Identification of key genes of papillary thyroid cancer using integrated bioinformatics analysis

OBJECTIVE

To identify novel clinically relevant genes in papillary thyroid carcinoma from public databases.

METHODS

Four original microarray datasets, GSE3678, GSE3467, GSE33630 and GSE58545, were downloaded. Differentially expressed genes (DEGs) were filtered from integrated data. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed, followed by protein-protein interaction (PPI) network construction. The CentiScape pug-in was performed to scale degree. The genes at the top of the degree distribution (≥ 95% percentile) in the significantly perturbed networks were defined as central genes. UALCAN and The Cancer Genome Atlas Clinical Explorer were used to verify clinically relevant genes and perform survival analysis.

RESULT

225 commonly changed DEGs (111 up-regulated and 114 down-regulated) were identified. The DEGs were classified into three groups by GO terms. KEGG pathway enrichment analysis showed DEGs mainly enriched in the PI3K-Akt signaling pathway, pathways in cancer, focal adhesion and proteoglycans in cancer. DEGs' protein-protein interaction (PPI) network complex was developed; six central genes (BCL2, CCND1, FN1, IRS1, COL1A1, CXCL12) were identified. Among them, BCL2, CCND1 and COL1A1 were identified as clinically relevant genes.

CONCLUSION

BCL2, CCND1 and COL1A1 may be key genes for papillary thyroid carcinoma. Further molecular biological experiments are required to confirm the function of the identified genes.

Genetic association of the ACACB gene with milk yield and composition traits in dairy cattle

Previously, we re-sequenced the whole genomes of eight Holstein bulls with high or low milk protein and fat percentage, and we detected two indels in the ACACB (acetyl-CoA carboxylase beta) gene that were polymorphic between the two groups. Thus, we considered ACACB as a promising candidate gene potentially affecting milk composition traits. Herein, we verified the genetic effects of ACACB on five milk traits in a Chinese Holstein population. We identified six SNPs in the 5'-promoter region, five in the 5'- untranslated region (UTR), 11 in exons, four in the 3'-UTR and three in the 3'-flanking region by re-sequencing the entire coding and regulatory regions of ACACB. One of these SNPs (ss1987461005) is reported here for the first time, and three of the SNPs (rs109482081, rs110819816 and rs109281947) were predicted to result in amino acid replacements. Genotype-phenotype association analyses showed that all the identified SNPs, except for ss1987461005, rs208919019 and rs134447911, were significantly associated with milk yield, fat yield, fat percentage, protein yield or protein percentage (P < 0.0001 to 0.0484). Linkage disequilibrium analyses were conducted among the identified SNPs to confirm the genetic associations. Two SNPs-rs135874354 (g.66218726T>C) and rs210928430 (g.66218117G>A)-were predicted to alter transcription factor binding sites in the 5'-promoter region of ACACB. A luciferase activity assay showed that the promoter activity of haplotype TG was significantly higher than that of CG (P = 0.0002) and that the promoter activity of haplotype TA was remarkably higher than that of CA (P = 7.4285E-09), showing that the T allele of rs135874354 increased promoter activity. Thus, rs135874354 was considered to be a potentially functional mutation. Our findings have, for the first time, profiled the genetic effect of ACACB on milk production traits in dairy cattle and revealed a potentially causal mutation that requires further the in-depth validation.

[Experimental study on the immune response of fusion tumor vaccine of HepG2 and dendritic cells in vitro]

Objective: To estimate the immune response of HepG2/dendritic cell (DC) fusion cells vaccines against HepG2 cells in vitro. Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donors by Ficoll-Hypaque density-gradient centrifugation.Then DC were obtain from PBMCs by culturing in medium containing granulocyte macrophage colony-stimulating factor (GM-CSF) and interleukin-4 (IL-4) for 5 days.DC and HepG2 fusion cells were induced by polythyleneglycol (PEG). The fusion cells were examined under fluorescence microscope by labeling DCs and HepG2 with green and red fluorescein, respectively, and then the fusion rates were analyzed by flow cytometry.The capacity of fusion cells to secrete interleukin (IL)-12 and stimulate the proliferation of T lymphocyte was assessed by ELISA and Flow cytometry, respectively.ELISPOT was used to assess the interferon gamma (IFN-γ) produced by cytotoxicity T lymphocyte (CTL), and the specific killing ability of fusion cells induce-CTL targeting HepG2 was estimated. Results: The fusion rate of HepG2/DC was 54.5%, and the fusion cells expressed a higher levels of DC mature marker CD80 and costimulatory molecules CD83, CD86 and MHC-Ⅰ, MHC-Ⅱ molecules HLA-ABC and HLA-DR than those in immature DCs (P<0.01). HepG2/DC showed a greater capacity to secrete high level of IL-12 (P<0.05) and activate proliferation of lymphocytes in vitro, as compared with DCs alone and DCs mix HepG2 (P<0.01). The HepG2/DC -activated CTL generated higher IFN-γ level and had a specific killing ability against HepG2 cells at the effecter/target ratio 30∶1 (31.4%±2.4%) and 100∶1 (57.6%±7.3%) (P<0.01). Conclusions: HepG2/DC fusion cells could efficiently stimulate T lymphocytes to generate specific CTL targeting HepG2 cells.It might be a promising strategy of immunotherapy for HCC.

Distance travelled to purchase alcohol and the mediating effect of price

OBJECTIVES

Little research has been done into the distance travelled by consumers to purchase alcohol, whether this is influenced by demographic characteristics or drinking levels of consumers, and the effect of price on purchase distance. This study aimed to explore distances drinkers were prepared to travel to purchase alcohol at on- and off-site outlets and how these decisions were affected by price discounting.

STUDY DESIGN

Online survey.

METHODS

The study, including 831 alcohol consumers aged 18 years and older living in Australian capital cities, was undertaken in 2012. The survey was used to gather data on the distances which participants anticipated that they usually travelled to purchase alcohol. The data provided insight into which factors influence where participants would choose to purchase alcohol and the possible effects of price discounts on purchase distance.

RESULTS

Most participants would choose to travel less than 10 km to purchase alcohol. Data indicated that price discounting might increase the purchase distance that most participants would be prepared to travel to purchase alcohol; this was more marked regarding off-site outlets and among high-risk drinking groups including young males and participants with risky drinking levels.

CONCLUSIONS

Price discounting affects hypothetical purchase distance choices, indicating the importance of price when implementing alcohol control policies. Purchase distance might be more affected by price discounting among consumers visiting off-site outlets, but less useful when exploring associations with on-site outlets.

Molecular and pathological evaluation of cryopreserved colorectal cancerous tissues: Effects of freezing method and cryoprotection

BACKGROUND

Snap freezing and RNAlater stabilization are methods that were wildly used in biospecimen depositories to preserve cancer tissues. Both methods have its own limitations. An ideal method for preservation of diseased tissues should permit the broader uses of stored tissue samples, including not just for molecular diagnostic analysis, histopathological evaluation, but also for the recovery of functional live cells and tissues as well as the regeneration of patient-derived xenograft (PDX) models for the drug screening study.

MATERIALS AND METHODS

This study investigated molecular and pathological evaluation of cryopreserved colorectal cancer tissues, with an emphasis on effects of freezing method and cryoprotection. Global gene expression analysis with microarrays and histological examination of tissue samples were performed to compare tissue specimens after snap freezing, cryoprotectant permeation and subsequent cryopreservation.

RESULTS

Compared with the fresh tissue samples (immediately stabilized in RNAlater after collection), samples preserved by snap freezing exhibited the largest number of differentially-expressed genes. Some genes relate to neuron, drug addiction and drug binding, but the rest of differentially-expressed genes were functionally dispersive. Cryoprotectant permeation into tissue samples and subsequent cryopreservation via a rate-controlled freezing resulted in much less differentially expressed genes. Histological structures of tissue specimens were both well preserved by snap freezing and cryoproservation.

CONCLUSION

Snap freezing may not be as reliable as commonly considered. The pilot study demonstrates the feasibility of using cryopreservation to retain viable diseased tissues for multiple applications.

Multi-functional thermo-crosslinkable collagen-metal nanoparticle composites for tissue regeneration: nanosilver vs. nanogold

Collagen–silver/gold biomimetic matrices were developed for cardiac tissue engineering.