that mutations were mainly distributed in circadian entrainment, insulin secretion, and glutamatergic synapse. Further, we identified 723 SNV and Indel genes with high frequency mutations including TTN, OBSCN, and hydrocephalus-inducing protein homolog (HYDIN) across all tissues of liver metastases. The GO analysis showed that the mutated genes in liver metastatic tissues were mainly concentrated in cell, cell part, and cellular process. The KEGG pathway analysis showed that high frequency mutation genes were focused on gastric acid secretion, bile secretion, and melanogenesis. CONCLUSIONS: This study found some candidate genes related to the occurrence of CRC and liver metastasis through whole-exome sequencing of relevant tissues in CRC patients with liver metastasis, which is expected to provide new markers and therapeutic targets for such patients.

Depressed expression of FAE1 and FAD2 genes modifies fatty acid profiles and storage compounds accumulation in Brassica napus seeds.

In plants, the enzymes fatty acid dehydrogenase 2 (FAD2) and fatty acid elongase 1 (FAE1) have been shown in previous studies to play important roles in the de novo biosynthesis of fatty acids. However, the effects of depressed expression of FAD2 and FAE1 on seed storage compounds accumulation remains to be elucidated. In this study, we produced RNA interfering transgenic rapeseeds lines, BnFAD2-Ri, BnFAE1-Ri and BnFAD2/BnFAE1-Ri, which exhibited depressed expression of the BnFAD2 and BnFAE1 genes under the control of seed-specific napin A promoter. These transgenic rapeseeds showed normal growth and development as compared with the wild type (CY2). Depressed expression of BnFAD2 and BnFAE1 genes modified fatty acid profiles, leading to increased oleic acid and decreased erucic acid contents in transgenic seeds. Consistent with these results, the ratios of C18:1/C18:2 and C18:1/C18:3 in C18 unsaturated fatty acids were greatly increased due to increased oleic acid content in transgenic seeds. Moreover, depressed expression of BnFAD2 and BnFAE1 genes resulted in slightly decreased oil contents and increased protein contents in transgenic seeds. Our results demonstrated that depressed expression of BnFAD2 and BnFAE1 greatly improves seed nutritional quality by modulating the fatty acid metabolism and storage products accumulation and that BnFAD2 and BnFAE1 are reliable targets for genetic improvement of rapeseed in seed nutritional quality.

Embryonal Control of Yellow Seed Coat Locus ECY1 Is Related to Alanine and Phenylalanine Metabolism in the Seed Embryo of Brassica napus.

Seed coat color is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds such as seed dormancy, longevity, oil content, protein content and fiber content. In Brassica napus, inheritance of seed coat color is related to maternal effects and pollen effects (xenia effects). In this research we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus, which is named Embryonal Control of Yellow seed coat 1 (Ecy1). Microscopy of transverse sections of the mature seed show that pigment is deposited only in the outer layer of the seed coat. Using Illumina Hisequation 2000 sequencing technology, a total of 12 GB clean data, 116× coverage of coding sequences of B. napus, was achieved from seeds 26 d after pollination (DAP). It was assembled into 172,238 independent transcripts, and 55,637 unigenes. A total of 139 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus Only 49 of the TT orthologous genes are transcribed in seeds. However transcription of all orthologs was independent of embryonal control of seed coat color. Only 55 genes were found to be differentially expressed between brown seeds and the yellow mutant. Of these 55, 50 were upregulated and five were downregulated in yellow seeds as compared to their brown counterparts. By KEGG classification, 14 metabolic pathways were significantly enriched. Of these, five pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways, and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were present at higher levels in the embryos of yellow seeds as compared to those of brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the embryo. The pigment substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe, and disappearance of pigment in the yellow seeded mutant, suggests that embryonal control of seed coat color is related with Phe and Ala metabolism in the embryo of B. napus.

RNAi knockdown of fatty acid elongase1 alters fatty acid composition in Brassica napus.

The quality and end-use of oil from oilseed crops is determined by its fatty acid composition. In particular, the relative proportions of erucic and oleic acids are key selection traits for breeders. The goal of our research is to genetically improve the nutritional quality of Brassica napus cultivar CY2, the oil of which is high in erucic acid (about 40%) and low in oleic acid (about 20%). Here, we report the use of a seed-specific napin A promoter to drive the knockdown of BnFAE1 in transgenic CY2. Southern blotting results confirmed the presence of the transgene. RT-PCR analysis showed that the levels of BnFAE1 were greatly decreased in BnFAE1-Ri lines compared with the CY2 cultivar. Knockdown of BnFAE1 sharply decreased the levels of erucic acid (less than 3%), largely increased the contents of oleic acid (more than 60%) and slightly increased the polyunsaturated chain fatty acids. Compared with high erucic acid parents, expression of BnFAE1 was dramatically decreased in developing F1 seeds derived from reciprocally crossed BnFAE1-Ri lines and high erucic acid cultivars. In addition, F1 seeds derived from reciprocal crosses between BnFAE1-Ri lines and high erucic acid cultivars showed significantly increased oleic acid (more than 52%) and sharply decreased erucic acid (less than 4%), demonstrating that the RNAi construct of BnFAE1 can effectively interfere with the target gene in F1 seeds. Taken together, our results demonstrate that BnFAE1 is a reliable target for genetic improvement of rapeseed in seed oil quality promotion.

Microsatellite primers in red bayberry, Myrica rubra (Myricaceae).

PREMISE OF THE STUDY: Microsatellite markers were developed in Myrica rubra to investigate potential hybridization events within or between M. rubra and its closely related species. METHODS AND RESULTS: Using an ISSR-suppression PCR method, 12 primer pairs were temporarily developed with GSG(GT)(6) as the primer for enriching microsatellite sequences and the genomic DNA of M. rubra cv. 'Heijing' as template. The average allele number per locus was 4.9 within 26 individuals including two species, M. rubra and M. nana. Three pairs of primers produced species-specific alleles, and the other nine showed polymorphisms among 26 accessions. CONCLUSIONS: Results indicated that the ISSR-suppression PCR method is suitable for developing microsatellite markers, especially for this species with little understanding of genomic information. The developed microsatellite markers provide a useful tool for further studies of population structure within or between M. rubra and M. nana or other closely related species.

[Raising fat content in transgenic rice by anti-PEP gene transformation].

Gene for phosphoenolpyruvate carboxylase (PEPCase) was incorporated in antisense orientation into genome of japonica rice variety Xiushui 11 through Agrobacterium tumefaciens-mediated transformation of mature seeds-derived embryogenic calli, and a total of 95 transgenic plants were regenerated, which were confirmed by histochemical detection of GUS activity (Fig.2), PCR assay (Fig.3) and Southern hybridization analysis (Fig.4). The transgene was inherited by the T1 progeny and Mendelian 3:1 segregation ratio was observed in most transgenic lines. It was found that the fat content of hulled grains of T2 transgenic lines was 0.37 +/- 0.12 per cent higher than that of the control, most of which were statistically very significant (Table 2).

Highly efficient transformation and plant regeneration of tall fescue mediated by Agrobacterium tumefaciens.

An efficient and reproducible system has been developed for the production of transgenic plants in tall fescue (Festuca arundinacea Schreb.) using A. tumefaciens-mediated transformation. Two-months-old suspension cultures served as excellent explants for transformation. The explants were inoculated with an A. tumefaciens strain EHA105 carrying a plasmid pDBA121 containing genes for hygromycin phosphotransferase (hpt) and phosphinotricin acetyltransferase (bar). The commercial herbicide Basta was used as a selective agent. Inclusion of acetosyringone (ACS) 20 mg/L in the co-culture medium led to an increase in transformation efficiency. The efficiency of transformation was highly dependent on the genotype, the explant, the culture medium and selective agent used. Tall fescue transformation efficiency is 2.85-10.9 plants per gram fresh weight (FW) of suspension cultures. This is much higher than the corresponding values reported before (2-5 plants). So far more than 300 transgenic plants have been obtained, the fertility of some transgenic plants had decreased. Stable integration and high expression of the transgenes were confirmed by PCR analysis and Southern blot hybridization or herbicide Basta spraying test.