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Bamba K, Ozawa M, Daitoku H, Kohara A. Diverting the food-freezing technology improves the cryopreservation efficiency of induced pluripotent stem cells and derived neurospheres. Regen Ther 2024; 27:83-91. [PMID: 38525239 PMCID: PMC10957518 DOI: 10.1016/j.reth.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 02/19/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Recent advances in induced pluripotent stem (iPS) technology and regenerative medicine require effective cryopreservation of iPSC-derived differentiated cells and three-dimensional cell aggregates (eg. Spheroids and organoids). Moreover, innovative freezing technologies for keeping food fresh over the long-term rapidly developed in the food industry. Therefore, we examined whether one of such freezing technologies, called "Dynamic Effect Powerful Antioxidation Keeping (DEPAK)," could be effective for the cryopreservation of biological materials. Methods We evaluated the efficiency of cryopreservation using DEPAK and Proton freezers, both of which are used in the food industry, compared with conventional slow-freezing methods using a programmable freezer and a cell-freezing vessel. As they are highly susceptible cells to freeze-thaw damage, we selected two suspension cell lines (KHYG-1 derived from human natural killer cell leukemia and THP-1 derived from human acute monocyte leukemia) and two adherent cell lines (OVMANA derived from human ovarian tumors and HuH-7 derived from human hepatocarcinoma). We used two human iPS cell lines, 201B7-Ff and 1231A3, which were either undifferentiated or differentiated into neurospheres. After freezing using the above methods, the frozen cells and neurospheres were immediately transferred to liquid nitrogen. After thawing, we assessed the cryopreservation efficiency of cell viability, proliferation, neurosphere formation, and neurite outgrowth after thawing. Results Among the four cryopreservation methods, DEPAK freezing resulted in the highest cell proliferation in suspension and adherent cell lines. Similar results were obtained for the cryopreservation of undifferentiated human iPS cells. In addition, we demonstrated that the DEPAK freezing method sustained the neurosphere formation capacity of differentiated iPS cells to the same extent as unfrozen controls. In addition, we observed that DEPAK-frozen neurospheres exhibited higher viability after thawing and underwent neural differentiation more efficiently than slow-freezing methods. Conclusions Our results suggest that diversifying food-freezing technologies can overcome the difficulties associated with the cryopreservation of various biological materials, including three-dimensional cell aggregates.
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Yamada M, Suzuki T, Kohara A, Honma M. Carcinogenic risk of food additive AF-2 banned in Japan: a case study on reassessment of genotoxicity. Genes Environ 2023; 45:33. [PMID: 38053221 PMCID: PMC10696715 DOI: 10.1186/s41021-023-00292-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Carcinogenic risk assessment studies have been repeatedly improved and are still being debated to find a goal. Evaluation might be changed if new approaches would be applied to some chemicals which means that new approaches may change the final assessment. In this paper, the risk assessment of a chemical, in particular the proper carcinogenicity, is examined using the long-banned food additive, 2-(2-furyl)-3-(5-nitro-2-furyl)-acrylamide, AF-2, as a case study. RESULTS First, Ames tests were carried out using strains TA1535, TA100, TA1538, and TA98 and their nitroreductase-deficient strains YG7127, YG7128, YG7129, and YG7130. The results showed that mutagenic activity was reduced by about 50% in the nitroreductase-deficient strains, indicating that part of the mutagenic activity shown in Ames test was due to bacterial metabolism. Second, in vivo genotoxicity tests were conducted, including the one that had not been developed in 1970's. Both a micronucleus test and a gene mutation assay using transgenic mice were negative. Third, assuming it is a genotoxic carcinogen, the virtual safety dose of 550 μg/day was calculated from the TD50 in rats with a probability of 10-5. CONCLUSION AF-2 has been shown to be carcinogenic to rodents and has previously been indicated to be genotoxic in vitro. However, the present in vivo genotoxicity study, it was negative in the forestomach, a target organ for cancer, particularly in the gene mutation assay in transgenic mice. Considering the daily intake of AF-2 in the 1970s and its virtually safety dose, the carcinogenic risk of AF-2 could be considered acceptable.
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Konishi K, Yamaji T, Sakuma C, Kasai F, Endo T, Kohara A, Hanada K, Osada N. Whole-Genome Sequencing of Vero E6 (VERO C1008) and Comparative Analysis of Four Vero Cell Sublines. Front Genet 2022; 13:801382. [PMID: 35391802 PMCID: PMC8981525 DOI: 10.3389/fgene.2022.801382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The Vero cell line is an immortalized cell line established from kidney epithelial cells of the African green monkey. A variety of Vero sublines have been developed and can be classified into four major cell lineages. In this study, we determined the whole-genome sequence of Vero E6 (VERO C1008), which is one of the most widely used cell lines for the proliferation and isolation of severe acute respiratory syndrome coronaviruses (SARS-CoVs), and performed comparative analysis among Vero JCRB0111, Vero CCL-81, Vero 76, and Vero E6. Analysis of the copy number changes and loss of heterozygosity revealed that these four sublines share a large deletion and loss of heterozygosity on chromosome 12, which harbors type I interferon and CDKN2 gene clusters. We identified a substantial number of genetic differences among the sublines including single nucleotide variants, indels, and copy number variations. The spectrum of single nucleotide variants indicated a close genetic relationship between Vero JCRB0111 and Vero CCL-81, and between Vero 76 and Vero E6, and a considerable genetic gap between the former two and the latter two lines. In contrast, we confirmed the pattern of genomic integration sites of simian endogenous retroviral sequences, which was consistent among the sublines. We identified subline-specific/enriched loss of function and missense variants, which potentially contribute to the differences in response to viral infection among the Vero sublines. In particular, we identified four genes (IL1RAP, TRIM25, RB1CC1, and ATG2A) that contained missense variants specific or enriched in Vero E6. In addition, we found that V739I variants of ACE2, which functions as the receptor for SARS-CoVs, were heterozygous in Vero JCRB0111, Vero CCL-81, and Vero 76; however, Vero E6 harbored only the allele with isoleucine, resulting from the loss of one of the X chromosomes.
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Kasai F, Hirayama N, Fukushima M, Kohara A, Nakamura Y. THP
‐1 reference data: proposal of an
in vitro
branched evolution model for cancer cell lines. Int J Cancer 2022; 151:463-472. [DOI: 10.1002/ijc.34019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 03/09/2022] [Accepted: 03/22/2022] [Indexed: 11/12/2022]
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Kasai F, Hirayama N, Kohara A. TK6 genome profile compared with WIL2-NS: Reference data to improve the reproducibility of genotoxicity studies. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 858-860:503236. [PMID: 33198927 DOI: 10.1016/j.mrgentox.2020.503236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
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.
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Kitamura Y, Suzuki T, Kohara A, Saeki KI. Hepatocarcinogen 4-methylquinoline induced G:C to C:G transversions in the cII gene in the liver of lambda/lacZ transgenic mice (Muta™Mouse). Mutat Res 2020; 821:111709. [PMID: 32497932 DOI: 10.1016/j.mrfmmm.2020.111709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 11/19/2022]
Abstract
We have previously reported that quinoline increased the mutation frequency of the cII gene in the liver of lambda/lacZ transgenic mice (Muta™Mouse), and G:C to C:G transversions were the molecular signature of quinoline-induced mutations. 4-Methylquinoline (4-MeQ) has the highest mutagenicity among quinoline and isomeric methylquinolines according to the Ames test using Salmonella typhimurium TA 100, in the presence of rat liver microsomal enzymes. In this report, we examined the effect of 4-MeQ on mutagenesis in the lambda cII gene in the liver of the Muta™Mouse, and we analyzed the sequences of the mutated genes. The mutation frequency of the liver cII gene was seven times higher in 4-MeQ-treated mice than in control mice. Sequence analysis revealed that 4-MeQ primarily induced G:C to C:G transversions (37 of 45). The specificities of 4-MeQ for target organ and mutation pattern were very consistent with those of quinoline. Thus, we showed that 4-MeQ was also genotoxic in the liver of the Muta™Mouse, and as with quinoline, the G:C to C:G transversion was the molecular signature of the 4-MeQ-induced mutations.
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Unno T, Tanaka H, Kohara A. Consumption of young barley leaf extract increases fecal short-chain fatty acid levels: a before-after clinical trial. FOOD RESEARCH 2020. [DOI: 10.26656/fr.2017.4(4).062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Short-chain fatty acids (SCFAs) bacterially produced in the intestine provide a variety of
physiological effects for the host. The present before-after clinical trial was conducted to
investigate the effects of young barley leaf extract (YBL) on fecal SCFA levels. For 4
weeks, female health subjects were asked to ingest two sticks (8 g) of test sample daily.
Feces were collected before and after the period of treatment with YBL. Results
demonstrated that YBL significantly elevated the fecal concentrations of acetate from
23.6±7.5 to 36.4±8.1 μmol/g (p<0.001) and propionate from 10.0±5.2 to 13.6±7.1 μmol/g
(p<0.05) but, did not give an advantage in fecal bacterial composition. Interestingly, YBL
also raised the fecal moisture by 3.9% point from the baseline (p<0.05).
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Kasai F, Asou H, Ozawa M, Kobayashi K, Kuramitsu H, Satoh M, Kohara A, Kaneko Y, Kawamura M. Kasumi leukemia cell lines: characterization of tumor genomes with ethnic origin and scales of genomic alterations. Hum Cell 2020; 33:868-876. [PMID: 32180206 PMCID: PMC7324421 DOI: 10.1007/s13577-020-00347-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/05/2020] [Indexed: 01/08/2023]
Abstract
Kasumi-1 has played an important role in an experimental model with t(8;21) translocation, which is a representative example of leukemia cell lines. However, previous studies using Kasumi-1 show discrepancies in the genome profile. The wide use of leukemia cell lines is limited to lines that are well-characterized. The use of additional cell lines extends research to various types of leukemia, and to further explore leukemia pathogenesis, which can be achieved by uncovering the fundamental features of each cell line with accurate data. In this study, ten Kasumi cell lines established in Japan, including five that were previously unknown, have been characterized by SNP microarray and targeted sequencing. SNP genotyping suggested that the genetic ancestry in four of the ten Kasumi cell lines was not classified as Japanese but covered several different east-Asian ethnicities, suggesting that patients in Japan are genetically diverse. TP53 mutations were detected in two cell lines with complex array profiles, indicating chromosomal instability (CIN). A quantitative assessment of tumor genomes at the chromosomal level was newly introduced to reveal total DNA sizes and Scales of Genomic Alterations (SGA) for each cell line. Kasumi-1 and 6 derived from relapsed phases demonstrated high levels of SGA, implying that the level of SGA would reflect on the tumor progression and could serve as an index of CIN. Our results extend the leukemia cellular resources with an additional five cell lines and provide reference genome data with ethnic identities for the ten Kasumi cell lines.
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Suzuki T, Tsukumo Y, Furihata C, Naito M, Kohara A. Preparation of the standard cell lines for reference mutations in cancer gene-panels by genome editing in HEK 293 T/17 cells. Genes Environ 2020; 42:8. [PMID: 32071619 PMCID: PMC7014756 DOI: 10.1186/s41021-020-0147-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/31/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Next Generation Sequencer (NGS) is a powerful tool for a high-throughput sequencing of human genome. It is important to ensure reliability and sensitivity of the sequence data for a clinical use of the NGS. Various cancer-related gene panels such as Oncomine™ or NCC OncoPanel have been developed and used for clinical studies. Because these panels contain multiple genes, it is difficult to ensure the performance of mutation detection for every gene. In addition, various platforms of NGS are developed and their cross-platform validation has become necessity. In order to create mutant standards in a defined background, we have used CRISPR/Cas9 genome-editing system in HEK 293 T/17 cells. RESULTS Cancer-related genes that are frequently used in NGS-based cancer panels were selected as the target genes. Target mutations were selected based on their frequency reported in database, and clinical significance and on the applicability of CRISPR/Cas9 by considering distance from PAM site, and off-targets. We have successfully generated 88 hetero- and homozygous mutant cell lines at the targeted sites of 36 genes representing a total of 125 mutations. CONCLUSIONS These knock-in HEK293T/17 cells can be used as the reference mutant standards with a steady and continuous supply for NGS-based cancer panel tests from the JCRB cell bank. In addition, these cell lines can provide a tool for the functional analysis of targeted mutations in cancer-related genes in the isogenic background.
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Kondo J, Ekawa T, Endo H, Yamazaki K, Tanaka N, Kukita Y, Okuyama H, Okami J, Imamura F, Ohue M, Kato K, Nomura T, Kohara A, Mori S, Dan S, Inoue M. High-throughput screening in colorectal cancer tissue-originated spheroids. Cancer Sci 2018; 110:345-355. [PMID: 30343529 PMCID: PMC6317944 DOI: 10.1111/cas.13843] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/12/2018] [Accepted: 10/19/2018] [Indexed: 12/13/2022] Open
Abstract
Patient‐derived cancer organoid culture is an important live material that reflects clinical heterogeneity. However, the limited amount of organoids available for each case as well as the considerable amount of time and cost to expand in vitro makes it impractical to perform high‐throughput drug screening using organoid cultures from multiple patients. Here, we report an advanced system for the high‐throughput screening of 2427 drugs using the cancer tissue‐originated spheroid (CTOS) method. In this system, we apply the CTOS method in an ex vivo platform from xenograft tumors, using machines to handle CTOS and reagents, and testing a CTOS reference panel of multiple CTOS lines for the hit drugs. CTOS passages in xenograft tumors resulted in minimal changes of morphological and genomic status, and xenograft tumor generation efficiently expanded the number of CTOS to evaluate multiple drugs. Our panel of colorectal cancer CTOS lines exhibited diverse sensitivities to the hit compounds, demonstrating the usefulness of this system for investigating highly heterogeneous disease.
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Kasai F, Pereira JC, Kohara A, Ferguson-Smith MA. Homologue-specific chromosome sequencing characterizes translocation junctions and permits allelic assignment. DNA Res 2018. [PMID: 29518182 PMCID: PMC6105103 DOI: 10.1093/dnares/dsy007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chromosome translocations can be detected by cytogenetic analysis, but it is hard to characterize the breakpoints at the sequence level. Chromosome sorting by flow cytometry produces flow karyotypes that enable the isolation of abnormal chromosomes and the generation of chromosome-specific DNA. In this study, a derivative chromosome t(9; 14) and its homologous normal chromosomes 9 and 14 from the Ishikawa 3-H-12 cell line were sorted to collect homologue-specific samples. Chromosome sequencing identified the breakpoint junction in the der(9) at 9p24.3 and 14q13.1 and uncovered the formation of a fusion gene, WASH1–NPAS3. Amplicon sequencing targeted for neighbouring genes at the fusion breakpoint revealed that the variant frequencies correlate with the allelic copy number. Sequencing of sorted chromosomes permits the assignment of allelic variants and can lead to the characterization of abnormal chromosomes. We show that allele-specific chromosome sequencing of homologues is a robust technique for distinguishing alleles and this provides an efficient approach for the comprehensive analysis of genomic changes.
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Kohara A, Matsumoto M, Hirose A, Hayashi M, Honma M, Suzuki T. Mutagenic properties of dimethylaniline isomers in mice as evaluated by comet, micronucleus and transgenic mutation assays. Genes Environ 2018; 40:18. [PMID: 30151062 PMCID: PMC6103965 DOI: 10.1186/s41021-018-0106-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/17/2018] [Indexed: 11/10/2022] Open
Abstract
Background The carcinogenic potential of dimethylaniline (DMA) isomers in rodents and humans has been previously reported, and there is sufficient evidence for the carcinogenicity of 2,6-DMA in experimental animals. The target organ of carcinogenesis of 2,6-DMA is the nasal cavity. In the current study, six DMA isomers, 2,3-, 2,4-, 2,5-, 2,6-, 3,4- and 3,5-DMA, were evaluated for mutagenic properties. Results Male ddY mice (3/group) were treated intragastrically (i.g.) with 200 mg/kg of one of the six DMAs, and a comet assay was performed on samples of bone marrow, kidney, liver and lung at 3 and 24 h after the treatment. Positive responses were observed in the kidney, liver and lungs of mice from all of the DMA treatment groups after 3 h and in the bone marrow of mice treated with either 3,4- or 3,5-DMA after 3 h; however, these effects were diminished at the 24 h time point. The micronucleus induction in the bone marrow was analysed in the same mouse at 24 h after the treatment. No induction of micronucleated polychromatic erythrocytes was observed after treatment with any of the DMAs.Male transgenic Muta™ mice (five/group) were treated i.g. with 2,5-, 2,6- or 3,5-DMA at 100 mg/kg bw weekly for 4 weeks, and the lacZ and the cII mutation frequencies were examined in the nasal cavity, liver and bone marrow at 7 days after the last treatment. Statistically significant increases in the mutation frequencies of the lacZ and/or cII genes were observed in the nasal cavity of 2,5-DMA or 2,6-DMA treated mice. Sequence analysis showed increased incidences of AT to GC and GC to TA mutations in the nasal tissues. Conclusions These findings suggest that the carcinogenic activities of DMAs are associated with mutagenic events.
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Kasai F, Hirayama N, Ozawa M, Satoh M, Kohara A. HuH-7 reference genome profile: complex karyotype composed of massive loss of heterozygosity. Hum Cell 2018; 31:261-267. [PMID: 29774518 PMCID: PMC6002425 DOI: 10.1007/s13577-018-0212-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/12/2018] [Indexed: 12/24/2022]
Abstract
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.
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Shioda S, Kasai F, Watanabe K, Kawakami K, Ohtani A, Iemura M, Ozawa M, Arakawa A, Hirayama N, Kawaguchi E, Tano T, Miyata S, Satoh M, Shimizu N, Kohara A. Screening for 15 pathogenic viruses in human cell lines registered at the JCRB Cell Bank: characterization of in vitro human cells by viral infection. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172472. [PMID: 29892436 PMCID: PMC5990783 DOI: 10.1098/rsos.172472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/23/2018] [Indexed: 05/04/2023]
Abstract
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.
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Tada M, Hirata M, Sasaki M, Sakate R, Kohara A, Takahashi I, Kameoka Y, Masui T, Matsuyama A. The Rare Disease Bank of Japan: establishment, current status and future challenges. Hum Cell 2018; 31:183-188. [PMID: 29611131 DOI: 10.1007/s13577-018-0204-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/12/2018] [Indexed: 12/13/2022]
Abstract
Research on rare diseases cannot be performed without appropriate samples from patients with such diseases. Due to the limited number of such patients, securing biosamples of sufficient quality for extensive research is a challenge and represents an important barrier to the advancement of research on rare diseases. To tackle this problem, the Rare Disease Bank (RDB) was established in 2009 at the National Institute of Biomedical Innovation (NIBIO; currently, the National Institutes of Biomedical Innovation, Health and Nutrition in Japan). Since then, the RDB has focused on three objectives: (1) emphasizing the importance of collecting biosamples from patients with rare diseases, together with appropriate clinical information, from various medical facilities nationwide; (2) maintaining strict high-quality sample management standards; and (3) sharing biosamples with research scientists across Japan for the advancement of research on rare diseases. As of August 2017, the bank has collected 4147 biosamples from patients with rare diseases, including DNA, serum, plasma, and cell samples from various university hospitals and other medical institutions across the country, and provided various research institutions with 13,686 biosample aliquots from 2850 cases. In addition, the management committee has successfully established a bank system that provides high-quality biosamples together with the results of human leukocyte antigen analysis. It is anticipated that the RDB, through the collection and sharing of biosamples with the medical research community, will enhance the understanding, prevention, and treatment of rare diseases in Japan and the world at large.
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Shioda S, Kasai F, Ozawa M, Hirayama N, Satoh M, Kameoka Y, Watanabe K, Shimizu N, Tang H, Mori Y, Kohara A. The human vascular endothelial cell line HUV-EC-C harbors the integrated HHV-6B genome which remains stable in long term culture. Cytotechnology 2017; 70:141-152. [PMID: 28755030 PMCID: PMC5809643 DOI: 10.1007/s10616-017-0119-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/29/2017] [Indexed: 01/02/2023] Open
Abstract
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.
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Kuroi A, Sugimura K, Kumagai A, Kohara A, Nagaoka Y, Kawahara H, Yamahara M, Kawahara N, Takemori H, Fuchino H. The Importance of 11α-OH, 15-oxo, and 16-en Moieties of 11α-Hydroxy-15-oxo-kaur-16-en-19-oic Acid in Its Inhibitory Activity on Melanogenesis. Skin Pharmacol Physiol 2017; 30:205-215. [DOI: 10.1159/000475471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 04/03/2017] [Indexed: 12/18/2022]
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Lorge E, Moore MM, Clements J, O'Donovan M, Fellows MD, Honma M, Kohara A, Galloway S, Armstrong MJ, Thybaud V, Gollapudi B, Aardema MJ, Tanir JY. Standardized cell sources and recommendations for good cell culture practices in genotoxicity testing. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2016; 809:1-15. [PMID: 27692294 DOI: 10.1016/j.mrgentox.2016.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 11/16/2022]
Abstract
Good cell culture practice and characterization of the cell lines used are of critical importance in in vitro genotoxicity testing. The objective of this initiative was to make continuously available stocks of the characterized isolates of the most frequently used mammalian cell lines in genotoxicity testing anywhere in the world ('IVGT' cell lines). This project was organized under the auspices of the International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) Project Committee on the Relevance and Follow-up of Positive Results in In Vitro Genetic Toxicity (IVGT) Testing. First, cell isolates were identified that are as close as possible to the isolate described in the initial publications reporting their use in genotoxicity testing. The depositors of these cell lines managed their characterization and their expansion for preparing continuously available stocks of these cells that are stored at the European Collection of Cell Cultures (ECACC, UK) and the Japanese Collection of Research Bioresources (JCRB, Japan). This publication describes how the four 'IVGT' cell lines, i.e. L5178Y TK+/- 3.7.2C, TK6, CHO-WBL and CHL/IU, were prepared for deposit at the ECACC and JCRB cell banks. Recommendations for handling these cell lines and monitoring their characteristics are also described. The growth characteristics of these cell lines (growth rates and cell cycles), their identity (karyotypes and genetic status) and ranges of background frequencies of select endpoints are also reported to help in the routine practice of genotoxicity testing using these cell lines.
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Kasai F, Hirayama N, Ozawa M, Iemura M, Kohara A. 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. Genomics 2016; 107:259-66. [PMID: 27107655 DOI: 10.1016/j.ygeno.2016.04.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 01/17/2023]
Abstract
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.
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Iida R, Garrett K, Alberola-lla J, Kohara A, Kincade P. Dynamic expression of B7 family molecules on hematopoietic stem cells. Exp Hematol 2015. [DOI: 10.1016/j.exphem.2015.06.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Osada N, Kohara A, Yamaji T, Hirayama N, Kasai F, Sekizuka T, Kuroda M, Hanada K. The genome landscape of the african green monkey kidney-derived vero cell line. DNA Res 2014; 21:673-83. [PMID: 25267831 PMCID: PMC4263300 DOI: 10.1093/dnares/dsu029] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
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.
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Capes-Davis A, Alston-Roberts C, Kerrigan L, Reid YA, Barrett T, Burnett EC, Cooper JR, Dirks WG, MacLeod RAF, Drexler HG, Freshney RI, Healy L, Kohara A, Korch C, Masters JRW, Nakamura Y, Nims RW, Storts DR. Beware imposters: MA-1, a novel MALT lymphoma cell line, is misidentified and corresponds to Pfeiffer, a diffuse large B-cell lymphoma cell line. Genes Chromosomes Cancer 2013; 52:986-8. [DOI: 10.1002/gcc.22094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 06/25/2013] [Indexed: 11/06/2022] Open
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Capes-Davis A, Reid YA, Kline MC, Storts DR, Strauss E, Dirks WG, Drexler HG, MacLeod RA, Sykes G, Kohara A, Nakamura Y, Elmore E, Nims RW, Alston-Roberts C, Barallon R, Los GV, Nardone RM, Price PJ, Steuer A, Thomson J, Masters JR, Kerrigan L. Match criteria for human cell line authentication: Where do we draw the line? Int J Cancer 2012; 132:2510-9. [DOI: 10.1002/ijc.27931] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 09/26/2012] [Indexed: 12/18/2022]
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Shofuda T, Kanematsu D, Fukusumi H, Yamamoto A, Bamba Y, Yoshitatsu S, Suemizu H, Nakamura M, Sugimoto Y, Furue MK, Kohara A, Akamatsu W, Okada Y, Okano H, Yamasaki M, Kanemura Y. Human Decidua-Derived Mesenchymal Cells Are a Promising Source for the Generation and Cell Banking of Human Induced Pluripotent Stem Cells. CELL MEDICINE 2012; 4:125-47. [PMID: 26858858 DOI: 10.3727/215517912x658918] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Placental tissue is a biomaterial with remarkable potential for use in regenerative medicine. It has a three-layer structure derived from the fetus (amnion and chorion) and the mother (decidua), and it contains huge numbers of cells. Moreover, placental tissue can be collected without any physical danger to the donor and can be matched with a variety of HLA types. The decidua-derived mesenchymal cells (DMCs) are highly proliferative fibroblast-like cells that express a similar pattern of CD antigens as bone marrow-derived mesenchymal cells (BM-MSCs). Here we demonstrated that induced pluripotent stem (iPS) cells could be efficiently generated from DMCs by retroviral transfer of reprogramming factor genes. DMC-hiPS cells showed equivalent characteristics to human embryonic stem cells (hESCs) in colony morphology, global gene expression profile (including human pluripotent stem cell markers), DNA methylation status of the OCT3/4 and NANOG promoters, and ability to differentiate into components of the three germ layers in vitro and in vivo. The RNA expression of XIST and the methylation status of its promoter region suggested that DMC-iPSCs, when maintained undifferentiated and pluripotent, had three distinct states: (1) complete X-chromosome reactivation, (2) one inactive X-chromosome, or (3) an epigenetic aberration. Because DMCs are derived from the maternal portion of the placenta, they can be collected with the full consent of the adult donor and have considerable ethical advantages for cell banking and the subsequent generation of human iPS cells for regenerative applications.
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Shofuda T, Kanematsu D, Fukusumi H, Yamamoto A, Bamba Y, Yoshitatsu S, Suemizu H, Nakamura M, Sugimoto Y, Furue MK, Kohara A, Akamatsu W, Okada Y, Okano H, Yamasaki M, Kanemura Y. Human Decidua-Derived Mesenchymal Cells are a Promising Source for the Generation and Cell Banking of Human Induced Pluripotent Stem Cells. CELL MEDICINE 2012. [DOI: 10.3727/215517911x658918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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