Gene expression profiling analysis of keloids with and without hydrocortisone treatment.

The present study aimed to investigate the genetic effects of hydrocortisone (HC) treatment on keloids and screen medicines to be used in a combination therapy of keloids with HC. The dataset GSE7890 was downloaded from Gene Expression Omnibus. It contained data regarding 4 fibroblast samples from normal scar tissue and 5 samples from keloid tissue with HC treatment, as well as 5 samples from normal scar and 5 samples from keloids without HC treatment. Following the identification of differentially expressed genes (DEGs), the functions of these DEGs were analyzed by Gene Ontology (GO) and pathway enrichment analyses. Furthermore, adverse effects of HC were identified using WebGestalt. Additionally, candidate small molecule drugs associated with keloids were selected from a connectivity map database. A total of 166 and 41 DEGs, with and without HC treatment respectively, were only present in dermal fibroblasts from keloids (termed genesets A and B, respectively). A set of 26 DEGs was present following both treatments (geneset C). A number of DEGs in geneset B (COL18A1 and JAG1) were associated with endothelial cell differentiation. However, in genesets A and C, certain genes (CCNB1 and CCNB2) were involved in the cell cycle and p53 signaling pathways, and a number of genes (IL1R1 and COL1A1) were associated with bone loss. Additionally, numerous small molecule drugs (including acemetacin) were associated with keloids. Thus, it has been determined that HC may treat keloids by targeting genes associated to endothelial cell differentiation (COL18A1 and JAG1). However, HC has a number of adverse effects, including bone loss. Acemetacin may be applied in a combination therapy, along with HC, to treat keloids.

Screening for genes, transcription factors and miRNAs associated with the myogenic and osteogenic differentiation of human adipose tissue-derived stem cells.

In the present study, we aimed to reveal the molecular mechanisms responsible for the differentiation of human adipose tissue-derived stem cells (hASCs) into myocytes and osteoblasts. Microarray data GSE37329 were obtained from the Gene Expression Omnibus database, including three hASC cell lines from healthy donors, two osteogenic lineages and two myogenic lineages from the in vitro­induction of hASCs. Differentially expressed genes (DEGs) in the two lineages were firstly screened. Subsequently, the underlying functions of the two sets of DEGs were investigated by Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, followed by protein-protein interaction (PPI) network construction. Regulatory relationships between transcription factors (TFs) and microRNAs (miRNAs or miRs) with target genes were finally explored using different algorithms. A total of 665 and 485 DEGs were identified from the hASC­derived myogenic and osteogenic lineages, respectively. The shared upregulated genes (n=205) in the two sets of DEGs were mainly involved in metabolism-related pathways, whereas the shared downregulated genes (n=128) were significantly enriched in the transforming growth factor-ß (TGF-ß) signaling pathway. Four genes, vascular endothelial growth factor A (VEGFA), fibroblast growth factor 2 (FGF2), nerve growth factor (NGF) and interleukin 1B (IL1B), presented with relatively higher degrees in both PPI networks. The transcription factor RAD21 was predicted to target shared upregulated and downregulated genes as well as specific downregulated genes in the myogenic and the osteogenic lineages. In addition, miRNA-DEG interaction analysis revealed that hsa-miR-1 regulated the most shared DEGs in the two lineages. There may be a correlation between the four genes, VEGFA, FGF2, IL1B and NGF, and the differentiation of hASCs into myocytes and osteoblasts. The TF RAD21 and hsa-miR-1 may play important roles in regulating the expression of differentiation-associated genes.

Vacuum Sealing Drainage Treatment Combined with Antibiotic-Impregnated Bone Cement for Treatment of Soft Tissue Defects and Infection.

BACKGROUND This study aimed to evaluate the combined effect of vacuum sealing drainage (VSD) and antibiotic-loaded bone cement on soft tissue defects and infection. MATERIAL AND METHODS This prospective non-blinded study recruited 46 patients with soft tissue defects and infection from January 2010 to May 2014 and randomly divided them into experimental and control groups (n=23). Patients in the experimental group were treated with VSD and antibiotic-loaded bone cement, while the patients in the control group were treated with VSD only. RESULTS In the experimental group, the wound was healed in 23 cases at 4 weeks postoperatively, of which direct suture was performed in 12 cases, and additional free flap transplantation or skin grafting was performed in 6 cases and 5 cases, respectively. No infection reoccurred in 1-year follow-up. In the control group, the wound was healed in 15 cases at 6 weeks postoperatively, of which direct suture was performed in 8 cases, and additional free flap transplantation or skin grafting was performed in 3 cases and 4 cases, respectively. In the other 8 cases the wound was healed at 8 weeks postoperatively. Infection reoccurred in 3 cases during the follow-up. The experimental group had significantly fewer VSD dressing renewals, shorter time needed until the wound was ready for surgery, shorter duration of antibiotic administration, faster wound healing, and shorter hospital stay than the control group (p<0.01). CONCLUSIONS The combination of VSD and antibiotic bone cement might be a better method for treatment of soft tissue defects and infection.

Gene expression profiling analysis contributes to understanding the association between non-syndromic cleft lip and palate, and cancer.

The present study aimed to investigate the molecular mechanisms underlying non­syndromic cleft lip, with or without cleft palate (NSCL/P), and the association between this disease and cancer. The GSE42589 data set was downloaded from the Gene Expression Omnibus database, and contained seven dental pulp stem cell samples from children with NSCL/P in the exfoliation period, and six controls. Differentially expressed genes (DEGs) were screened using the RankProd method, and their potential functions were revealed by pathway enrichment analysis and construction of a pathway interaction network. Subsequently, cancer genes were obtained from six cancer databases, and the cancer­associated protein­protein interaction network for the DEGs was visualized using Cytoscape. In total, 452 upregulated and 1,288 downregulated DEGs were screened. The upregulated DEGs were significantly enriched in the arachidonic acid metabolism pathway, including PTGDS, CYP4F2 and PLA2G16; and transforming growth factor (TGF)­ß signaling pathway, including SMAD3 and TGFB2. The downregulated DEGs were distinctly involved in the pathways of DNA replication, including MCM2 and POLA1; cell cycle, including CDK1 and STAG1; and viral carcinogenesis, including PIK3CA and HIST1H2BF. Furthermore, the pathways of cell cycle and viral carcinogenesis, with higher degrees of interaction were found to interact with other pathways, including DNA replication, transcriptional misregulation in cancer, and the TGF­ß signaling pathway. Additionally, TP53, CDK1, SMAD3, PIK3R1 and CASP3, with higher degrees, interacted with the cancer genes. In conclusion, the DEGs for NSCL/P were implicated predominantly in the TGF­ß signaling pathway, the cell cycle and in viral carcinogenesis. The TP53, CDK1, SMAD3, PIK3R1 and CASP3 genes were found to be associated, not only with NSCL/P, but also with cancer. These results may contribute to a better understanding of the molecular mechanisms of NSCL/P.

Identification of the interaction network of hub genes for melanoma treated with vemurafenib based on microarray data.

AIMS AND BACKGROUND: The objective of this study was to identify possible biomarkers and to explore the mechanisms of suppression of vemurafenib on melanoma progression. METHODS: GSE42872 affymetrix microarray data were downloaded from the Gene Expression Omnibus database for further analysis. Differentially expressed genes (DEGs) between vehicle-treated samples and vemurafenib-treated samples were identified. Gene ontology and pathway enrichment analysis of DEGs were performed, followed by protein-protein interaction (PPI) network construction. Furthermore, the functional modules of the PPI network were screened using BioNet analysis tool. Finally, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed for DEGs in the module. RESULTS: In total, 794 upregulated transcripts corresponding to 214 genes and 977 downregulated transcripts corresponding to 325 genes were screened. The downregulated DEGs were significantly enriched in pathways such as cell cycle, DNA replication, and p53 signaling pathway. Upregulated DEGs were significantly enriched in phosphatidylinositol signaling system and inositol phosphate metabolism. Significantly enriched functions of downregulated DEGs were mitotic cell cycle, nuclear division, DNA metabolic process, cell cycle, and mitosis. Upregulated DEGs were mainly enriched in single multicellular organism process and multicellular organismal process. Moreover, cell division cycle 6, checkpoint kinase 1 (CHEK1), E2F transcription factor 1 (E2F1), epidermal growth factor receptor (EGFR), and phosphoinositide-3-kinase, regulatory subunit 1-α (PIK3R1) of the module were remarkably enriched in pathways such as cell cycle, apoptosis, focal adhesion, and DNA replication. CONCLUSIONS: Cell division cycle 6, CHEK1, E2F1, EGFR, and PIK3R1 of the module and their relative pathways, cell cycle, and focal adhesion might play important roles of suppression of vemurafenib on melanoma progression.

Identification of Target Genes Regulated by KSHV miRNAs in KSHV-Infected Lymphoma Cells.

This study aimed to identify target genes regulated by KSHV miRNAs in KSHV-infected lymphoma cells. Original Ago HITS-CLIP data of BC-3 and BCBL-1 cell lines were downloaded from SRA database in NCBI, including mRNA and miRNA samples. The raw mRNA reads were mapped into human reference genome hg19 via TopHat for read alignment. PCR duplicates were removed via the SAM tool and the peaks of reads were analyzed via Cufflinks. For miRNA data, the raw data were mapped to the mature miRNA sequences based on miRBase via Bowtie. Peak intersection was computed by using intersectBed in BEDtools. Then, the mature miRNA seeds were identified and then were aligned with 3' UTR merged peaks. The regulationships of miRNAs and their corresponding genes were analyzed based on the signal of RNA-induced silencing complex. Totally, 7 KSHV-related genes regulated by KSHV miRNAs were identified, including IPO5, EDA, NT5C3, WSB1, KCNS1, PRAM1 and MTRNR2L6. Among them, EDA, MTRNR2L6 and IPO5 were regulated by multiple KSHV miRNAs, such as kshv-miR-K12-1-5p, kshv-miR-K12-4-3p and kshv-miR-K12-3-5p, respectively. Furthermore, expression of kshv-miR-K12-1-5p and kshv-miR-K12-3-5p in BCBL-1 cell line were lower than that in BC-3 cell line, conversely, expression of kshv-miR-K12-4-3p in BCBL-1 cell line were higher than that in BC-3 cell line. In conclusion, potential target genes regulated by KSHV miRNAs in KSHV-infected lymphoma cells might play key roles in the nosogenesis of this disease. These findings might provide the basis for deep understanding of KSHV-infected tumors and further molecular experiments.

Toxic shock syndrome toxin-1 (TSST-1) antibody levels in Japanese children.

Children with burns have a greater risk of developing toxic shock syndrome (TSS) than adults. This risk is thought to be associated with colonisation by toxic shock syndrome toxin-1 (TSST-1)-producing Staphylococcus aureus in children with insufficient antibody titers. The diagnosis of TSS is difficult because, in the early stages, its signs and symptoms resemble those of other common childhood illnesses such as scarlet fever. If the condition is not treated promptly, the mortality rate is high. This study was designed to determine the titers of TSST-1 serum antibody in Japanese children, in order to prevent TSS and facilitate its early diagnosis. Between May 2006 and May 2007, we studied 119 patients who were treated in the Department of Plastic and Reconstructive Surgery of Kanazawa Medical University Hospital. An enzyme-linked immunosorbent assay (ELISA) was used to test the level of the IgG antibody to TSST-1 in the patients' serum samples. The percentage of cases testing for TSST-1 antibody in the patients under 6 months old was 78.6%, and it was lowest (21.3%) in the age group from 6 to 12 months old. The group of patients older than 41 years showed the highest rate of positivity (100.0%) for TSST-1 antibody. Higher titers of TSST-1 antibody were found within the first 6 months after birth, and lower titers were found between 6 months and 2 years old. The titers began to increase again after age three. The high morbidity of TSS in children around 2 years of age was proven to be related to changes in the titers of TSST-1 antibody. Infants under 6 months old are protected from TSS because of the high level of TSST-1 antibody they receive from their mother. Children are at risk of developing staphylococcal toxic shock syndrome when their immune system is immature and they have no protective circulating anti-TSS antibodies.