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Comprehensive transcriptome data to identify downstream genes of testosterone signalling in dermal papilla cells. Sci Data 2022; 9:731. [PMID: 36446804 PMCID: PMC9709033 DOI: 10.1038/s41597-022-01846-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Testosterone-related steroid hormones are associated with various types of diseases, including prostate cancer and androgenetic alopecia (AGA). The testosterone or dihydroxy testosterone (DHT) circulates through the blood, binds to the androgen receptor (AR) in the cytoplasm, and finally enters the nucleus to activate downstream target genes. We previously found that immortalized dermal papilla cells (DPCs) lost AR expression, which may be explained by the repeated cell passages of DPCs. To compensate for the AR expression, DPCs that express AR exogenously were established. In this study, we performed an RNA-Seq analysis of the AR-expressing and non-AR-expressing DPCs in the presence or absence of DHT to identify the downstream target genes regulated by AR signalling. Furthermore, we treated DPCs with minoxidil sulphate, which has the potential to treat AGA. This is the first comprehensive analysis to identify the downstream genes involved in testosterone signalling in DPCs. Our manuscript provides high-priority data for the discovery of molecular targets for prostate cancer and AGA.
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Endo Y, Kamei KI, Hasegawa K, Okita K, Ito H, Terada S, Inoue-Murayama M. Generation and gene expression profiles of Grevy's zebra induced Pluripotent Stem Cells. Stem Cells Dev 2022; 31:250-257. [PMID: 35316100 DOI: 10.1089/scd.2021.0253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) can serve as a biological resource for functional and conservation research for various species. This realisation has led to the generation of iPSCs from many species, including those identified as endangered. However, the understanding of species variation in mammalian iPSCs remains largely unknown. To gain insight into species variation in iPSCs, we generated iPSCs from a new species Grevy's zebra (Equus grevyi; gz-iPSCs), which has been listed as endangered in the IUCN (International Union for Conservation of Nature) Red List. We isolated primary fibroblast cells from an individual and successfully reprogrammed them into iPSCs. The generated gz-iPSCs continued to grow under primed-type culture condition and showed pluripotency and differentiation potential. To describe the molecular characteristics of gz-iPSCs, we performed RNA sequencing analysis. The gz-iPSC transcriptome showed robust expression of pluripotency associated genes reported in human and mouse, suggesting evolutionary conservation among the species. This study provides insight into the iPSCs from a rare species and helps the understanding of the gene expression basis underlying mammalian PSCs.
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Affiliation(s)
| | - Ken-Ichiro Kamei
- Kyoto University - Yoshida Campus, 12918, Kyoto, Japan, 606-8501;
| | | | | | | | - Shiho Terada
- Kyoto University - Yoshida Campus, 12918, Kyoto, Japan;
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Furuya K, Fujibayashi S, Wu T, Takahashi K, Takase S, Orimoto A, Sugano E, Tomita H, Kashiwagi S, Kiyono T, Ishii T, Fukuda T. Transcriptome analysis to identify the downstream genes of androgen receptor in dermal papilla cells. BMC Genom Data 2022; 23:2. [PMID: 34983378 PMCID: PMC8725446 DOI: 10.1186/s12863-021-01018-6] [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: 05/31/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Testosterone signaling mediates various diseases, such as androgenetic alopecia and prostate cancer. Testosterone signaling is mediated by the androgen receptor (AR). In this study, we fortuitously found that primary and immortalized dermal papilla cells suppressed AR expression, although dermal papilla cells express AR in vivo. To analyze the AR signaling pathway, we exogenously introduced the AR gene via a retrovirus into immortalized dermal papilla cells and comprehensively compared their expression profiles with and without AR expression. Results Whole-transcriptome profiling revealed that the focal adhesion pathway was mainly affected by the activation of AR signaling. In particular, we found that caveolin-1 gene expression was downregulated in AR-expressing cells, suggesting that caveolin-1 is controlled by AR. Conclusion Our whole transcriptome data is critical resources for discovery of new therapeutic targets for testosterone-related diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-01018-6. The comprehensive gene expression profiling were obtained by RNA-Seq analysis about AR negative and AR positive dermal papilla cells. The bioinformatics analysis suggested that caveolin-1 and EGF receptors are the downstream of AR signaling. Our study showed the combination of pinpoint mutant cells and global transcriptome is effective to identify the downstream genes.
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Affiliation(s)
- Kai Furuya
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - So Fujibayashi
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Tao Wu
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Kouhei Takahashi
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Shin Takase
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Ai Orimoto
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Eriko Sugano
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Hiroshi Tomita
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Sayo Kashiwagi
- Rohto Pharmaceutical Co., Ltd., Basic Research Development Division, 6-5-4 Kunimidai, Kizugawa, Kyoto, 619-0216, Japan
| | - Tohru Kiyono
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Tsuyoshi Ishii
- Rohto Pharmaceutical Co., Ltd., Basic Research Development Division, 6-5-4 Kunimidai, Kizugawa, Kyoto, 619-0216, Japan.
| | - Tomokazu Fukuda
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan.
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Furuya K, Wu T, Orimoto A, Sugano E, Tomita H, Kiyono T, Kurose T, Takai Y, Fukuda T. The transcriptome of wild-type and immortalized corneal epithelial cells. Sci Data 2021; 8:126. [PMID: 33963195 PMCID: PMC8105388 DOI: 10.1038/s41597-021-00908-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
Cellular immortalization enables indefinite expansion of cultured cells. However, the process of cell immortalization sometimes changes the original nature of primary cells. In this study, we performed expression profiling of poly A-tailed RNA from primary and immortalized corneal epithelial cells expressing Simian virus 40 large T antigen (SV40) or the combination of mutant cyclin-dependent kinase 4 (CDK4), cyclin D1, and telomere reverse transcriptase (TERT). Furthermore, we studied the expression profile of SV40 cells cultured in medium with or without serum. The profiling of whole expression pattern revealed that immortalized corneal epithelial cells with SV40 showed a distinct expression pattern from wild-type cells regardless of the presence or absence of serum, while corneal epithelial cells with combinatorial expression showed an expression pattern relatively closer to that of wild-type cells. Measurement(s) | Molecular Profiling | Technology Type(s) | RNA sequencing | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14093807
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Affiliation(s)
- Kai Furuya
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Tao Wu
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Ai Orimoto
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Eriko Sugano
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Hiroshi Tomita
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan
| | - Tohru Kiyono
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Takahiro Kurose
- Rohto Pharmaceutical Co., Ltd., Basic Research Development Division, 6-5-4 Kunimidai, Kizugawa, Kyoto, 619-0216, Japan
| | - Yoshihiro Takai
- Rohto Pharmaceutical Co., Ltd., Basic Research Development Division, 6-5-4 Kunimidai, Kizugawa, Kyoto, 619-0216, Japan.
| | - Tomokazu Fukuda
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551, Japan.
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Fukuda T, Furuya K, Takahashi K, Orimoto A, Sugano E, Tomita H, Kashiwagi S, Kiyono T, Ishii T. Combinatorial expression of cell cycle regulators is more suitable for immortalization than oncogenic methods in dermal papilla cells. iScience 2021; 24:101929. [PMID: 33437932 PMCID: PMC7788094 DOI: 10.1016/j.isci.2020.101929] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/05/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
The immortalized cell is an essential research tool that uses robust growth properties for the functional investigation of gene products. Immortalized mammalian cells have mainly been established using three methods: expression of simian vacuolating virus 40 T antigen (the SV40 method); human papilloma virus-derived oncoprotein E6/E7 (the E6/E7 method); or combinatorial expression of R24C mutant cyclin-dependent kinase 4, cyclin D1, and telomerase reverse transcriptase (the K4DT method). However, it is unclear as to which method is optimal for an in vitro model. Here, we compared the biological characteristics and genome-wide expression profiles of immortalized human dermal papilla cells generated by the SV40, E6/E7, or K4DT method. To our knowledge, this is the first study to comprehensively compare expression profiles to determine the optimal immortalization method for maintaining the original nature of the wild-type cells. These data would be valuable to scientists aiming to establish new immortalized cell lines.
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Affiliation(s)
- Tomokazu Fukuda
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551 Japan
| | - Kai Furuya
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551 Japan
| | - Kouhei Takahashi
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551 Japan
| | - Ai Orimoto
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551 Japan
| | - Eriko Sugano
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551 Japan
| | - Hiroshi Tomita
- Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate, 020-8551 Japan
| | - Sayo Kashiwagi
- Rohto Pharmaceutical Co., Ltd., Basic Research Development Division, 6-5-4 Kunimidai, Kizugawa, Kyoto, 619-0216, Japan
| | - Tohru Kiyono
- Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa-city, Chiba, 277-8577, Japan
| | - Tsuyoshi Ishii
- Rohto Pharmaceutical Co., Ltd., Basic Research Development Division, 6-5-4 Kunimidai, Kizugawa, Kyoto, 619-0216, Japan
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Haraguchi S, Dang-Nguyen TQ, Wells D, Fuchimoto D, Fukuda T, Tokunaga T. Establishment of porcine nuclear transfer-derived embryonic stem cells using induced pluripotent stem cells as donor nuclei. J Reprod Dev 2020; 66:163-174. [PMID: 31983707 PMCID: PMC7175389 DOI: 10.1262/jrd.2019-137] [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] [Indexed: 11/20/2022] Open
Abstract
We investigated whether sequential reprogramming via porcine induced pluripotent stem cells (piPSCs) or exposure to oocyte cytoplasm following nuclear transfer could generate nuclear transfer-derived ESCs (piPSCs-ntESCs). Nuclear transfer embryos were reconstructed with piPSCs possessing a ZsGreen fluorescent marker for expression of exogenous Nanog and Lin28. Reconstructed oocytes developed to morphologically normal 8-cell/morulae (35/93, 37.6%) and blastocysts (12/93, 12.9%). Although most green fluorescent protein-positive blastocysts showed efficient outgrowth (8/10, 80%), none formed primary colonies and all cultures degenerated. Conversely, 15% of fluorescent positive 8-cell/morula stage embryos showed outgrowth (6/40), with three forming primary colonies (7.5%). All three were expanded and maintained as piPSC-ntESC lines. These cell lines expressed stem cell marker genes and proteins. Despite inactivation of one X chromosome, all piPSC-ntESC lines formed teratomas comprising derivatives from all three embryonic germ layers. Strong SSEA1, 3, and 4 expression was detected at the 8-cell/morula stage in embryos reconstructed from both piPSCs and porcine embryonic fibroblasts (PEFs). SSEA3 was notably absent from IVF controls at pre-implantation embryo stages. Finally, we attempted to establish ntESCs from 8-cell/morulae reconstructed with PEFs using the same culture conditions as those for piPSC-ntESC derivation. Although eight primary colonies arose from 107 embryos (7.5%), they all degenerated after the first passage culture. Early and sustained expression of key reprogramming regulatory factors may be critical for pluripotent stem cell derivation to derive piPSC-ntESCs from 8-cell/morula stages, while the expression of SSEAs may be involved in the initial stem cell colony formation phases.
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Affiliation(s)
- Seiki Haraguchi
- Animal Biotechnology Unit, Institute of Agrobiological Sciences, NARO, Ibaraki 305-0901, Japan
| | - Thanh Quang Dang-Nguyen
- Reproductive Biology Unit, Institute of Agrobiological Sciences, NARO, Ibaraki 305-0901, Japan
| | - David Wells
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand
| | - Daiichiro Fuchimoto
- Animal Biotechnology Unit, Institute of Agrobiological Sciences, NARO, Ibaraki 305-0901, Japan
| | - Tomokazu Fukuda
- Laboratory of Cell Engineering and Molecular Genetics, Iwate University, Iwate 020-8550, Japan
| | - Tomoyuki Tokunaga
- Animal Biotechnology Unit, Institute of Agrobiological Sciences, NARO, Ibaraki 305-0901, Japan
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Glanzner WG, Gutierrez K, Rissi VB, de Macedo MP, Lopez R, Currin L, Dicks N, Baldassarre H, Agellon LB, Bordignon V. Histone Lysine Demethylases KDM5B and KDM5C Modulate Genome Activation and Stability in Porcine Embryos. Front Cell Dev Biol 2020; 8:151. [PMID: 32211412 PMCID: PMC7076052 DOI: 10.3389/fcell.2020.00151] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/24/2020] [Indexed: 12/16/2022] Open
Abstract
The lysine demethylases KDM5B and KDM5C are highly, but transiently, expressed in porcine embryos around the genome activation stage. Attenuation of KDM5B and KDM5C mRNA hampered embryo development to the blastocyst stage in fertilized, parthenogenetically activated and nuclear transfer embryos. While KDM5B attenuation increased H3K4me2-3 levels on D3 embryos and H3K4me1-2-3 on D5 embryos, KDM5C attenuation increased H3K9me1 on D3 embryos, and H3K9me1 and H3K4me1 on D5 embryos. The relative mRNA abundance of EIF1AX and EIF2A on D3 embryos, and the proportion of D4 embryos presenting a fluorescent signal for uridine incorporation were severely reduced in both KDM5B- and KDM5C-attenuated compared to control embryos, which indicate a delay in the initiation of the embryo transcriptional activity. Moreover, KDM5B and KDM5C attenuation affected DNA damage response and increased DNA double-strand breaks (DSBs), and decreased development of UV-irradiated embryos. Findings from this study revealed that both KDM5B and KDM5C are important regulators of early development in porcine embryos as their attenuation altered H3K4 and H3K9 methylation patterns, perturbed embryo genome activation, and decreased DNA damage repair capacity.
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Affiliation(s)
- Werner Giehl Glanzner
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Karina Gutierrez
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Vitor Braga Rissi
- Laboratory of Biotechnology and Animal Reproduction - BioRep, Federal University of Santa Maria (UFSM), Santa Maria, Brazil
| | | | - Rosalba Lopez
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Luke Currin
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Naomi Dicks
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Hernan Baldassarre
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Luis B Agellon
- School of Human Nutrition, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Vilceu Bordignon
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
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