A major issue in the use of immune checkpoint inhibitors is their lack of efficacy in many patients. Previous studies have reported that the T cell inflamed signature can help predict the response to immunotherapy. Thus, many studies have investigated mechanisms of immunotherapy resistance by defining the tumor microenvironment based on T cell inflamed and non–T cell inflamed subsets. Although methods of calculating T cell inflamed subsets have been developed, valid screening tools for distinguishing T cell inflamed from non–T cell inflamed subsets using gene expression data are still needed, since general researchers who are unfamiliar with the details of the equations can experience difficulties using extant scoring formulas to conduct analyses. Thus, we introduce TcellInflamedDetector, an R package for distinguishing T cell inflamed from non–T cell inflamed samples using cancer gene expression data via bulk RNA sequencing.

The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in twoand- a-half dimensions (2.5D) as an alternative to three dimensional (3D) visualizations. Such visualization allows user to display different groups of clustered nodes, in different parallel planes, and to see a detailed view of a group of objects in focus and its place in the context of the whole system. This tool is an extended version of J2dPathway.
Hypogonadism ; Metabolic Networks and Pathways ; Mitochondrial Diseases ; Ophthalmoplegia

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
Computational Biology ; Databases, Protein ; Indonesia ; Proteins ; Software

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
Computational Biology ; Databases, Protein ; Indonesia ; Proteins ; Software

OBJECTIVE: The purpose of this study was to evaluate the validity and reliability of Korean version of Addiction Severity Index for the systematic diagnosis and evaluation of alcoholism. METHODS: The authors selected 65 alcoholic patients with the criteria of DSM-VI. RESULTS: The results were as follows: 1) The exception of the significant correlation between psychiatric and the family/social problem area, the 6 sections of ASI were mutually independent. 2) There was significant inter-rater reliability in all sections of ASI. 3) In medical, alcohol use, family/social and psychiatry section, the calculation of composite score showed reasonable level of item consistency. In all sections, there was significant correlation between composite scores and severity ratings of corresponding section. 4) The important items of each section were most highly correlated with their corresponding severity ratings except two sections. 5) In the multiple regression analysis, the amount of variance accounted far by the most important 4 items were 83% in medical section, 45% in employment/support,43% in alcohol use section, 55% in legal section,53% in family/social section and 84% in psychiatric section. 6) Severity rating of psychiatric section was significantly correlated with the scores of MMFI, MAST and SCL-90-R. CONCLUSION: The result suggests that Korean version of the ASI showed relatively reasonable reliability and validity and it can be used in treatment and study of alcoholic patients.
Alcoholics* ; Alcoholism ; Diagnosis ; Humans ; Reproducibility of Results*

PURPOSE: Ovarian cancer (OC) is the most fatal of gynecological malignancies with a high rate of recurrence. We aimed to evaluate the expression of solute carrier family 6, member 12 (SLC6A12) and methylation of its promoter CpG sites in a xenograft mouse model of metastatic OC, and to investigate the regulatory mechanisms that promote aggressive properties during OC progression. MATERIALS AND METHODS: Expression of SLC6A12 mRNA was determined by reverse-transcription quantitative polymerase chain reaction (RT-qPCR), and DNA methylation status of its promoter CpGs was detected by quantitative methylation-specific PCR. The metastatic potential of SLC6A12 was evaluated by in vitro migration/invasion transwell assays. Gene expression and DNA methylation of SLC6A12 and clinical outcomes were further investigated from publicly available databases from curatedOvarianData and The Cancer Genome Atlas. RESULTS: SLC6A12 expression was 8.1–14.0-fold upregulated and its DNA methylation of promoter CpG sites was 41–62% decreased in tumor metastases. After treatment with DNA methyltransferase inhibitor and/or histone deacetylase inhibitor, the expression of SLC6A12 was profoundly enhanced (~8.0-fold), strongly supporting DNA methylation-dependent epigenetic regulation of SLC6A12. Overexpression of SLC6A12 led to increased migration and invasion of ovarian carcinoma cells in vitro, approximately 2.0-fold and 3.3-fold, respectively. The meta-analysis showed that high expression of SLC6A12 was significantly associated with poor overall survival [hazard ratio (HR)=1.07, p value=0.016] and that low DNA methylation levels of SLC6A12 at specific promoter CpG site negatively affected patient survival. CONCLUSION: Our findings provide novel evidence for the biological and clinical significance of SLC6A12 as a metastasis-promoting gene.
Animals ; Carrier Proteins/genetics/*metabolism ; Cell Line, Tumor ; Cell Migration Assays ; *CpG Islands ; *DNA Methylation ; Disease Progression ; Epigenesis, Genetic ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Mice ; Neoplasm Invasiveness ; Neoplasm Transplantation ; Ovarian Neoplasms/genetics/*metabolism/mortality/pathology ; Polymerase Chain Reaction ; Prognosis ; *Promoter Regions, Genetic ; RNA, Messenger/*metabolism ; Up-Regulation

PURPOSE: Lymphatic invasion (LI) is regarded as a predictor of the aggressiveness of ovarian cancer (OC). However, LI is not always the major determinant of long-term patient survival. To establish proper diagnosis and treatment for OC, we analyzed differentially expressed genes (DEGs) for patients with serous epithelial OC, with or without LI, who did or did not survive for 5 years. MATERIALS AND METHODS: Gene expression data from 63 patients with OC and LI, and 35 patients with OC but without LI, were investigated using an Affymetrix Human Genome U133 Array and analyzed using The Cancer Genome Atlas (TCGA) database. Among these 98 patients, 16 survived for 5 years or more. DEGs were identified using the Bioconductor R package, and their functions were analyzed using the DAVID web tool. RESULTS: We found 55 significant DEGs (p<0.01) from the patients with LI and 20 highly significant DEGs (p<0.001) from those without it. Pathway analysis showed that DEGs associated with carbohydrate metabolism or with renal cell carcinoma pathways were enriched in the patients with and without LI, respectively. Using the top five prognostic marker genes, we generated survival scores that could be used to predict the 5-year survival of patients with OC without LI. CONCLUSION: The DEGs identified in this study could be used to elucidate the mechanism of tumor progression and to guide the prognosis and treatment of patients with serous OC but without LI.
Cystadenocarcinoma, Serous/*genetics/*mortality/pathology ; Databases, Genetic ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Microarray Analysis ; Middle Aged ; Ovarian Neoplasms/*genetics/*mortality/pathology ; Prognosis ; Regression Analysis ; Retrospective Studies ; Survival Rate

Metastasis is a major cause of therapeutic failure in ovarian cancer. To elucidate molecular mechanisms of ovarian cancer metastasis, we previously established a metastatic xenograft mouse model using human ovarian carcinoma SK-OV-3 cells. Using gene expression profiling, we found that γ-aminobutyric acid (GABA)A receptor π subunit (GABRP) expression was upregulated (>4-fold) in metastatic tissues from our xenograft mice compared with SK-OV-3 cells. Importantly, GABRP knockdown diminished the migration and invasion of SK-OV-3 cells, and reduced extracellular signal-regulated kinase (ERK) activation while overexpression of GABRP exhibited significantly increased cell migration, invasion and ERK activation. Moreover, treatment with the mitogen-activated protein kinase (MAPK)/ERK kinase (MEK) inhibitor U0126 similarly suppressed the migration and invasion of SK-OV-3 cells, implying that GABRP promotes these cellular behaviors by activating the MAPK/ERK pathway. Using genome-wide DNA methylation profiling, we identified hypomethylated CpG sites in the GABRP promoter in metastatic tissues from the xenograft mice compared with SK-OV-3 cells. Treatment with a DNA methyltransferase inhibitor demonstrated that methylation at −963 bp from the GABRP transcription start site (−963 CpG site) was critical for the epigenetic regulation of GABRP. Finally, we analyzed human ovarian cancer patient samples and showed DNA hypomethylation at the GABRP −963 CpG site in advanced stage, but not early-stage, primary tumors compared with their paired normal tissues. These findings suggest that GABRP enhances the aggressive phenotype of ovarian cancer cells, and that the DNA methylation status of the GABRP −963 CpG site may be useful for predicting the metastatic potential in ovarian cancer patients.
Animals ; Cell Movement ; DNA ; DNA Methylation ; Epigenomics* ; Gene Expression Profiling ; Heterografts ; Humans ; Methylation ; Mice ; Neoplasm Metastasis ; Ovarian Neoplasms* ; Phenotype* ; Phosphotransferases ; Protein Kinases ; Transcription Initiation Site

The explosion in biological data resulting from highthroughput experiments requires new software tools to manipulate and display pathways in a way that can integrate disparate sources of information. A visual Java-based CAD tool for drawing and annotating biological pathways with semiautomatic image-processing features is described in this paper. The result of the image-editing process is an XML file for the appropriate links. This tool integrates the pathway images and XML file sources. The system has facilities for linking graphical objects to external databases and is capable of reproducing existing visual representations of pathway maps.
Computational Biology ; Computer-Aided Design ; Explosions ; Software ; Systems Biology

An extracellular matrix protein plays an important role in skin wound healing. In the present study, we engineered a recombinant protein encompassing the 9th and 10th type III domains of fibronectin, and 4th FAS1 domain of beta ig-h3. This recombinant protein, in total, harbors four known-cell adhesion motifs for integrins: Pro-His-Ser-Arg-Asn (PHSRN) and Arg-Gly-Asp (RGD) in 9th and 10th type III domains of fibronectin, respectively, and Glu-Pro-Asp-Ile-Met (EPDIM) and Try-His (YH) in 4th FAS1 domain of big-h3, were designated to tetra-cell adhesion motifs (T-CAM). In vitro studies showed T-CAM supporting adhesion, migration and proliferation of different cell types including keratinocytes and fibroblasts. In an animal model of full-thickness skin wound, T-CAM exhibited excellent wound healing effects, superior to both 4th FAS1 domain of beta ig-h3 or 9th and 10th type III domains of fibronectin. Based on these results, T-CAM can be applied where enhancement of cell adhesion, migration and proliferation are desired, and it could be developed into novel wound healing drug.
Amino Acid Motifs ; Animals ; Cell Adhesion/*drug effects ; Cell Line ; Cell Movement/*drug effects ; Cell Proliferation/*drug effects ; Extracellular Matrix Proteins/chemistry/genetics/pharmacology ; Fibroblasts/cytology/drug effects/physiology ; Fibronectins/chemistry/genetics/*pharmacology ; Humans ; Keratinocytes/cytology/drug effects/physiology ; Mice ; NIH 3T3 Cells ; Rabbits ; Recombinant Fusion Proteins/chemistry/genetics/pharmacology ; Transforming Growth Factor beta/chemistry/genetics/pharmacology ; Wound Healing/*drug effects/physiology