Microarray Analysis of Long Non-coding RNA Expression Profile Associated with 5-Fluorouracil-Based Chemoradiation Resistance in Colorectal Cancer Cells

Xiong, Wei,Jiang, Yong-Xin,Ai, Yi-Qin,Liu, Shan,Wu, Xing-Rao,Cui, Jian-Guo,Qin, Ji-Yong,Liu, Yan,Xia, Yao-Xiong,Ju, Yun-He,He, Wen-Jie,Wang, Yong,Li, Yun-Fen,Hou, Yu,Wang, Li,Li, Wen-Hui Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.8

Background: Preoperative 5-fluorouracil (5-FU)-based chemoradiotherapy is a standard treatment for locally advanced colorectal cancer (CRC). However, CRC cells often develop chemoradiation resistance (CRR). Recent studies have shown that long non-coding RNA (lncRNA) plays critical roles in a myriad of biological processes and human diseases, as well as chemotherapy resistance. Since the roles of lncRNAs in 5-FU-based CRR in human CRC cells remain unknown, they were investigated in this study. Materials and Methods: A 5-FU-based concurrent CRR cell model was established using human CRC cell line HCT116. Microarray expression profiling of lncRNAs and mRNAs was undertaken in parental HCT116 and 5-FU-based CRR cell lines. Results: In total, 2,662 differentially expressed lncRNAs and 2,398 mRNAs were identified in 5-FU-based CRR HCT116 cells when compared with those in parental HCT116. Moreover, 6 lncRNAs and 6 mRNAs found to be differentially expressed were validated by quantitative real time PCR (qRT-PCR). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for the differentially expressed mRNAs indicated involvement of many, such as Jak-STAT, PI3K-Akt and NF-kappa B signaling pathways. To better understand the molecular basis of 5-FU-based CRR in CRC cells, correlated expression networks were constructed based on 8 intergenic lncRNAs and their nearby coding genes. Conclusions: Changes in lncRNA expression are involved in 5-FU-based CRR in CRC cells. These findings may provide novel insight for the prognosis and prediction of response to therapy in CRC patients.

Sleep Duration and Cancer Risk: a Systematic Review and Meta-analysis of Prospective Studies

Zhao, Hao,Yin, Jie-Yun,Yang, Wan-Shui,Qin, Qin,Li, Ting-Ting,Shi, Yun,Deng, Qin,Wei, Sheng,Liu, Li,Wang, Xin,Nie, Shao-Fa Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.12

To assess the risk of cancers associated with sleep duration using meta-analysis of published cohort studies, we performed a comprehensive search using PubMed, Embase and Web of Science through October 2013. We combined hazard ratios (HRs) from individual studies using meta-analysis approaches. A random effect dose-response analysis was used to evaluate the relationship between sleep duration and cancer risk. Subgroup analyses and sensitivity analyses were also performed. Publication bias was evaluated using Funnel plots and Begg's test. A total of 13 cohorts from 12 studies were included in this meta-analysis, which included 723, 337 participants with 15, 156 reported cancer outcomes during a follow-up period ranging from 7.5 to 22 years. The pooled adjusted HRs were 1.06 (95% CI: 0.92, 1.23; P for heterogeneity =0.003) for short sleep duration, 0.91 (95% CI: 0.78, 1.07; P for heterogeneity <0.0001) for long sleep duration. In subgroup analyses stratified by cancer type, long duration of sleep showed an inverse relation with hormone-related cancer (HR=0.79; 95% CI: 0.65, 0.97; P for heterogeneity =0.009) and a greater risk of colorectal cancer (HR=1.29; 95% CI: 1.09, 1.52; P for heterogeneity =0.346). Further meta-analysis on dose-response relationships showed that the relative risks of cancer were 1.00 (95% CI: 0.99, 1.01; P for linear trend=0.9151) for one hour of sleep increment per day, and 1.00 (95% CI: 0.98, 1.01; P for linear trend=0.7749) for one hour of sleep increment per night. No significant dose-response relationship between sleep duration and cancer was found on non-linearity testing (P=0.5053). Our meta-analysis suggests a positive association between long sleep duration and colorectal cancer, and an inverse association with incidence of hormone related cancers like those in the breast. Studies with larger sample size, longer follow-up times, more cancer types and detailed measure of sleep duration are warranted to confirm these results.

Effects of Defaunation on Fermentation Characteristics, Degradation of Ryegrass Hay and Methane Production by Rumen Microbes In Vitro When Incubated with Plant Oils

Qin, Wei-Ze,Li, Cheng-Yun,Choi, Seong-Ho,Jugder, Shinekhuu,Kim, Hyun-Ju,Lee, Sang-Suk,Song, Man-Kang The Korean Society of Grassland and Forage Science 2014 한국초지조사료학회지 Vol.34 No.3

This study was conducted to examine the effects of defaunation (removal of live protozoa) on fermentation characteristics, degradation of ryegrass hay and $CH_4$ (methane) production by rumen microbes when incubated with plant oils (SO, sunflower oil and LO, linseed oil) in vitro. Sodium lauryl sulfate (0.000375 g/ml) as a defaunation reagent was added into the culture solution and incubated anaerobically up to 24 h at $39^{\circ}C$. pH from defaunation was increased for all treatments from 6 h incubation times (p<0.01-0.001) compared with those from fauantion. Concentration of ammonia-N from defaunation is higher than that from faunation at 3 h (p<0.001), 12 h (p<0.05) and 24 h (p<0.001) incubation times. Defaunation decreased (p<0.01-0.001) total volatile fatty acid concentration at all incubation times. Molar proportions of $C_2$ (acetate, p<0.05-0.001) and butyrate (p<0.01-0.001) were also decreased by defaunation at all incubation times. Molar proportion of $C_3$ (propionate), however, was increased by defaunation at all incubation times (p<0.001). Thus the rate of $C_2$ to $C_3$ was decreased by defaunation at all incubation times (p<0.001). Defaunation decreased ED (effective degradability) of dry matter (p<0.001) and ED of neutral detergent fiber (p<0.001) of ryegrass hay. Defaunation decreased total gas, $CH_4$ production, $CH_4$ % in total gas and $CH_4/CO_2$ at all incubation times (p<0.001). Oil supplementation decreased total gas (p<0.05-0.001), $CH_4$ production (p<0.001) and $CH_4$ % in total gas (p<0.001) compared with control at all incubation times. The result of this study showed that defaunation combined with oil supplementation may cause an alteration of microbial communities and further medicate the fermentation pattern, resulting in both reduction of degradation of ryegrass hay and $CH_4$ production. No difference, however, was observed in all the examinations between SO and LO.

Mechanisms of Hela Cell Apoptosis Induced by Abnormal Savda Munziq Total Phenolics Combined with Chemotherapeutic Agents

Zhang, Yun-Xia,Abliz, Guzalnur,Ye, Wei-Jun,Mutalipu, Zuohelaguli,Li, Xiao-Wen,Wang, Hai-Qin,Buranjiang, Gulimire,Upur, Halmurat Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.2

Objective: To investigate the effects of abnormal Savda Munziq (ASMq) total phenolics combined with cisplatin and docetaxel on the Hela cell growth. Methods: In vivo cultured Hela cells were treated with cisplatin, docetaxel, total phenolics, cisplatin+total phenolics or docetaxel+total phenolics. MTT was performed to assess inhibition of cell proliferation, flow cytometry to detect apoptosis, and semi-quantitative RT-PCR to test for survivin and Bcl-2 expression. Results: The total phenolics, cisplatin and docetaxel had significant inhibitory and apoptosis-promoting effects on Hela cells (P<0.05), with the early apoptotic rates of $12.8{\pm}0.70%$, $18.9{\pm}3.79%$ and $15.8{\pm}3.8%$; the total phenolics, cisplatin and docetaxel significantly decreased the expression of Bcl-2 and survivin (all P<0.01), especially when used in combination. Conclusion: ASMq total phenolics, combined with cisplatin and docetaxel, could promote the apoptosis of Hela cells possibly through reducing the expression of Bcl-2 and survivin.

Impact of Co-transfection with Livin and Survivin shRNA Expression Vectors on Biological Behavior of HepG2 Cells

Xu, Wei,Chang, Hong,Qin, Cheng-Kun,Zhai, Yun-Peng Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.9

Objective: To construct short hairpin RNA (shRNA) eukaryotic expression vectors targeting Livin and Survivin genes, and to explore the impact of co-transfection of Livin and Survivin shRNA expression vectors on the biological behavior of HepG2 cells. Methods: shRNA eukaryotic expression vectors pSD11-Livin and pSD11-Survivin were designed and constructed then transfected into HepG2 cells separately or in combination. mRNA and protein expression in transfected cells was assessed by quantitative fluorescence PCR and Western blotting, respectively. Cell proliferation was measured by MTT assay and cell apoptosis by TUNEL assay. Results: The Livin and Survivin shRNA eukaryotic expression vectors were successfully constructed and transfected into HepG2 cells. The relative mRNA expression levels of Livin and Survivin in HepG2 cells co-transfected with pSD11-Livin and pSD11-Survivin were $0.12{\pm}0.02$ and $0.33{\pm}0.13$, respectively, which was significantly lower than levels in cells transfected with either pSD11-Livin or pSD11-Survivin (P<0.05). The relative protein expression levels of Livin and Survivin in the co-transfected cells were also significantly decreased compared to single-transfection (P<0.05). The inhibition rate of cell growth in the co-transfection group was higher than that in the single-transfection groups at 48 h, 60 h, or 72 h after transfection (P<0.01). The apoptotic rate increased to the greatest extent in the co-transfection group relative to any other group (P<0.05). Conclusions: Co-transfection with pSD11-Livin and pSD11-Survivin was more efficient than transfection with either vector alone in reducing the mRNA and protein expression of Livin and Survivin genes in HepG2 cells. Co-transfection also inhibited the proliferation of transfected cells more than the other groups, and induced cellular apoptosis more effectively.

Anti-proliferative Effects of Atractylis lancea (Thunb.) DC. via Down-regulation of the c-myc/hTERT/Telomerase Pathway in Hep-G2 Cells

Guo, Wei-Qiang,Li, Liang-Zhi,He, Zhuo-Yang,Zhang, Qi,Liu, Jia,Hu, Cui-Ying,Qin, Fen-Ju,Wang, Tao-Yun Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.11

Atractylis lancea (Thunb.) DC. (AL), an important medicinal herb in Asia, has been shown to have anti-tumor effects on cancer cells, but the involved mechanisms are poorly understood. This study focused on potential effects and molecular mechanisms of AL on the proliferation of the Hep-G2 liver cancer cell line in vitro. Cell viability was assessed by MTT test in Hep-G2 cells incubated with an ethanol extract of AL. Then, the effects of AL on apoptosis and cell cycle progression were determined by flow cytometry. Telomeric repeat amplification protocol (TRAP) assays was performed to investigate telomerase activity. The mRNA and protein expression of human telomerase reverse transcriptase (hTERT) and c-myc were determined by real-time RT-PCR and Western blotting. Our results show that AL effectively inhibits proliferation in Hep-G2 cells in a concentrationand time-dependent manner. When Hep-G2 cells were treated with AL after 48h,the $IC_{50}$ was about 72.1 ${\mu}g/mL$. Apoptosis was induced by AL via arresting the cells in the G1 phase. Furthermore, AL effectively reduced telomerase activity through inhibition of mRNA and protein expression of hTERT and c-myc. Hence, these data demonstrate that AL exerts anti-proliferative effects in Hep-G2 cells via down-regulation of the c-myc/hTERT/telomerase pathway.

Photoactivation and inactivation of <i>Arabidopsis</i> cryptochrome 2

Wang, Qin,Zuo, Zecheng,Wang, Xu,Gu, Lianfeng,Yoshizumi, Takeshi,Yang, Zhaohe,Yang, Liang,Liu, Qing,Liu, Wei,Han, Yun-Jeong,Kim, Jeong-Il,Liu, Bin,Wohlschlegel, James A.,Matsui, Minami,Oka, Yoshito,Lin American Association for the Advancement of Scienc 2016 Science Vol.354 No.6310

<P>Cryptochromes are blue-light receptors that regulate development and the circadian clock in plants and animals. We found that Arabidopsis cryptochrome 2 (CRY2) undergoes blue light-dependent homodimerization to become physiologically active. We identified BIC1 (blue-light inhibitor of cryptochromes 1) as an inhibitor of plant cryptochromes that binds to CRY2 to suppress the blue light-dependent dimerization, photobody formation, phosphorylation, degradation, and physiological activities of CRY2. We hypothesize that regulated dimerization governs homeostasis of the active cryptochromes in plants and other evolutionary lineages.</P>

Mechanical behavior of rock-coal-rock specimens with different coal thicknesses

Guo, Wei-Yao,Tan, Yun-Liang,Yu, Feng-Hai,Zhao, Tong-Bin,Hu, Shan-Chao,Huang, Dong-Mei,Qin, Zhe Techno-Press 2018 Geomechanics & engineering Vol.15 No.4

To explore the influence of coal thickness on the mechanical behavior and the failure characteristics of rock-coal-rock (RCR) mass, the experimental investigation of uniaxial compressive tests was conducted first and then a systematic numerical simulation by particle flow code (PFC2D) was performed to deeply analyze the failure mechanical behavior of RCR specimens with different coal thicknesses in conventional compression tests. The overall elastic modulus and peak stress of RCR specimens lie between the rock and the coal. Inter-particle properties were calibrated to match the physical sample strength and the stiffness response. Numerical simulation results show that the deformation and strength behaviors of RCR specimens depend not only on the coal thickness, but also on the confining pressure. Under low confining pressures, the overall failure mechanism of RCR specimen is the serious damage of coal section when the coal thickness is smaller than 30 mm, but it is shear failure of coal section when the coal thickness is larger than 30 mm. Whereas under high confining pressures, obvious shear bands exist in both the coal section and the rock section when the coal thickness is larger than 30 mm, but when the coal thickness is smaller than 30mm, the failure mechanism is serious damage of coal section and shear failure of rock section.

Genome-wide analysis of codon usage bias patterns in an enterotoxigenic Escherichia coli F18 strain

Ri Wei Xia,Wen Bin Bao,Xue Mei Yin,Wei Yun Qin,Guo Qiang Zhu,Sheng Long Wu 한국유전학회 2017 Genes & Genomics Vol.39 No.11

Enterogenic Escherichia coli (ETEC) F18 strains are the main pathogenic bacteria causing severe diarrhea in humans and domestic animals. However, the information about synonymous codon usage pattern of ETEC F18 genome remains unclear. We conducted a genome-wide analysis of synonymous codon usage patterns in the ETEC F18 strain SRA: SAMN02471895. After filtering of the complete genome sequence, 4327 coding sequences were analyzed using multivariate statistical methods to calculate synonymous codon usage patterns and to evaluate the influence of various factors in shaping the codon usage. The mean GC content was 51.38%, with a slight preference for G/C-ending codons. Twenty-two codons were determined as ‘‘optimal codons”. ENC plots showed some of the genes were on or close to the expected curve, while only points with low-ENC values were below the curve. PR2 analysis showed that GC and AT were not used proportionally, suggesting major roles for mutational pressure and natural selection in shaping usage. Neutrality plots showed a significant correlation between GC12 and GC3, suggesting that mutational pressure is responsible for nucleotide composition in shaping the strength of codon usage. Translational selection was the main factor shaping the codon usage pattern of ETEC F18 genome, while other factors such as protein length, GRAVY and ARO values also influenced codon usage to some extent. We analyzed the codon usage pattern systematically and identified the factors shaping codon usage bias in the ETEC F18 genome. Such information further elucidates the mechanisms of synonymous codon usage bias and provides the basis of molecular genetic engineering and evolutionary studies.

SSR and SCAR mapping of a multiple-allele male-sterile gene in Chinese cabbage (Brassica rapa L.)

Feng, Hui,Wei, Peng,Piao, Zhong-Yun,Liu, Zhi-Yong,Li, Cheng-Yu,Wang, Yu-Gang,Ji, Rui-Qin,Ji, Shu-Juan,Zou, Ting,Choi, Su-Ryun,Lim, Yong-Pyo Springer-Verlag 2009 TAG. Theoretical and applied genetics. Theoretisch Vol.119 No.2