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Li X, Gao B, Gao B, Li X, Xia X. Transcriptome profiling reveals dysregulation of inflammatory and protein synthesis genes in PCOS. Sci Rep 2024; 14:16596. [PMID: 39025980 PMCID: PMC11258128 DOI: 10.1038/s41598-024-67461-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
To analyze the differential expression genes of polycystic ovary syndrome (PCOS), clarify their functions and pathways, as well as the protein-protein interaction network, identify HUB genes, and explore the pathological mechanism. PCOS microarray datasets were screened from the GEO database. Common differentially expressed genes (co-DEGs) were obtained using GEO2R and Venn analysis. Enrichment and pathway analyses were conducted using the DAVID online tool, with results presented in bubble charts. Protein-protein interaction analysis was performed using the STRING tool. HUB genes were identified using Cytoscape software and further interpreted with the assistance of the GeneCards database. A total of two sets of co-DEGs (108 and 102), key proteins (15 and 55), and hub genes (10 and 10) were obtained. The co-DEGs: (1) regulated inflammatory responses and extracellular matrix, TNF, and IL-17 signaling pathways; (2) regulated ribosomes and protein translation, ribosome and immune pathways. The key proteins: (1) regulated inflammation, immunity, transcription, matrix metabolism, proliferation/differentiation, energy, and repair; (2) regulated ubiquitination, enzymes, companion proteins, respiratory chain components, and fusion proteins. The Hub genes: (1) encoded transcription factors and cytokines, playing vital roles in development and proliferation; (2) encoded ribosomes and protein synthesis, influencing hormone and protein synthesis, associated with development and infertility. The dysregulated expression of inflammation and protein synthesis genes in PCOS may be the key mechanism underlying its onset and progression.
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Affiliation(s)
- Xilian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, China
| | - Biao Gao
- Teaching and Research Support Center, Naval Medical University, Shanghai, 200433, China.
| | - Bingsi Gao
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, China
| | - Xin Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, China
| | - Xian Xia
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, China.
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Nakamura M, Kyoda T, Yoshida H, Takebayashi-Suzuki K, Koike R, Takahashi E, Moriyama Y, Wlizla M, Horb ME, Suzuki A. Injury-induced cooperation of InhibinβA and JunB is essential for cell proliferation in Xenopus tadpole tail regeneration. Sci Rep 2024; 14:3679. [PMID: 38355764 PMCID: PMC10867027 DOI: 10.1038/s41598-024-54280-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 02/10/2024] [Indexed: 02/16/2024] Open
Abstract
In animal species that have the capability of regenerating tissues and limbs, cell proliferation is enhanced after wound healing and is essential for the reconstruction of injured tissue. Although the ability to induce cell proliferation is a common feature of such species, the molecular mechanisms that regulate the transition from wound healing to regenerative cell proliferation remain unclear. Here, we show that upon injury, InhibinβA and JunB cooperatively function for this transition during Xenopus tadpole tail regeneration. We found that the expression of inhibin subunit beta A (inhba) and junB proto-oncogene (junb) is induced by injury-activated TGF-β/Smad and MEK/ERK signaling in regenerating tails. Similarly to junb knockout (KO) tadpoles, inhba KO tadpoles show a delay in tail regeneration, and inhba/junb double KO (DKO) tadpoles exhibit severe impairment of tail regeneration compared with either inhba KO or junb KO tadpoles. Importantly, this impairment is associated with a significant reduction of cell proliferation in regenerating tissue. Moreover, JunB regulates tail regeneration via FGF signaling, while InhibinβA likely acts through different mechanisms. These results demonstrate that the cooperation of injury-induced InhibinβA and JunB is critical for regenerative cell proliferation, which is necessary for re-outgrowth of regenerating Xenopus tadpole tails.
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Affiliation(s)
- Makoto Nakamura
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, CA, 94158, USA
| | - Tatsuya Kyoda
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Hitoshi Yoshida
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Kimiko Takebayashi-Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Ryota Koike
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Eri Takahashi
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Yuka Moriyama
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Marcin Wlizla
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Embryology, Charles River Laboratories, Wilmington, MA, 01887, USA
| | - Marko E Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Atsushi Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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The AP-1 transcription factor JunB functions in Xenopus tail regeneration by positively regulating cell proliferation. Biochem Biophys Res Commun 2019; 522:990-995. [PMID: 31812242 DOI: 10.1016/j.bbrc.2019.11.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022]
Abstract
Xenopus tropicalis tadpoles can regenerate an amputated tail, including spinal cord, muscle and notochord, through cell proliferation and differentiation. However, the molecular mechanisms that regulate cell proliferation during tail regeneration are largely unknown. Here we show that JunB plays an important role in tail regeneration by regulating cell proliferation. The expression of junb is rapidly activated and sustained during tail regeneration. Knockout (KO) of junb causes a delay in tail regeneration and tissue differentiation. In junb KO tadpoles, cell proliferation is prevented before tissue differentiation. Furthermore, TGF-β signaling, which is activated just after tail amputation, regulates the induction and maintenance of junb expression. These findings demonstrate that JunB, a downstream component of TGF-β signaling, works as a positive regulator of cell proliferation during Xenopus tail regeneration.
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Virgirinia RP, Jahan N, Okada M, Takebayashi‐Suzuki K, Yoshida H, Nakamura M, Akao H, Yoshimoto Y, Fatchiyah F, Ueno N, Suzuki A. Cdc2‐like kinase 2 (Clk2) promotes early neural development inXenopusembryos. Dev Growth Differ 2019; 61:365-377. [DOI: 10.1111/dgd.12619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Regina Putri Virgirinia
- Amphibian Research Center Graduate School of Science Hiroshima University Higashi-Hiroshima Japan
| | - Nusrat Jahan
- Amphibian Research Center Graduate School of Science Hiroshima University Higashi-Hiroshima Japan
| | - Maya Okada
- Amphibian Research Center Graduate School of Science Hiroshima University Higashi-Hiroshima Japan
| | | | - Hitoshi Yoshida
- Amphibian Research Center Graduate School of Science Hiroshima University Higashi-Hiroshima Japan
| | - Makoto Nakamura
- Amphibian Research Center Graduate School of Science Hiroshima University Higashi-Hiroshima Japan
| | - Hajime Akao
- Amphibian Research Center Graduate School of Science Hiroshima University Higashi-Hiroshima Japan
| | - Yuta Yoshimoto
- Amphibian Research Center Graduate School of Science Hiroshima University Higashi-Hiroshima Japan
| | - Fatchiyah Fatchiyah
- Department of Biology Faculty of Mathematics and Natural Sciences Brawijaya University Malang Indonesia
| | - Naoto Ueno
- Division of Morphogenesis National Institute for Basic Biology Okazaki Japan
| | - Atsushi Suzuki
- Amphibian Research Center Graduate School of Science Hiroshima University Higashi-Hiroshima Japan
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Takebayashi-Suzuki K, Konishi H, Miyamoto T, Nagata T, Uchida M, Suzuki A. Coordinated regulation of the dorsal-ventral and anterior-posterior patterning ofXenopusembryos by the BTB/POZ zinc finger protein Zbtb14. Dev Growth Differ 2018; 60:158-173. [DOI: 10.1111/dgd.12431] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/09/2018] [Accepted: 02/22/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Kimiko Takebayashi-Suzuki
- Amphibian Research Center; Graduate School of Science; Hiroshima University; Higashi-Hiroshima Japan
| | - Hidenori Konishi
- Amphibian Research Center; Graduate School of Science; Hiroshima University; Higashi-Hiroshima Japan
| | - Tatsuo Miyamoto
- Amphibian Research Center; Graduate School of Science; Hiroshima University; Higashi-Hiroshima Japan
| | - Tomoko Nagata
- Amphibian Research Center; Graduate School of Science; Hiroshima University; Higashi-Hiroshima Japan
| | - Misa Uchida
- Amphibian Research Center; Graduate School of Science; Hiroshima University; Higashi-Hiroshima Japan
| | - Atsushi Suzuki
- Amphibian Research Center; Graduate School of Science; Hiroshima University; Higashi-Hiroshima Japan
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Yin L, Guo X, Zhang C, Cai Z, Xu C. In silico analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat. Oncotarget 2018; 9:11794-11804. [PMID: 29545936 PMCID: PMC5837750 DOI: 10.18632/oncotarget.24370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 12/05/2017] [Indexed: 12/13/2022] Open
Abstract
The priming stage is the first step of liver regeneration (LR). This stage is characterized by the transition from G0 to cell cycle for 4 hours in rat. In this study, individual gene level and gene set level (GSEA) was performed to identify the candidate genes and significantly changed biological processes at 2 h after partial hepatectomy (PH). The leading edge analysis is performed to identify the key genes and iRegulon was employed for transcription factor (TF) analysis. A total of 53 differentially expressed genes were identified using RMA package based on R language at 2 h after PH, including the transcription factor, enzyme and cytokine. As the most important genes in our analysis, Socs3 was selected with a special analysis so as to find the pathways correlate to the expression of it. The changed significantly pathways in LR involved response to stress, ATP metabolism, and regulation of cell cycle mainly. Several transcription factors were identified including Stat5a, Cnot3 and zfp384. Taken together, at the early priming stage of LR in rat, the liver is experiencing some changes including response to stress, activated ATP metabolism and inhibition of cell cycle. Our analysis provided a detailed and comprehensive map for further research of the early priming stage of LR in rat.
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Affiliation(s)
- Li Yin
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, Henan Province, China.,Luohe Medical College, Luohe 462002, Henan Province, China
| | - Xueqiang Guo
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Chunyan Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Zhihui Cai
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.,Luohe Medical College, Luohe 462002, Henan Province, China
| | - Cunshuan Xu
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development, Henan Normal University, Xinxiang 453007, Henan Province, China
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