THP-1 reference data: Proposal of an in vitro branched evolution model for cancer cell lines.

THP-1 is a representative leukemia cell line and is registered with four different numbers in JCRB and RIKEN BRC cell banks. However, differences between these four lines remain unclear. In our study, these four THP-1 cell lines, JCRB0112, JCRB0112.1 (corresponding to ATCC TIB-202), RCB1189 (DSMZ ACC-16) and RCB3686, have been compared at chromosome and DNA sequence levels. Our results reveal that ploidy has been changed in JCRB0112 and RCB1189, which are triploid and tetraploid, respectively. Patterns of variant frequencies from target sequencing are unique to each ploidy, estimating whole genomic status based on partial sequence data. SNP microarrays showed four distinct profiles with a large-scale loss of heterozygosity, reflected in subtle differences in STR genotypes. Transcriptome patterns suggest that JCRB0112.1 has diverged highly from the other three lines. RCB1189 and JCRB0112.1 responded to PMA faster than RCB3686 and JCRB0112. We have identified RCB3686 as the closest to the original THP-1, which can be an optimal model of AML-M5. These four THP-1 genomes and transcriptomes exhibit significant differences, indicating four independent sublines and demonstrating the influence of genetic drift on gene expression. As these cells share the same name, THP-1 must be accompanied by their registration number of each cell repository. Our data provide genomic features of four THP-1 sublines and serve as a reference profile to classify widely spread THP-1 progenies, which could be distinguished by a comparison of 24 STR markers. Multiple sublines can be generated by separate cell cultures, which would be explained by in vitro branched evolution.

Changes of heterogeneous cell populations in the Ishikawa cell line during long-term culture: Proposal for an in vitro clonal evolution model of tumor cells.

Genomic changes in tumor cell lines can occur during culture, leading to differences between cell lines carrying the same name. In this study, genome profiles between low and high passages were investigated in the Ishikawa 3-H-12 cell line (JCRB1505). Cells contained between 43 and 46 chromosomes and the modal number changed from 46 to 45 during culture. Cytogenetic analysis revealed that a translocation t(9;14), observed in all metaphases, is a robust marker for this cell line. Single-nucleotide polymorphism microarrays showed a heterogeneous copy number in the early passages and distinct profiles at late passages. These results demonstrate that cell culture can lead to elimination of ancestral clones by sequential selection, resulting in extensive replacement with a novel clone. Our observations on Ishikawa cells in vitro are different from the in vivo heterogeneity in which ancestral clones are often retained during tumor evolution and suggest a model for in vitro clonal evolution.

Heme oxygenase-1 promoter polymorphism is associated with risk of malignant mesothelioma.

BACKGROUND: Malignant mesothelioma is an aggressive tumor of serosal surfaces that is closely associated with asbestos exposure which induces oxidative stress. Heme oxygenase (HO)-1, a rate-limiting enzyme of heme degradation, plays a protective role against oxidative stress. The HO-1 gene promoter carries (GT)n repeats whose number is inversely related to transcriptional activity of the HO-1 gene. METHODS: To investigate the relationship between the length polymorphism of (GT)n repeats and mesothelioma susceptibility, we analyzed the HO-1 promoter in 44 asbestos-exposed subjects without mesothelioma and 78 asbestos-exposed subjects with mesothelioma using PCR-based genotyping. RESULTS: The number of repeats ranged from 16 to 38, with two peaks at 23 and 30 repeats. Polymorphisms of (GT)n repeats were grouped into two classes of alleles, short (S) (<24) and long (L) (≥24), and three genotypes: L/L, L/S, and S/S. The proportions of allele frequencies in class L as well as genotypic frequencies of L allele carriers (L/L and L/S) were significantly higher in the asbestos-exposed subjects with mesothelioma than in those without mesothelioma. CONCLUSION: The findings of this study suggest that long (GT)n repeats in the HO-1 gene promoter are associated with a higher risk of malignant mesothelioma in the Japanese population.

TK6 genome profile compared with WIL2-NS: Reference data to improve the reproducibility of genotoxicity studies.

The TK6 cell line has been widely used for genotoxicity screening by taking advantage of the TK1 mutations. A number of publications have employed TK6 as a tool for the assay; however, its characterization is limited. Because genomes of cell lines are often changed during cell culture, differences in TK6 genomes could be observed between laboratories, which would cause potential problems with reproducibility using TK6. In this study, TK6(IVGT) (JCRB1435), registered with the JCRB Cell Bank as the standard for TK6, has been characterized by karyotyping, SNP microarray and targeted sequencing, and were then compared to WIL2-NS (JCRB9063), a subline derived from a common ancestor with TK6. Changes at the chromosome level were quantitatively assessed by the microarray data, which were shown by DNA sizes and Scales of Genomic Alterations (SGA). An extinct common ancestral cell line, WI-L2 originated from hereditary spherocytosis, has been extrapolated from analysis of genomic signatures shared between TK6 and WIL2-NS, revealing a point mutation in SPTA1, related to the disease. DNA size is calculated to be 102.6 %, 103.1 % and 103.9 % for WI-L2, TK6(IVGT) and WIL2-NS respectively, with the reference values of a normal diploid genome, and each genome shows SGA of 2.8 %, 4.5 % and 4.2 % respectively. Differences between TK6(IVGT) and WIL2-NS are due to regions and sizes of gains, implying that genomes of both cells tend to increase their DNA size independently. Our data provide fundamental genomic features of TK6 and serve as a reference profile of the standardized TK6 cell line, which leads to an increase in robustness of assays using the TK6 cells.

HuH-7 reference genome profile: complex karyotype composed of massive loss of heterozygosity.

Human cell lines represent a valuable resource as in vitro experimental models. A hepatoma cell line, HuH-7 (JCRB0403), has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. However, an accurate genome profile, which can be served as a reliable reference, has not been available. In this study, we performed M-FISH, SNP microarray and amplicon sequencing to characterize the cell line. Single cell analysis of metaphases revealed a high level of heterogeneity with a mode of 60 chromosomes. Cytogenetic results demonstrated chromosome abnormalities involving every chromosome in addition to a massive loss of heterozygosity, which accounts for 55.3% of the genome, consistent with the homozygous variants seen in the sequence analysis. We provide empirical data that the HuH-7 cell line is composed of highly heterogeneous cell populations, suggesting that besides cell line authentication, the quality of cell lines needs to be taken into consideration in the future use of tumor cell lines.

The human vascular endothelial cell line HUV-EC-C harbors the integrated HHV-6B genome which remains stable in long term culture.

Human herpes virus 6 (HHV-6) is a common human pathogen that is most often detected in hematopoietic cells. Although human cells harboring chromosomally integrated HHV-6 can be generated in vitro, the availability of such cell lines originating from in vivo tissues is limited. In this study, chromosomally integrated HHV-6B has been identified in a human vascular endothelial cell line, HUV-EC-C (IFO50271), derived from normal umbilical cord tissue. Sequence analysis revealed that the viral genome was similar to the HHV-6B HST strain. FISH analysis using a HHV-6 DNA probe showed one signal in each cell, detected at the distal end of the long arm of chromosome 9. This was consistent with a digital PCR assay, validating one copy of the viral DNA. Because exposure of HUV-EC-C to chemicals did not cause viral reactivation, long term cell culture of HUV-EC-C was carried out to assess the stability of viral integration. The growth rate was altered depending on passage numbers, and morphology also changed during culture. SNP microarray profiles showed some differences between low and high passages, implying that the HUV-EC-C genome had changed during culture. However, no detectable change was observed in chromosome 9, where HHV-6B integration and the viral copy number remained unchanged. Our results suggest that integrated HHV-6B is stable in HUV-EC-C despite genome instability.

Screening for 15 pathogenic viruses in human cell lines registered at the JCRB Cell Bank: characterization of in vitro human cells by viral infection.

Human cell lines have been used in a variety of research fields as an in vitro model. These cells are all derived from human tissue samples, thus there is a possibility of virus infection. Virus tests are routinely performed in clinical practice, but are limited in cell lines. In this study, we investigated 15 kinds of viruses in 844 human cell lines registered at the Japanese Collection of Research Bioresources (JCRB) Cell Bank. Our real-time PCR analysis revealed that six viruses, EBV, HTLV-1, HBV, B19V, HHV-6 and HHV-7, were detected in 43 cell lines. Of them, 20 cell lines were transformed by intentional infection in vitro with EBV or HTLV-1. Viruses in the other 23 cell lines and one EBV transformed cell line are derived from an in vivo infection, including five de novo identifications of EBV, B19V or HHV-7 carriers. Among them, 17 cell lines were established from patients diagnosed with virus-associated diseases. However, the other seven cell lines originated from in vivo cells unrelated to disease or cellular tropism. Our approach to screen for a set of 15 viruses in each cell line has worked efficiently to identify these rare cases. Virus tests in cell lines contribute not only to safety assessments but also to investigation of in vivo viral infection which can be a characteristic feature of cell lines.

Antitumor effects of synthetic VEGF-receptor binding antagonist, VGA1155.

Vascular endothelial growth factor (VEGF) plays key roles in tumor angiogenesis. Therefore, VEGF and its receptors are considered to be primary targets for antiangiogenic strategy during cancer chemotherapy. Our previous study reported that VGA1155, a low-molecular-weight inhibitor of the binding of VEGF, inhibited VEGF binding to KDR/Flk-1 receptor-overexpressing cells. In the present study, the antitumor effects and antimetastatic effect of VGA1155 were examined in vivo. VGA1155 suppressed the growth of human lung, breast, colon and epidermoid cancers (LC-6, HT29, MX-1, Col-1 and A431) in the nude mouse xenograft model, and pulmonary metastasis of melanoma in the spontaneous metastasis model. These results suggest that VGA1155 has antitumor effects in vivo through the inhibition of VEGF binding to its receptors.

A novel low molecular weight antagonist of vascular endothelial growth factor receptor binding: VGA1155.

Vascular endothelial growth factor (VEGF) plays a pivotal role in the processes of angiogenesis, which is essential for the growth of solid tumors and their metastasis. Because VEGF is a critical factor in tumor survival, inhibiting VEGF would provide significant benefits in tumor therapy. To identify a compound that inhibits the binding of VEGF to its receptor, we used a high throughput screening method, finding that small molecular compounds inhibited VEGF binding. Among active compounds, 5-[N-methyl-N-(4-octadecyloxyphenyl)acetyl]amino-2-methylthiobenzoic acid (VGA1155) was selected for its potent inhibition of binding. VGA1155 inhibited [(125)I] VEGF binding to two cell lines, NIH3T3-fms-like tyrosine kinase-1 (VEGF receptor 1 transfected) cells and NIH3T3-kinase insert domain containing receptor/fetal liver kinase-1 (KDR/Flk-1; VEGF receptor 2 transfected), in a concentration-dependent manner. VGA1155 did not inhibit the binding of several other growth factors or cytokines to their receptors. Based on the results of surface plasmon resonance analysis using Biacore S51 system, it appears that this binding inhibitory property may be based on the association of VGA1155 with VEGF receptor 2 (KDR/Flk-1). Further, the interference in VEGF binding by VGA1155 in turn induces the inhibition of VEGF-induced KDR/Flk-1 autophosphorylation. VGA1155 also reduced intradermal VEGF-induced vascular permeability in guinea pigs. These findings indicate that VGA1155 inhibits not only VEGF binding to its receptors through association with KDR/Flk-1 but also VEGF function in vivo. These VGA1155 activities may provide a useful basis for the development of antiangiogenic and antitumor agents.

A novel low molecular weight VEGF receptor-binding antagonist, VGA1102, inhibits the function of VEGF and in vivo tumor growth.

Vascular endothelial cell growth factor (VEGF) plays an important role in the processes of angiogenesis. Angiogenesis appears to be essential for the growth of solid tumors and their metastasis. VEGF plays a principal role in tumor angiogenesis. To identify a compound that inhibits the binding of VEGF to its receptor, we used a high-throughput screening method and found that oxydibenzoic acid derivatives inhibited VEGF binding to its receptors. Among the active compounds, 5-[3-[4-(octadecyloxy)phenyl]propionylamino]-2,4'-oxydibenzoic acid (VGA1102) was selected based on its potent binding inhibitory activity. VGA1102 inhibited [(125)I]VEGF binding to both of two VEGF receptor-transfected cell lines, NIH-Flt-1 and NIH-KDR/Flk-1, in a concentration-dependent manner, with IC(50) values of 0.66+/-0.07 and 0.61+/-0.16 micro M, respectively. VGA1102 (10 micro M) exhibited inhibitory activity against VEGF-induced receptor autophosphorylation. VGA1102 also inhibited VEGF-induced growth of rat liver sinusoidal endothelial cells (IC(50)=0.89+/-0.16 micro M) as well as VEGF-induced tube formation of HUVEC in vitro. VGA1102 reduced intradermal VEGF-induced vascular permeability in guinea pigs. Treatment with VGA1102 (50 mg/kg, i.p., days 0-20) significantly increased the lifespan of MM2-bearing mice with an increase in lifespan of >195.8%, and all such mice were long-term survivors on day 71. Furthermore, VGA1102 (50 mg/kg, i.p.) administered daily suppressed the growth of nude mice transplanted with LC-6 human non-small-cell lung cancer. These results suggest that VGA1102 inhibits VEGF function resulting in inhibition of tumor angiogenesis, which led to suppression of growth of human tumors transplanted into nude mice.

VGA1155, a novel binding antagonist of VEGF, inhibits angiogenesis in vitro and in vivo.

The process of angiogenesis involves the formation of new blood vessels from established vasculature and is essential for progressive tumor growth and metastasis. Since vascular endothelial growth factor (VEGF) plays a pivotal role in tumor angiogenesis, it is reasonable to expect that antagonizing VEGF binding to its receptor may be effective in cancer therapy. Our previous study found that a novel low molecular weight compound, VGA1155, inhibited binding between radioisotope-labelled VEGF and cells overexpressing its two receptors, Flt-1 and KDR/Flk-1, that is, NIH3T3-Flt-1 and NIH3T3-KDR, respectively. In the present study, we investigated the anti-angiogenic effects of VGA1155 based on VEGF inhibition. VGA1155 inhibited VEGF-induced DNA synthesis of human umbilical vein endothelial cells (HUVEC) and human retinal endothelial cells (HREC) in a concentration-dependent manner. VGA1155 also inhibited VEGF-induced tube formation of HUVEC in vitro and tumor angiogenesis toward B16-BL6 melanoma after orthotopic implantation into the skin of the back. On the other hand, VGA 1155 did not affect the proliferation of human epidermoid carcinoma (KB) cells and mouse mammary carcinoma (MM2) cells. It also had no effect on the activity of several cytosolic kinases such as p55fyn and p56lck. These findings suggest that VGA1155 inhibits endothelial cell growth and angiogenesis by inhibiting VEGF function but not non-specific cytotoxicity. VGA1155 thus exhibits promise as an antiangiogenic or anti-tumor agent with fewer side-effects.

Crude oil bioremediation field experiment in the Sea of Japan.

Experimental bioremediation of crude oil was conducted for approximately 3 months in the intertidal zone of the Sea of Japan, Hyogo Prefecture. Artificial mixtures of weathered Arabian light crude oil and sand taken from the experimental site were wrapped in polyester net envelopes. The envelopes were placed in drum-shaped acrylic vessels with perforated sides to facilitate seawater exchange. The vessels were laid in the intertidal area. Slow release nitrogen and phosphorus synthetic fertilizer granules were added to the oil-sand mixtures in three different amounts. Some oil-sand mixtures were unfertilized controls. The oil-sand mixtures were periodically sampled and changes in the composition of the residual oils were monitored. Oil samples were subjected to gas chromatography coupled with mass spectrometry for analysis of some representative semi-volatile aliphatic and aromatic compounds. All values for each analyte were normalized against that of hopane to evaluate the extent of oil biodegradation. Significant increases in the concentrations of both nitrogen and phosphorus were found in the fertilized sections in accordance with the amounts of added fertilizers. Although significant natural attenuation of oil was observed in the unfertilized sections, fertilization stimulated the degradation rate of the oil in the early stage of the experimental term. The extent of the oil biodegradation increased as the amount of added fertilizer increased. However, the final degradation efficiencies for each oil component in the fertilized sections were not significantly different from those in the unfertilized sections, and the degradation of each oil component had almost ceased after 6 weeks. We conclude that excessive amounts of macronutrients are required to accelerate oil biodegradation and that fertilization is only effective in the early stages.

The genome landscape of the african green monkey kidney-derived vero cell line.

Continuous cell lines that originate from mammalian tissues serve as not only invaluable tools for life sciences, but also important animal cell substrates for the production of various types of biological pharmaceuticals. Vero cells are susceptible to various types of microbes and toxins and have widely contributed to not only microbiology, but also the production of vaccines for human use. We here showed the genome landscape of a Vero cell line, in which 25,877 putative protein-coding genes were identified in the 2.97-Gb genome sequence. A homozygous ∼9-Mb deletion on chromosome 12 caused the loss of the type I interferon gene cluster and cyclin-dependent kinase inhibitor genes in Vero cells. In addition, an ∼59-Mb loss of heterozygosity around this deleted region suggested that the homozygosity of the deletion was established by a large-scale conversion. Moreover, a genomic analysis of Vero cells revealed a female Chlorocebus sabaeus origin and proviral variations of the endogenous simian type D retrovirus. These results revealed the genomic basis for the non-tumourigenic permanent Vero cell lineage susceptible to various pathogens and will be useful for generating new sub-lines and developing new tools in the quality control of Vero cells.

Methotrexate and gemcitabine combination chemotherapy for the treatment of malignant pleural mesothelioma.

Malignant pleural mesothelioma (MPM) is an aggressive tumor of serosal surfaces with a poor prognosis. Methotrexate and gemcitabine have exhibited single-agent activity in MPM. We evaluated the feasibility of sequential administration of these agents in the treatment of MPM. A total of 21 patients with MPM received a 30-min infusion of 100 mg/m2 methotrexate and, 30 min later, a 30-min infusion of 800 mg/m2 gemcitabine. Twenty-four hours following the administration of methotrexate, leucovorin rescue therapy was initiated (10 mg/m2 leucovorin administered 4 times at 6-h intervals). These treatments were administered weekly, with 4 weekly administrations constituting a cycle of therapy. A total of 88 cycles were administered to the 21 patients, with each patient receiving 1-10 cycles (median, 4.2 cycles). Eight patients (38.1%) exhibited a partial response, 10 patients (47.6%) had stable disease and 3 patients (14.3%) had progressive disease. The median overall survival was 19.4 months (range, 02-41 months). One-year and 2-year survival rates were 61.9 and 38.1%, respectively. Hematological toxicity was considered acceptable, with grade 3-4 toxicities occurring in 3 (14.3%) patients. Non-hematologic toxicity was generally mild. There was no treatment-related mortality. Our results suggest that methotrexate and gemcitabine combination therapy is feasible and effective in the treatment of MPM. This regimen may offer an alternative to platinum-based chemotherapy and a prospective trial including a larger cohort of patients is recommended to confirm these results.

Protein kinase C regulates human pluripotent stem cell self-renewal.

BACKGROUND: The self-renewal of human pluripotent stem (hPS) cells including embryonic stem and induced pluripotent stem cells have been reported to be supported by various signal pathways. Among them, fibroblast growth factor-2 (FGF-2) appears indispensable to maintain self-renewal of hPS cells. However, downstream signaling of FGF-2 has not yet been clearly understood in hPS cells. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we screened a kinase inhibitor library using a high-throughput alkaline phosphatase (ALP) activity-based assay in a minimal growth factor-defined medium to understand FGF-2-related molecular mechanisms regulating self-renewal of hPS cells. We found that in the presence of FGF-2, an inhibitor of protein kinase C (PKC), GF109203X (GFX), increased ALP activity. GFX inhibited FGF-2-induced phosphorylation of glycogen synthase kinase-3ß (GSK-3ß), suggesting that FGF-2 induced PKC and then PKC inhibited the activity of GSK-3ß. Addition of activin A increased phosphorylation of GSK-3ß and extracellular signal-regulated kinase-1/2 (ERK-1/2) synergistically with FGF-2 whereas activin A alone did not. GFX negated differentiation of hPS cells induced by the PKC activator, phorbol 12-myristate 13-acetate whereas Gö6976, a selective inhibitor of PKCα, ß, and γ isoforms could not counteract the effect of PMA. Intriguingly, functional gene analysis by RNA interference revealed that the phosphorylation of GSK-3ß was reduced by siRNA of PKCδ, PKCε, and ζ, the phosphorylation of ERK-1/2 was reduced by siRNA of PKCε and ζ, and the phosphorylation of AKT was reduced by PKCε in hPS cells. CONCLUSIONS/SIGNIFICANCE: Our study suggested complicated cross-talk in hPS cells that FGF-2 induced the phosphorylation of phosphatidylinositol-3 kinase (PI3K)/AKT, mitogen-activated protein kinase/ERK-1/2 kinase (MEK), PKC/ERK-1/2 kinase, and PKC/GSK-3ß. Addition of GFX with a MEK inhibitor, U0126, in the presence of FGF-2 and activin A provided a long-term stable undifferentiated state of hPS cells even though hPS cells were dissociated into single cells for passage. This study untangles the cross-talk between molecular mechanisms regulating self-renewal and differentiation of hPS cells.

Pleural effusion VEGF levels as a prognostic factor of malignant pleural mesothelioma.

BACKGROUND: Malignant pleural mesothelioma (MPM) is an aggressive malignant tumor of mesothelial origin associated with asbestos exposure. MPM has a limited response to conventional chemotherapy and radiotherapy so early diagnosis of MPM is very important. Vascular endothelial growth factor (VEGF), a potent mitogen for the vascular endothelium, is also known to be an autocrine growth factor for MPM. Here, we investigated the pleural effusion VEGF levels in patients with MPM and compared them to those of a population with a non-malignant pleuritis or lung cancer involving malignant pleural effusion. METHODS: The pleural effusion VEGF concentrations were measured in 46 MPM patients and 45 individuals with non-MPM individuals (25 individuals with non-malignant pleural effusions, and 20 individuals with lung cancer involving malignant pleural effusion). RESULTS: We demonstrated that patients with MPM had significantly higher pleural effusion VEGF levels than a population with non-malignant pleuritis or lung cancer involving malignant pleural effusion, and the patients with advanced stage MPM showed higher levels of VEGF than the early stage MPM patients. The difference in overall survival between the groups with pleural effusion VEGF levels lower and higher than the assumed cut-off of 2000pg/ml was significant. CONCLUSIONS: Our data suggest that the pleural effusion VEGF concentration could be useful as an aid for the diagnosis of MPM and as a prognostic factor.

Clinical significance of serum vascular endothelial growth factor in malignant pleural mesothelioma.

INTRODUCTION: Malignant pleural mesothelioma (MPM) is an aggressive malignant tumor of mesothelial origin associated with asbestos exposure. MPM has a limited response to conventional chemotherapy and radiotherapy so diagnosing MPM early is very important. Vascular endothelial growth factor (VEGF) is an autocrine growth factor for MPM. Here, we investigated the serum levels of VEGF in patients with MPM in comparison with a population that had been exposed to asbestos without developing MPM. METHODS: Serum concentrations of VEGF were measured in 51 patients with MPM and 42 individuals with benign asbestos-related diseases (asbestosis or pleural plaques) or who were healthy despite asbestos exposure. RESULTS: We demonstrated that patients with MPM had significantly higher serum levels of VEGF than a population who had been exposed to asbestos but had not developed MPM, and the patients with advanced stage MPM showed higher levels of VEGF than the early stage patients with MPM. The difference in overall survival between the groups with VEGF serum levels lower and higher than the assumed cutoff of 460 pg/ml was significant. CONCLUSIONS: Our data suggest that the VEGF serum concentration could be a useful marker for screening MPM among asbestos-exposed individuals and as a prognostic factor.