Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress respo

Xiao‑Xiao Gong,Bing‑Yu Yan,Jin Hu,Cui‑Ping Yang,Yi‑Jian Li,Jin‑Ping Liu,Wen‑Bin Liao 한국유전학회 2018 Genes & Genomics Vol.40 No.11

Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at 4 °C for 2 h) and LT24 (cold treatment at 4 °C for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. Quantitative real time PCR (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. A total of 1457 and 2328 differentially expressed genes (DEGs) in LT2 and LT24 compared with CT were respectively detected. Most significantly enriched KEGG pathways included flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, phenylalanine metabolism and starch and sucrose metabolism. A total of 239 transcription factors (TFs) were differentially expressed following 2 h or/and 24 h of cold treatment. Cold-response transcription factor families included ARR-B, B3, BES1, bHLH, C2H, CO-like, Dof, ERF, FAR1, G2-like, GRAS, GRF, HD-ZIP, HSF, LBD, MIKC-MADS, M-type MADS, MYB, MYB-related, NAC, RAV, SRS, TALE, TCP, Trihelix, WOX, WRKY, YABBY and ZF-HD. The genome-wide transcriptional response of rubber tree to the cold treatments were determined and a large number of DEGs were characterized including 239 transcription factors, providing important clues for further elucidation of the mechanisms of cold stress responses in rubber tree.

The USP21/YY1/SNHG16 axis contributes to tumor proliferation, migration, and invasion of non-small-cell lung cancer

Pei Xu,Haibo Xiao,Qi Yang,Rui Hu,Lianyong Jiang,Rui Bi,Xueyan Jiang,Lei Wang,Ju Mei,Fangbao Ding,Jianbing Huang 생화학분자생물학회 2020 Experimental and molecular medicine Vol.52 No.-

Deubiquitinases (DUBs) and noncoding RNAs have been the subjects of recent extensive studies regarding their roles in lung cancer, but the mechanisms involved are largely unknown. In our study, we used The Cancer Genome Atlas data set and bioinformatics analyses and identified USP21, a DUB, as a potential contributor to oncogenesis in nonsmall-cell lung cancer (NSCLC). We further demonstrated that USP21 was highly expressed in NSCLCs. We then conducted a series of in vitro and in vivo assays to explore the effect of USP21 on NSCLC progression and the underlying mechanism involved. USP21 promoted NSCLC cell proliferation, migration, and invasion and in vivo tumor growth by stabilizing a well-known oncogene, Yin Yang-1 (YY1), via mediating its deubiquitination. Furthermore, YY1 transcriptionally regulates the expression of SNHG16. Moreover, StarBase bioinformatics analyses predicted that miR4500 targets SNHG16 and USP21. A series of in vitro experiments indicated that SNHG16 increased the expression of USP21 through miR-4500. In summary, the USP21/YY1/SNHG16 axis plays a role in promoting the progression of NSCLC. Therefore, the USP21/YY1/SNHG16/miR-4500 axis may be a potential therapeutic target in NSCLC treatment.

Relationship Between the SER Treatment Period and Prognosis of Patients with Small Cell Lung Cancer

Xiao, Xiao-Guang,Wang, Shu-Jing,Hu, Li-Ya,Chu, Qian,Wei, Yao,Li, Yang,Mei, Qi,Chen, Yuan Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.15

Purpose: To explore the relationship between SER (time between the start of any treatment and the end of radiation therapy) and the survival of patients with limited-stage small cell lung cancer. Materials and Methods: Between 2008 and 2013, 135 cases of limited-stage small cell lung cancer (LS-SCLC) treated with consecutively curative chemoradiotherapy were included in this retrospective analysis. In terms of SER, patients were divided into early radiotherapy group (SER<30 days, n=76) and late radiotherapy group ($SER{\geq}30$ days, n=59) with a cut-off of SER 30 days. Outcomes of the two groups were compared for overall survival. Results: For all analyzable patients, median follow-up time was 23.8 months and median overall survival time was 16.8 months. Although there was no significant differences in distant metastasis free survival between the two groups, patients in early radiotherapy group had a significantly better PFS (p=0.003) and OS (p=0.000). Conclusions: A short SER may be a good prognostic factor for LD-SCLC patients treated with concurrent chemoradiotherapy.

Use of antibiotics and other treatments in Chinese adults with acute cough: An online survey

Xiao-yang Hu,Ru-yu Xia,Michael Moore,Beth Stuart,Wen Ling-Zi,Bertrand Graz,Lai Lily,Liu Jian-Ping,Yu-tong Fei,Merlin Willcox 한국한의학연구원 2023 Integrative Medicine Research Vol.12 No.1

Background: Acute respiratory tract infections are common worldwide and there has been a rapid in- crease in antibiotic consumption. This study aimed to identify use of various treatments and their as- sociation with the use of antibiotics and patient reported clinical recovery in Chinese adults with acute cough. Methods: An online survey recruiting people who had recently experienced cough was conducted. Their sociodemographic, clinical characteristics, treatments received and their perceived changes in symptoms were collected. Factors influencing avoidance of antibiotics and improvement in symptoms were explored. Results: A total of 22,787 adults with recent acute cough completed the questionnaire, covering all 34 province-level administrative units in China. Most respondents were male (68.0%), young (89.4%, aged 18–45), educated to university/degree or postgraduate level (44.6%), with a median cough severity of 6/10 on a numerical rating scale. Nearly half of the participants (46.4%) reported using antibiotics, among which 93.1% were for presumed upper respiratory tract infections (URTIs). Pharmacies (48.8%) were the most common source of antibiotics. Fewer patients took antibiotics after taking CHM (14.9%), compared to those who started with home remedies (18.0%), or allopathic non-antibiotic medication (25.0%). An- tibiotics, allopathic non-antibiotic medications, CHM and home remedies were all perceived beneficial in relieving cough. Conclusions: Chinese adult responders report use of a considerable variety of treatments alone or in combination for acute cough. Patient-reported clinical recovery was similar regardless of treatment. There is likely a high proportion of inappropriate use of antibiotics for treatment of simple acute cough. As the majority of respondents did not use antibiotics as a first-line, and use of CHM was associated with relief of cough symptoms and reduction in the use of antibiotics, this presents an important opportunity for prudent antibiotic stewardship in China.

Effect of Trichostatin A on CNE2 Nasopharyngeal Carcinoma Cells - Genome-wide DNA Methylation Alteration

Yang, Xiao-Li,Zhang, Cheng-Dong,Wu, Hua-Yu,Wu, Yong-Hu,Zhang, Yue-Ning,Qin, Meng-Bin,Wu, Hua,Liu, Xiao-Chun,Lina, Xing,Lu, Shao-Ming Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.11

Trichostatin A (TSA) is a histone deacetylase (HDAC) inhibitor. We here investigated its effects on proliferation and apoptosis of the CNE2 carcinoma cell line, and attempted to establish genome-wide DNA methylation alteration due to differentially histone acetylation status. After cells were treated by TSA, the inhibitory rate of cell proliferation was examined with a CCK8 kit, and cell apoptosis was determined by flow cytometry. Compared to control, TSA inhibited CNE2 cell growth and induced apoptosis. Furthermore, TSA was found to induce genome-wide methylation alteration as assessed by genome-wide methylation array. Overall DNA methylation level of cells treated with TSA was higher than in controls. Function and pathway analysis revealed that many genes with methylation alteration were involved in key biological roles, such as apoptosis and cell proliferation. Three genes (DAP3, HSPB1 and CLDN) were independently confirmed by quantitative real-time PCR. Finally, we conclude that TSA inhibits CNE2 cell growth and induces apoptosis in vitro involving genome-wide DNA methylation alteration, so that it has promising application prospects in treatment of NPC in vivo. Although many unreported hypermethylated/hypomethylated genes should be further analyzed and validated, the pointers to new biomarkers and therapeutic strategies in the treatment of NPC should be stressed.

IGF-1 from Adipose-Derived Mesenchymal Stem Cells Promotes Radioresistance of Breast Cancer Cells

Yang, Hui-Ying,Qu, Rong-Mei,Lin, Xiao-Shan,Liu, Tong-Xin,Sun, Quan-Quan,Yang, Chun,Li, Xiao-Hong,Lu, Wei,Hu, Xiao-Fang,Dai, Jing-Xing,Yuan, Lin Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.23

Purpose: The aim of this study was to investigate effects of adipose-derived mesenchymal stem cells (AMSCs) on radioresistance of breast cancer cells. Materials and Methods: MTT assays were used to detect any influence of AMSC supernatants on proliferation of breast cancer cells; cell migration assays were used to determine the effect of breast cancer cells on the recruitment of AMSCs; the cell survival fraction post-irradiation was assessed by clonogenic survival assay; ${\gamma}$-H2AX foci number post-irradiation was determined via fluorescence microscopy; and expression of IGF-1R was detected by Western blotting. Results: AMSC supernatants promoted proliferation and radioresistance of breast cancer cells. Breast cancer cells could recruit AMSCs, especially after irradiation. IGF-1 derived from AMSCs might be responsible for the radioresistance of breast cancer cells. Conclusions: Our results suggest that AMSCs in the tumor microenvironment may affect the outcome of radiotherapy for breast cancer in vitro.

Experimental Investigations of Natural Convection in Wire-Woven Bulk Kagome

Yang, Xiao Hu,Bai, Jia Xi,Kang, Ki-Ju,Lu, Tian Jian,Kim, Tongbeum Springer-Verlag 2014 Transport in porous media Vol.105 No.1

Calpain-10 SNP43 and SNP19 Polymorphisms and Colorectal Cancer: a Matched Case-control Study

Hu, Xiao-Qin,Yuan, Ping,Luan, Rong-Sheng,Li, Xiao-Ling,Liu, Wen-Hui,Feng, Fei,Yan, Jin,Yang, Yan-Fang Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.11

Objective: Insulin resistance (IR) is an established risk factor for colorectal cancer (CRC). Given that CRC and IR physiologically overlap and the calpain-10 gene (CAPN10) is a candidate for IR, we explored the association between CAPN10 and CRC risk. Methods: Blood samples of 400 case-control pairs were genotyped, and the lifestyle and dietary habits of these pairs were recorded and collected. Unconditional logistic regression (LR) was used to assess the effects of CAPN10 SNP43 and SNP19, and environmental factors. Both generalized multifactor dimensionality reduction (GMDR) and the classification and regression tree (CART) were used to test gene-environment interactions for CRC risk. Results: The GA+AA genotype of SNP43 and the Del/Ins+Ins/Ins genotype of SNP19 were marginally related to CRC risk (GA+AA: OR = 1.35, 95% CI = 0.92-1.99; Del/Ins+Ins/Ins: OR = 1.31, 95% CI = 0.84-2.04). Notably, a high-order interaction was consistently identified by GMDR and CART analyses. In GMDR, the four-factor interaction model of SNP43, SNP19, red meat consumption, and smoked meat consumption was the best model, with a maximum cross-validation consistency of 10/10 and testing balance accuracy of 0.61 (P < 0.01). In LR, subjects with high red and smoked meat consumption and two risk genotypes had a 6.17-fold CRC risk (95% CI = 2.44-15.6) relative to that of subjects with low red and smoked meat consumption and null risk genotypes. In CART, individuals with high smoked and red meat consumption, SNP19 Del/Ins+Ins/Ins, and SNP43 GA+AA had higher CRC risk (OR = 4.56, 95%CI = 1.94-10.75) than those with low smoked and red meat consumption. Conclusions: Though the single loci of CAPN10 SNP43 and SNP19 are not enough to significantly increase the CRC susceptibility, the combination of SNP43, SNP19, red meat consumption, and smoked meat consumption is associated with elevated risk.

Expression profiles of circular RNAs in sheep skeletal muscle

Cao, Yang,You, Shuang,Yao, Yang,Liu, Zhi-Jin,Hazi, Wureli,Li, Cun-Yuan,Zhang, Xiang-Yu,Hou, Xiao-Xu,Wei, Jun-Chang,Li, Xiao-Yue,Wang, Da-Wei,Chen, Chuang-Fu,Zhang, Yun-Feng,Ni, Wei,Hu, Sheng-Wei Asian Australasian Association of Animal Productio 2018 Animal Bioscience Vol.31 No.10

Objective: Circular RNAs (circRNAs) are a newfound class of non-coding RNA in animals and plants. Recent studies have revealed that circRNAs play important roles in cell proliferation, differentiation, autophagy and apoptosis during development. However, there are few reports about muscle development-related circRNAs in livestock. Methods: RNA sequencing analysis was employed to identify and annotate circRNAs from longissimus dorsi of sheep. Reverse transcription followed by real-time quantitative (q) polymerase chain reaction (PCR) analysis verified the presence of these circRNAs. Targetscan7.0 and miRanda were used to analyse the interaction of circRNA-microRNA (miRNA). To investigate the function of circRNAs, an experiment was conducted to perform enrichment analysis hosting genes of circRNAs using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathways. Results: About 75.5 million sequences were obtained from RNA libraries of sheep skeletal muscle. These sequences were mapped to 729 genes in the sheep reference genome. We identified 886 circRNAs, including numerous circular intronic RNAs and exonic circRNAs. Reverse transcription PCR (RT-PCR) and DNA sequencing analysis confirmed the presence of several circRNAs. Real-Time RT-PCR analysis exhibited resistance of sheep circRNAs to RNase R digestion. We found that many circRNAs interacted with muscle-specific miRNAs involved in growth and development of muscle, especially circ776. The GO and KEGG enrichment analysis showed that hosting genes of circRNAs was involved in muscle cell development and signaling pathway. Conclusion: The study provides comprehensive expression profiles of circRNAs in sheep skeletal muscle. Our study offers a large number of circRNAs to facilitate a better understanding of their roles in muscle growth. Meanwhile, we suggested that circ776 could be analyzed in future study.

Lack of Association of Three Common Polymorphisms in Toll-like receptors (TLRs), TLR2+597T>C, +1350C>T and Arg753Gln with Cancer Risk: a Meta-analysis

Yang, Xin,Wang, Xiao-Xiao,Qiu, Man-Tang,Hu, Jing-Wen,Yin, Rong,Xu, Lin,Zhang, Qin Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.10

Background: Single nucleotide polymorphisms (SNPs) occurring in Toll-like receptors (TLRs) may contribute to cancer risk. Many polymorphisms of TLR2 have been studied for associations, but the findings are conflicting. Methodology/Principal Findings: We performed a meta-analysis of 14 studies to confirm the association between TLR2+597T>C (rs3804099), +1350C>T (rs3804100) and Arg753Gln (rs5743708) polymorphisms and cancer risk. Odds ratio (OR) and 95% confidence intervals (95% CI) were used to assess the strength of associations. There was no significant association between TLR2+597T>C and cancer risk in the codominant models (CC vs. TT: OR = 1.01, 95%CI = 0.86-1.17, $P_{heterogeneity}=0.148$; CT vs. TT: OR = 0.92, 95%CI = 0.69-1.23, $P_{heterogeneity}$ < 0.001), the recessive model (CC vs. CT+TT: OR = 0.86, 95%CI = 0.67-1.10, $P_{heterogeneity}=0.007$), the dominant model (CC+CT vs. TT: OR = 0.93, 95%CI = 0.76-1.15, $P_{heterogeneity}=0.001$) and the allele model (C vs. T: OR =0.93, 95%CI = 0.81-1.08, $P_{heterogeneity}=0.019$). Similarly, no significant associations between TLR2+1350C>T, Arg753Gln polymorphisms and cancer risk were found. However, in the sub-group analysis of ethnicities, the trend of pooled ORs in Asians was opposite to Caucasians. Conclusions: The present meta-analysis suggests that TLR2+597T>C (rs3804099), +1350C>T (rs3804100) and Arg753Gln (rs5743708) polymorphisms are not associated with cancer risk.