Jun-Woo Kim

Network signatures of cellular immortalization in human lymphoblastoid cell lines

Human lymphoblastoid cell line (LCL) has been used as an in vitro cell model in genetic and pharmacogenomic studies, as well as a good model for studying gene expression regulatory machinery using integrated genomic analyses. In this study, we aimed to identify biological networks of LCL immortalization from transcriptomic profiles of microRNAs and their target genes in LCLs. We first selected differentially expressed genes (DEGs) and microRNAs (DEmiRs) between early passage LCLs (eLCLs) and terminally differentiated late passage LCLs (tLCLs). The in silico and correlation analysis of these DEGs and DEmiRs revealed that 1098 DEG-DEmiR pairs were found to be positively (n=591 pairs) or negatively (n=507 pairs) correlated with each other. More than 41% of DEGs are possibly regulated by miRNAs in LCL immortalizations. The target DEGs of DEmiRs were enriched for cellular functions associated with apoptosis, immune response, cell death, JAK-STAT cascade and lymphocyte activation while non-miRNA target DEGs were over-represented for basic cell metabolisms. The target DEGs correlated negatively with miR-548a-3p and miR-219-5p were significantly associated with protein kinase cascade, and the lymphocyte proliferation and apoptosis, respectively. In addition, the miR-106a and miR-424 clusters located in the X chromosome were enriched in DEmiR-mRNA pairs for LCL immortalization. In this study, the integrated transcriptomic analysis of LCLs could identify functional networks of biologically active microRNAs and their target genes involved in LCL immortalization.

Bacterial Contamination of Blood DNA Samples is Associated with Donor's Health Condition

Bacterial contamination often occurs in human blood DNA samples, possibly due to bacteremia or an inappropriate procedure during sample preparation. This study aimed at analyzing the clinical significance of bacterial DNA contamination in human blood DNA samples and to assess its influence on experimental data. DNA samples (N = 1359) were randomly selected from population-based cohort samples to determine bacterial DNA contamination by polymerase chain reaction and direct DNA sequencing. Bacterial DNA contaminated samples (N = 150) were then assessed for experimental quality of single nucleotide polymorphism (SNP) chip data, compared with uncontaminated DNA samples (N = 1209). DNA sequencing data showed that a major source of bacterial contaminants was derived from Alcaligenes species. The occurrence of bacterial DNA contaminations was significantly associated with some clinical variables including a postprandial glucose level at 60 min, % body fat, and waist-to-hip ratio. It was also found that there was no difference of SNP call rates between bacterial DNA contaminated samples and uncontaminated DNA samples. This study showed that bacterial DNA contamination in human blood samples was related to donors health condition, suggesting that the occurrence of bacterial DNA contamination may provide useful health information of blood donors and a potential tool for human disease genomics.

Optimized Internal Control and Gene Expression Analysis in Epstein-Barr Virus-Transformed Lymphoblastoid Cell Lines

The Epstein-Barr virus-transformed lymphoblastoid cell line (LCL) is one of the major genomic resources for human genetics and immunological studies. Use of LCLs is currently extended to pharmacogenetic studies to investigate variations in human gene expression as well as drug responses between individuals. We evaluated four common internal controls for gene expression analysis of selected hematopoietic transcriptional regulatory genes between B cells and LCLs. In this study, the expression pattern analyses showed that TBP (TATA box-binding protein) is a suitable internal control for normalization, whereas GAPDH (glyceraldehyde-3-phosphate dehydrogenase) is not a good internal control for gene expression analyses of hematopoiesis-related genes between B cells and LCLs at different subculture passages. Using the TBP normalizer, we found significant gene expression changes in selected hematopoietic transcriptional regulatory genes (downregulation of RUNX1, RUNX3, CBFB, TLE1, and NOTCH2 ; upregulation of MSC and PLAGL2) between B cells and LCLs at different passage numbers. These results suggest that these hematopoietic transcriptional regulatory genes are potential cellular targets of EBV infection, contributing to EBV-mediated B-cell transformation and LCL immortalization.

ManBIF: a Program for Mining and Managing Biobank Impact Factor Data

Abstract Biobank Impact Factor (BIF), which is a very effective criterion to evaluate the activity of biobanks, can be es-timated by the citation information of biobanks from sci-entific papers. We have developed a program, ManBIF, to investigate the citation information from PDF files in the literature. The program manages a dictionary for ex-pressions to represent biobanks and their resources, mines the citation information by converting PDF files to text files and searching with a dictionary, and produces a statistical report file. It can be used as an important tool by biobanks. Availability: ManBIF and its manual are available at http://cgs.cdc.go.kr/manbifKeywords: biobank, Biobank Impact Factor Data Introduction Biobanks, as repository organizations, are getting more and more important, not only nationwide but also worldwide. As their roles and functions are being ex-panded to effectively maintain and distribute biological resources, international cooperation and competition is getting very active. BIF (Biobank Impact Factor), a comparative index of citation information of biobanks in scientific papers, is used as a major criterion of biobank activity (Zika, 2010). As a biobank can be represented with several names, including abbreviations and a full name, a dedicated program is required to search for multiple biobanks against multiple literature files. We have developed ManBIF, a program, to search for Biobank citation information from PDF files in the liter-ature to produce a summary report.