RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations.

Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships. However, a snapshot of single-cell CRISPR data may not lead to an accurate inference, since a gene knockout can influence multi-layered downstream over time. Here, we developed RENGE, a computational method that infers gene regulatory networks using a time-series single-cell CRISPR dataset. RENGE models the propagation process of the effects elicited by a gene knockout on its regulatory network. It can distinguish between direct and indirect regulations, which allows for the inference of regulations by genes that are not knocked out. RENGE therefore outperforms current methods in the accuracy of inferring gene regulatory networks. When used on a dataset we derived from human-induced pluripotent stem cells, RENGE yielded a network consistent with multiple databases and literature. Accurate inference of gene regulatory networks by RENGE would enable the identification of key factors for various biological systems.

Functional analysis of protein disulfide isomerase P5 in glioblastoma cells as a novel anticancer target.

P5, which is a member of the protein disulfide isomerase family, possesses isomerase and chaperone activity in vitro; however, the physiological functions of this enzyme in cells remain unclear. To understand the important roles of P5 in cancer cells, the present study examined its expression on the surface of normal and cancer cell lines by flow cytometry using an affinity­purified anti­P5 antibody labeled with 6­(fluorescein­5­carboxamido) hexanoic acid succinimidyl ester. P5 expression was increased on the surface of various cancer cell lines, including leukemia cells, and glioblastoma, breast, colon, ovarian and uterine cervical cancer cells, compared with normal cells. However, P5 was constantly expressed within both normal and cancer cell lysates, and its total expression levels were not significantly different between the cells. P5 knockdown in glioblastoma cells by small interfering RNA affected Bip promoter activation during cancer cell growth, and significantly inhibited cancer cell growth and migration. Immunoprecipitation using an anti­P5 antibody in cancer and normal cells demonstrated that vimentin was bound to P5, predominantly in U251 glioblastoma cells. P5 knockdown in glioblastoma cells did not affect the protein expression levels of vimentin; however, it did affect the expression of numerous epithelial­mesenchymal transition markers, including Snail and Slug. These results suggested that P5 may serve an important role in cancer cell growth, and may be considered an attractive and potent target for the treatment of glioblastoma.

Development of des-gamma-carboxy prothrombin (DCP) measuring reagent using the LiBASys clinical analyzer.

BACKGROUND: Des-gamma-carboxy prothrombin (DCP), Lens culinaris agglutinin-reactive alpha-fetoprotein ratio (AFP-L3) and total alpha-fetoprotein (AFP) are tumor markers useful for diagnosing and determining the prognosis of hepatocellular carcinoma (HCC). There is a real need for measurement of these three markers on a one-assay platform. METHODS: A method of DCP measurement in human serum was developed using liquid binding assay (LBA), which enables rapid antigen-antibody reaction and bound/free separation on the LiBASys clinical analyzer. RESULTS: The dilution curve for DCP was linear up to 500 ng/mL. The limit of detection of DCP concentration was 0.5 ng/mL. Intra- and inter-assay coefficients of variation of DCP were 0.7%-2.4% and 2.2%-6.5%, respectively. This method was free from interference by hemoglobin, bilirubin, ditaurobilirubin, intrafat, ascorbate, galactose, glucose and rheumatoid factor. The analytical recoveries of DCP added to serum were 91.7%-108.2%. DCP concentration measured with the LBA method was linear and was significantly correlated with that measured with the ELISA method. CONCLUSIONS: The LiBASys clinical analyzer made possible measurement of the complementary tumor markers, HCC, total AFP, AFP-L3 and DCP.