Multi-omics data-based analysis characterizes molecular alterations of the vesicle genes in human colorectal cancer.

The role of vesicular genes in the development of colorectal cancer (CRC) is crucial. Analyzing alterations in these genes at multi-omics can aid in understanding the molecular pathways behind colorectal carcinogenesis and identifying potential treatment targets. However, studies on the overall alteration of vesicular genes in CRC are still lacking. In this study, we aimed to investigate the relationship between vesicle genetic alterations and CRC progression. To achieve this, we analyzed molecular alterations in CRC vesicle genes at eight levels, including mRNA, protein, and epigenetic levels. Additionally, we examined CRC overall survival-related genes that were obtained from a public database. Our analysis of chromatin structural variants, DNA methylation, chromatin accessibility, and proteins (including phosphorylation, ubiquitination, and malonylation), along with RNA-seq data from the TCGA database, revealed multiple levels of alterations in CRC vesicle genes in the collected tissue samples. We progressively examined the alterations of vesicle genes in mRNA and protein levels in CRC and discovered the hub genes. Further investigation identified the probable essential transcription factors. This study contributes to a thorough knowledge of the connection between vesicle gene alterations at multiple levels and the development of CRC and offers a theoretical framework for the identification of novel treatment targets.

Optimization of lactic acid bacterial starter culture to improve the quality and flavor characteristics of traditional Hurood.

Hurood is a traditional fermented milk product prepared by traditional Mongolian techniques of fermenting raw milk, partial degreasing, heating, whey drainage, emulsification of curd, and molding. Currently, Hurood available in the market is generally prepared by small-scale enterprises at home or in open air. Therefore, lack of standardization of bacterial starter culture leads to variation in the flavor and sensory properties of Hurood from batch to batch. In this study, we aimed to assess the best starter culture combination obtained from 37 lactic acid bacterial strains isolated from traditional Hurood. The solidification state and sensory quality were used as indexes for determining the fermentation efficiency of the bacterial starter culture combinations. The yield and texture characteristics were used to determine the optimal ratio of bacterial strains in a combination and the processing conditions for traditional Hurood production. The most optimal bacterial culture combination was observed to be NF 9-3:NF 10-4:CH 3-1 in 5:4:1 ratio and in 3% amount. The most optimal whey temperature and heating-stirring temperature were observed to be 55°C to 60°C and 85°C to 90°C, respectively. Hurood prepared with the optimal combination of bacterial strains exhibited significantly enhanced sensory quality, flavor, and contents of AA and fatty acids. Therefore, the use of optimal starter culture of lactic acid bacteria could produce Hurood with significantly superior sensory qualities, making the product more acceptable to consumers.

A New Highly Oxygenated Polyketide Derivative from Trichoderma sp. and Its Antifungal Activity.

A new highly oxygenated polyketide derivative, trichodersine (1), together with fourteen known compounds (2-15) were isolated from Trichoderma sp. MWTGP-04. The structure of trichodersine (1) was established based on comprehensive spectroscopic data analysis, and biogenesis argument. The results of double culture experiments indicated that the strain exhibited potential antifungal activity. The antifungal activities of all isolated compounds were evaluated, among them compound 1 exhibited remarkable antifungal activities against Fusarium solani, Plectosphaerella cucumerina, Alternaria panax, and Aspergillus niger, with minimum inhibitory concentrations (MICs) of 4, 4, 16, and 32 µg/mL, respectively. In addition, the antifungal experiments of polyketide derivatives (1-3) disclosed that their degree of oxidation was a key factor affecting the antifungal activity.

Investigations of specialised metabolites of endophyte Diaporthe destruens hosted in Illigera orbiculata C. Y. Wu.

A chemical investigation of the endophytic fungus Diaporthe destruens from the Hernandiaceae plant Illigera orbiculata C. Y. Wu collected from southern Yunnan Province, China, led to the isolation of six undescribed compounds, including two azaphilone analogs, which are a pair of epimers (13R-hydroxy-chermesinone A and 13S-hydroxy-chermesinone A); a pyrrole derivative (1-(4-(methoxymethyl)-1H-pyrrol-3-yl)ethan-1-one); an isoindolone derivative (4-hydroxy-6-methoxyisoindolin-1-one); a benzylbenzene derivative (destruensine A) and a conjectural fragment of polyketide ((2R,4R)-2-(methoxymethyl)pentane-1,4-diol) along with nine known compounds. Their structures were elucidated by spectroscopic methods and HRESIMS, and the absolute configurations were further confirmed by electronic circular dichroism (ECD) and chemical derivatization. The antimicrobial activities, anti-acetylcholinesterase activities, antiproliferation, and NO production inhibitory effects of compounds 1-15 were evaluated.

Three new sesquiterpenes from the stems of Nicotiana tabacum and their bioactivities.

Three new sesquiterpenes, methyl 4-isopropyl-7-methoxy-6-methylnaphthalene-1-carboxylate (1), methyl 2-hydroxy-4-isopropyl-7-methoxy-6-methylnaphthalene-1-carboxylate (2), and methyl 2-hydroxy-6-(hydroxymethyl)-4-isopropyl-7-methoxynaphthalene-1-carboxylate (3), together with three known sesquiterpenes (4-6), were isolated from the stems of Nicotiana tabacum. Their structures were determined by means of HRESIMS and extensive 1D and 2D NMR spectroscopic studies. The results showed that compounds 2, 3, and 5 exhibited high anti-TMV activity with inhibition rates of 33.6, 35.8, and 36.7%. Compounds 1-6 showed weak inhibitory activities against some tested human tumor cell lines (NB4, A549, SHSY5Y, PC3, and MCF7) with IC50 values in the range of 6.7-9.6 µM.

[A new isobenzofuranone derivative from Phlomis betonicoides and its antibacterial activity].

A new isobenzofuranone derivative has been isolated from Phlomis betonicoides by using various chromatographic techniques, including silica gel, Sephadex LH-20, MCI-gel resin and RP-HPLC. This compound was determined as 5-(3-hydroxypropyl)-2,2-dimethyl-2H-furo[3,4-h]chromen-7(9H)-one (1) by NMR, MS, IR and UV spectroscopic data. Compound 1 showed potent antibacterial activity with an MIC90 value of (58.4 ± 4.2) mg·L⁻¹ for methicillin resistant Staphylococcus aureus (MRSA) strain [levofloxacin as a control with MIC90 value of (52.8±4.6) mg·L⁻¹].

Three new benzolactones from Lavandula angustifolia and their bioactivities.

Three new benzolactones (1-3), together with four known ones (4-7), were isolated from the whole herb of Lavandula angustifolia. Their structures were established on the basis of detailed spectroscopic analysis (1D- and 2D-NMR, HRESIMS, UV, and IR) and comparison with data reported in the literature. New compounds were evaluated for their anti-tobacco mosaic virus (TMV) activities and cytotoxic activities. The results revealed that compounds 1-3 showed obvious anti-TMV activities with inhibition rates of 26.9, 30.2, and 28.4%, which were at the same grade as positive control. Compounds 1-3 also showed weak inhibitory activities against some tested human tumor cell lines with IC50 values in the range of 32.1-7.6 µM.

Anti-TMV activity flavones from the leaves of Yunnan local air cured tobacco.

Four new flavones, tobaflavones E-H (1-4), together with two known flavones (5 and 6), were isolated from the leaves of Dali Tiandeng tobacco (a variety of Yunnan local air cured tobacco). Their structures were elucidated by spectroscopic methods, including extensive 1D- and 2D NMR techniques. Compound 2 is the first naturally occurring flavone bearing a (4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)methyl moiety. These compounds were also evaluated for their anti-tobacco mosaic virus (anti-TMV) activity. The results revealed that compounds 1 and 2 exhibited high anti-TMV activity with inhibition rate of 35.3% and 39.6%, respectively. The rates are higher than those of positive control. The other compounds also showed potential anti-TMV activity with inhibition rates in the range of 18.7-28.4%, respectively.

[The roles of Ku80/p53 pathway in silica-induced cell cycle changes in human embryo lung fibroblasts].

OBJECTIVE: To study the roles of Ku80/p53 pathway in silica-induced cell cycle changes in human embryo lung fibroblasts (HELF). METHODS: Ku80 siRNA expression vectors were transfected into HELF by lipofectamine. Flow cytometry was used to detect the distributions of cell cycle and western blot assay was used to determine the expression level of Ku80, p53 and p21 proteins or the phosphorylation levels of p53-ser15 after cells were exposed to silica. RESULTS: The expression levels of Ku80 protein increased in concentration-dependent and time-dependent manners after cells were exposed to silica. The proportion of G1 phases in H-NC cells (controls) decreased from 89.28% +/- 2.19% to 68.93% +/- 3.79% after exposure to silica, and the proportion of G1 phases in HELF cells (H-Ku80) decreased from 85.16% +/- 3.73% to 59.92% +/- 3.31% after exposure to silica (P<0.05). The expression levels of Ku80, p53 proteins or p21 proteins or phosphorylation level of p53-ser15 were obviously suppressed in H-Ku80, as compared with H-NC. CONCLUSION: Ku80/p53 pathway plays a role in the cell cycle charges induced by silica in human embryo lung fibroblasts.

DNA repair and synthetic lethality.

Tumors often have DNA repair defects, suggesting additional inhibition of other DNA repair pathways in tumors may lead to synthetic lethality. Accumulating data demonstrate that DNA repair-defective tumors, in particular homologous recombination (HR), are highly sensitive to DNA-damaging agents. Thus, HR-defective tumors exhibit potential vulnerability to the synthetic lethality approach, which may lead to new therapeutic strategies. It is well known that poly (adenosine diphosphate (ADP)-ribose) polymerase (PARP) inhibitors show the synthetically lethal effect in tumors defective in BRCA1 or BRCA2 genes encoded proteins that are required for efficient HR. In this review, we summarize the strategies of targeting DNA repair pathways and other DNA metabolic functions to cause synthetic lethality in HR-defective tumor cells.

[Roles of DNA dependent protein kinase in silica-induced cyclin E and CDK2 expressions and cell cycle changes in human embryo lung fibroblasts].

OBJECTIVE: To study the roles of DNA dependent protein kinase (DNA-PK)in silica-induced cell cycle changes and expressions of CyclinE and CDK2 in human embryo lung fibroblasts (HELF). METHODS: The expressions of Ku80 and DNA-PKcs proteins were inhibited by siRNA plasmids, respectively. Flow cytometry was used to detect the distributions of cell cycle and western blot assay was used to determine the expression levels of CyclinE and CDK2 after cells were exposed to 200 microg/ml silica for 0, 3, 6, 12, 24 h. RESULTS: The proportion of G1 phases in negative control cells decreased from 83.53% +/- 2.24% to 69.11% +/- 3.12% after exposure to silica; the proportion of G1 phases in H-Ku80 and H-PKcs cells exposed to silica decreased from 85.16% +/- 3.73% to 59.92% +/- 3.31% and from 75.06% +/- 2.23% to 58.32% +/- 1.35%, respectively (P < 0.05). The exposure to silica resulted in the increasing protein expression levels of CyclinE and CDK2 in negative control cells, and the expression levels of CyclinE were obviously suppressed in H-Ku80 and H-PKcs as compared with control cells. However, the expression level of CDK2 protein did not change significantly. CONCLUSION: DNA-PK might play a role in silica-induced alternations of cell cycle and regulate silica-induced overexpression of CyclinE in human embryo lung fibroblasts.

[Silica induce cell cycle changes by mitogen-activated protein kinases pathway].

OBJECTIVE: To investigate the roles of mitogen-activated protein kinases (MAPK) on silica-induced cell cycle changes. METHODS: After cells were treated with 200 microg/ml silica, Western blot and Immunofluorescence assays were utilized to detect the expression of cyclin D1, CDK4 and E2F-4, Flow cytometry was used to detect cell cycle progression, the dominant negative mutants techniques were used to investigate silica-induced signal pathway and the effects of which in silica-induced cell cycle changes. RESULTS: After cells were exposed to 200 microg/ml silica 24 h, the results of present study showed the proportion of cells in G1 phases was decreased. Silica-induced cell cycle alternation was markedly impaired by stable expression of a dominant negative mutants of ERK or JNK, but not p38. It was found that ERK and JNK were involved in silica-induced cyclin D1 and CDK4 overexpression and the decreased expression of E2F-4. CONCLUSION: ERK and JNK, but not p38, mediated silica-induced cell cycle changes in human embryo lung fibroblasts.

[The roles of activated protein-1 and cell cycle protein in silica-induced cell cycle changes].

OBJECTIVE: To investigate the roles of cyclin D1 and CDK4 in the cell cycle changes of human embryonic lung fibroblasts (HELFs) exposed to silica. METHODS: HELFs were divided into 4 groups: control group, curcumin (20 µmol/L for 1 h) group, silica (200 µg/ml for 24 h) group and curcumin plus silica group, i.e. after exposure to 20 µmol/L curcumin for 1h, the HELFs were treated with 200 µg/ml silica for 24 h. Western blot and Immunofluorescence assays were utilized to detect the expression levels of cyclin D1, CDK4 and E2F1/4. Flow cytometry was used to detect the cell cycle progression, the RNA transfection technique was used to investigate the silica-induced signal pathway and the roles of which in silica-induced cell cycle changes. RESULTS: The expression levels of cyclin D1 and CDK4 significantly increased and the expression level of E2F-4 decreased obviously, but the expression level of E2F-1 did not significantly change in silica group. The proportion of G1 phase cells obviously decreased and the proportion of S phase cells significantly increased in silica group, as compared with control group (P < 0.05). When suppressing the expression of cyclin D1 or CDK4, the proportions of cells in G1 phase in anti-D1 plus silica group and anti-K4 plus silica group did not obviously change, as compared with control group. When suppressing AP-1 activity, the cyclin D1 and CDK4 expression levels decreased and the E2F-4 expression level increased in curcumin plus silica group, as compared with silica group. CONCLUSION: The results of present suggested that 200 µg/ml silica could induce the high expression of cyclin D1 and CDK4 and the low expression of E2F-4, resulting in the cell cycle changes by AP-1/cyclin D1 pathway in HELFs.

[Roles of phosphatidylinositol 3 kinase in silica-induced DNA double strand breaks damage repair in human embryo lung fibroblasts].

OBJECTIVE: To study the role of Phosphatidylinositol 3 kinase (PI3K) in silica-induced DNA double strand break repair in human embryo lung fibroblasts (HELF). METHODS: Control HELF cells and DN-Deltap85 (HELF transfected with Dominant negative mutant of PI3K) were treated with 200 microg/ml silica for different times. The expression levels of phosphor-H2AX (H2AX), Ku70, Ku80 and DNA-PKcs were determined by Western blot. Furthermore, DNA double strand breaks were measured by neutral comet assay after cells were treated with 200 microg/ml silica for 0, 12 and 24 h. RESULTS: After treatment with 200 microg/ml silica for different times, the levels of H2AX were increased in a time-dependent manner and the expression levels of H2AX were obviously suppressed in DN-Deltap85 compared with control cells. The levels of Ku70 and Ku80 were also significantly suppressed in DN-Deltap85 (0.37 +/- 0.14, 0.55 +/- 0.17) compared with control cells (0.58 +/- 0.09, 0.95 +/- 0.21) after treatment with 200 microg/ml silica for 12 h (P < 0.05). Both the percentage of tail DNA in HELF and DN-Deltap85 increased significantly at 12 h (9.78 +/- 1.15, 11.79 +/- 4.90) compared with groups without treatment with silica (2.40 +/- 0.69, 3.31 +/- 1.35) and then decreased at 24 h (4.19 +/- 0.47, 7.58 +/- 4.32), but only the decrease of HELF at 24 h was significant compared with HELF at 12 h (P < 0.05). DNA repair competence of HELF was 75.74% and that of DN-Deltap85 declined to 49.64%. CONCLUSION: Silica dust can induce DNA double strand breaks in human embryo lung fibroblasts. PI3K might play a role in silica-induced DNA double strand break repair by regulating the expression levels of Ku70 and Ku80.

[Role of p53 in silica-induced cell cycle alternation and DNA double-strand break repair in human embryo lung fibroblasts].

OBJECTIVE: To study the role of p53 in silica-induced cell cycle alternation and DNA double strand breaks repair in human embryo lung fibroblasts (HELF). METHODS: Neutral comet assay was applied to detect silica-induced DNA double strand breaks. According to the neutral comet experimental result, the DNA repair competence was calculated. The expression levels and phosphorylation of protein in HELF were determined by Western blot. Cell cycle changes were identified by flow cytometry in HELF. RESULTS: After treatment with 200 microg/ml silica for different times (0, 1, 2, 6, 12 and 24 h), the expression levels and phosphorylation of p53 increased in a time-dependent manner, reaching maximum at 12 h and then decreasing at 24 h. After treatment with 0, 25, 50, 100, 200, 300 and 400 microg/ml silica for 12 h, the expression levels and phosphorylation of p53 increased in concentration-dependent manner. After p53 expression was inhibited, silica-induced DNA damage repair competence was markedly increased (DRC = 87.68%), compared with the negative control cell induced by silica (DRC = 57.19%). Silica increased the percentage of S phase (31.8 +/- 1.1)% compared with the controls (24.3 +/- 3.8)% (P < 0.05). When p53 expression was inhibited, the number of S phase cells was significantly increased, (41.4 +/- 0.6)% compared with the controls (25.4 +/- 1.9)% (P < 0.05). CONCLUSION: The silica dramatically increases the expression levels and phosphorylation of p53. The increased expression of p53 mediates silica-induced cell cycle change and inhibits silica-induced DNA double strand breaks repair.

[Role of DNA-dependent protein kinase catalytic subunit in silica-induced DNA double-strand break repair in human embryo lung fibroblasts].

OBJECTIVE: To study the role of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) in silica-induced DNA double-strand break repair in human embryo lung fibroblasts (HELF). METHODS: Two stable transfectants, HELF transfected with DNA-PKcs siRNA (HELF-PKcs) and with negative control siRNA (HELF-NC), were established. HELF cells were treated with 0, 25, 50, 100, 200, 300 and 400 microg/ml silica for 12 h and with 200 microg/ml silica for different times (0, 1, 2, 6, 12 and 24 h). HELF-PKcs and HELF-NC were treated with 200 microg/ml silica for 0, 12 and 24 h. The expression levels of DNA-PKcs and phosphor-H2AX (H2AX) were determined by Western blot. DNA double strand breaks were measured by neutral comet assay. RESULTS: After treatment with different doses of silica for 12 h, the levels of H2AX and the percentages of tail DNA increased in concentration-dependent manner. After treatment with 200 microg/ml silica for different times, the levels of H2AX increased in a time-dependent manner. The percentages of tail DNA increased significantly at 6 h, and reaching maximum at 12 h and then decreasing at 24 h. The expression level of DNA-PKcs was suppressed in HELF-PKcs. After treatment with silica at 12 h, the level of H2AX was lower in HELF-PKcs than in HELF-NC, and the percentages of tail DNA increased obviously in both HELF-PKcs and HELF-NC compared with non-treated cells, but no significant difference was found in the percentages of tail DNA between them. The percentages of tail DNA decreased markedly in silica-treated HELF-NC and was significantly lower than in HELF-PKcs at 24 h (P < 0.05). CONCLUSION: Silica can induce DNA double strand breaks in human embryo lung fibroblasts. DNA-PKcs might play a major role in silica-induced DNA double strand break repair. Silica-induced histone H2AX phosphorylation was dependent on DNA-PKcs.

[Effects of p53 in benzo (a) pyrene induced p21 and E2F-1 expression and cell cycle changes].

OBJECTIVE: To investigate the roles of p53 in cell cycle changes on human embryo lung fibroblasts (HELF) induced by benzo(a) pyrene[ B(a) P], and relationships between p53 and p21, E2F-1. METHODS: Cells transfected with p53 siRNA plasmid (p53-H) and CMV vector (HELF/CMV) were cultured with serum-free R/MINI-1640 for 48 hours, then treated with 2 micromol/L B(a)P for 24 hours. Flow cytometry assay was used for detecting the cell cycle alteration after being exposed to B(a)P. Changes of p53 and p21 expressions were checked using Western blot assay, and the cytoplasmic and nuclear extraction was used to observe the subcellular localizations of p53 and p21. The immunofluorescence assay was used to check changes of E2F-1 expression and the distribution of E2F-1 in nuclear and cytoplasm after exposed to B (a)P. p53siRNA plasmid and the chemical inhibitor of p53 [pifithrin-alpha (PFT)] were used to observe effects of p53 in B(a)P induced cell cycle changes and the relationships of p53 and p21, E2F-1. RESULTS: After 2 micromol/L B(a)P exposure, the ratio of G1 phase cells (71 +/- 5)% was decreased to (39 +/- 4)% (P < 0.05). p53, p21 and E2F-1 expressions were increased significantly, and over expressed proteins were mostly located in nuclear after B(a)P treatment. When p53 expression was inhibited by p53 siRNA or PFT, the decreases of G1 phase in response to B(a)P treatment still existed, and over expression of p21 induced by B(a)P was attenuated, especially in nuclear, but E2F-1 over expression was not changed significantly. CONCLUSION: B(a)P could induce cell cycle changes through p53 independent pathways. And p53 could regulate p21 expression positively, but not E2F-1.

[Activated protein 1-cyclin D1/E2F 1 pathways involved in cell cycle changes induced by benzo (a) pyrene].

OBJECTIVE: To investigate the roles of activated protein 1 (AP-1) in cell cycle changes on human embryo lung fibroblasts (HELF) induced by benzo (a) pyrene [B (a) P], and relationships between AP-1 and cyclin D1/CDK4-E2F-1/4. METHODS: Cells transfected with AP-1 luciferase reporter plasmid (AP-H) were cultured with serum-free RPMI1640 for 48 h, and treated with 2 micromol/L B (a) P for 24 h. AP-1 relative activity was detected by luciferase assay. Changes of cell cycle and the expression of cyclin D1, CDK4 and E2F-1/4 were checked using the flow cytometer and Western blot assay. RESULTS: After B (a) P was treated for 24 h, the ratio of G1 phase cells (71 +/- 2)% was decreased to (48 +/- 3)% (P < 0.05), and an increase was observed in the ratio of S phase. AP-1 activity and cyclin D1/E2F-1 expression were increased significantly, but CDK4/E2F-4 expression did not change after B (a) P treatment. When AP-1 activity was inhibited by curcumin, decreases of G1 phase in response to B (a) P treatment were blocked, and overexpression of cyclin D1/E2F-1 was attenuated, but CDK4/E2F-4 expression was not changed significantly. CONCLUSION: AP-1 is involved in B (a) P induced cell cycle changes, and is the upstream signals of cyclin D1/E2F-1, but not CDK4/E2F-4.

[ERK, JNK/AP-1 pathway was involved in silica-induced cell cycle changes].

OBJECTIVE: To investigate the alteration of activator protein-1 (AP-1) luciferase activity in human embryo lung fibroblasts (HELF) after exposed to silica, and the role of mitogen activated protein kinase (MAPK)/AP-1 pathway on silica-induced cell cycle changes. METHODS: After HELF cells were treated with 200 microg/ml silica, immunofluorescence assays were employed to detect the translocation and the phosphorylation level of extracellular signal-regulated protein kinase (ERK) and c-Jun N-terminal kinase (JNK), flow cytometry was used to detect the distributions of cell cycle, the dominant negative mutant of ERK, JNK and p38 were applied to detect the upstream or downstream relationship of signaling pathways. RESULTS: After HELF-AP-1 cells were exposed to 200 microg/ml silica 6, 12, 24 h respectively, silica exposure lead to AP-1 activation in a time-dependent manner, inducing significant AP-1 activation at 6 h, reaching a maximum activation at 12 h, and having a little decrease at 24 h. After silica exposure 1 h, phosphorylation level of ERK and JNK increased mainly in cytoplasm, however, after exposure 2 h, they translocated to nucleus. The proportion of cells in G1 phases was decreased from (63.80 +/- 9.57)% to (32.23 +/- 7.22)%, and the proportion of cells in S phases was increased from (35.17 +/- 10.33)% to (66.00 +/- 8.07)% after exposed to silica 24 h. Curcumin, a chemical inhibitor of AP-1, impaired the decrease of cells in G1 phases. Furthermore we found expression of dominant-negative mutant of ERK and JNK impaired silica-induced AP-1 activation, whereas, dominant-negative mutant of p38 did not show the effect. CONCLUSION: These result suggested that 200 microg/ml silica exposure can induce AP-1 activation, induce cell cycle changes through ERK, JNK/AP-1-dependent pathway.