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Borg J, Loy C, Kim J, Buhagiar A, Chin C, Damle N, De Vlaminck I, Felice A, Liu T, Matei I, Meydan C, Muratani M, Mzava O, Overbey E, Ryon KA, Smith SM, Tierney BT, Trudel G, Zwart SR, Beheshti A, Mason CE, Borg J. Spatiotemporal expression and control of haemoglobin in space. Nat Commun 2024; 15:4927. [PMID: 38862545 PMCID: PMC11166948 DOI: 10.1038/s41467-024-49289-8] [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: 06/19/2023] [Accepted: 05/31/2024] [Indexed: 06/13/2024] Open
Abstract
It is now widely recognised that the environment in space activates a diverse set of genes involved in regulating fundamental cellular pathways. This includes the activation of genes associated with blood homoeostasis and erythropoiesis, with a particular emphasis on those involved in globin chain production. Haemoglobin biology provides an intriguing model for studying space omics, as it has been extensively explored at multiple -omic levels, spanning DNA, RNA, and protein analyses, in both experimental and clinical contexts. In this study, we examined the developmental expression of haemoglobin over time and space using a unique suite of multi-omic datasets available on NASA GeneLab, from the NASA Twins Study, the JAXA CFE study, and the Inspiration4 mission. Our findings reveal significant variations in globin gene expression corresponding to the distinct spatiotemporal characteristics of the collected samples. This study sheds light on the dynamic nature of globin gene regulation in response to the space environment and provides valuable insights into the broader implications of space omics research.
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Affiliation(s)
- Josef Borg
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta
| | - Conor Loy
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alfred Buhagiar
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta
| | - Christopher Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Iwijn De Vlaminck
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alex Felice
- Department of Surgery, Faculty of Medicine and Surgery, University of Malta, Msida, MSD2080, Malta
| | - Tammy Liu
- Ottawa Hospital Research Institute, Department of Medicine, Ottawa, Ontario, Canada
| | - Irina Matei
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Masafumi Muratani
- Department of Genome Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Omary Mzava
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Eliah Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Scott M Smith
- Biomedical Research and Environmental Sciences Division, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
| | - Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Guy Trudel
- Ottawa Hospital Research Institute, Department of Medicine, Ottawa, Ontario, Canada
| | - Sara R Zwart
- Biomedical Research and Environmental Sciences Division, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
- University of Texas Medical Branch, Galveston, TX, USA
| | - Afshin Beheshti
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Joseph Borg
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta.
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2
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Zhang B, Li W, Cao J, Zhou Y, Yuan X. Prohibitin 2: A key regulator of cell function. Life Sci 2024; 338:122371. [PMID: 38142736 DOI: 10.1016/j.lfs.2023.122371] [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: 10/17/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
The PHB2 gene is located on chromosome 12p13 and encodes prohibitin 2, a highly conserved protein of 37 kDa. PHB2 is a dimer with antiparallel coils, possessing a unique negatively charged region crucial for its mitochondrial molecular chaperone functions. Thus, PHB2 plays a significant role in cell life activities such as mitosis, mitochondrial autophagy, signal transduction, and cell death. This review discusses how PHB2 inhibits transcription factors or nuclear receptors to maintain normal cell functions; how PHB2 in the cytoplasm or membrane ensures normal cell mitosis and regulates cell differentiation; how PHB2 affects mitochondrial structure, function, and cell apoptosis through mitochondrial intimal integrity and mitochondrial autophagy; how PHB2 affects mitochondrial stress and inhibits cell apoptosis by regulating cytochrome c migration and other pathways; how PHB2 affects cell growth, proliferation, and metastasis through a mitochondrial independent mechanism; and how PHB2 could be applied in disease treatment. We provide a theoretical basis and an innovative perspective for a comprehensive understanding of the role and mechanism of PHB2 in cell function regulation.
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Affiliation(s)
- Bingjie Zhang
- Gastroenterology and Urology Department II, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China; Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, Hunan 410011, China
| | - Wentao Li
- Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, Hunan 410011, China
| | - Jiaying Cao
- Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, Hunan 410011, China
| | - Yanhong Zhou
- Cancer Research Institute, Basic School of Medicine, Central South University, Changsha, Hunan 410011, China.
| | - Xia Yuan
- Gastroenterology and Urology Department II, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China.
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3
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Choi S, Son SH, Kim MY, Na I, Uversky VN, Kim CG. Improved prediction of protein-protein interactions by a modified strategy using three conventional docking software in combination. Int J Biol Macromol 2023; 252:126526. [PMID: 37633550 DOI: 10.1016/j.ijbiomac.2023.126526] [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: 06/30/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Proteins play a crucial role in many biological processes, where their interaction with other proteins are integral. Abnormal protein-protein interactions (PPIs) have been linked to various diseases including cancer, and thus targeting PPIs holds promise for drug development. However, experimental confirmation of the peculiarities of PPIs is challenging due to their dynamic and transient nature. As a complement to experimental technologies, multiple computational molecular docking (MD) methods have been developed to predict the structures of protein-protein complexes and their dynamics, still requiring further improvements in several issues. Here, we report an improved MD method, namely three-software docking (3SD), by employing three popular protein-peptide docking software (CABS-dock, HPEPDOCK, and HADDOCK) in combination to ensure constant quality for most targets. We validated our 3SD performance in known protein-peptide interactions (PpIs). We also enhanced MD performance in proteins having intrinsically disordered regions (IDRs) by applying the modified 3SD strategy, the three-software docking after removing random coiled IDR (3SD-RR), to the comparable crystal PpI structures. At the end, we applied 3SD-RR to the AlphaFold2-predicted receptors, yielding an efficient prediction of PpI pose with high relevance to the experimental data regardless of the presence of IDRs or the availability of receptor structures. Our study provides an improved solution to the challenges in studying PPIs through computational docking and has the potential to contribute to PPIs-targeted drug discovery. SIGNIFICANCE STATEMENT: Protein-protein interactions (PPIs) are integral to life, and abnormal PPIs are associated with diseases such as cancer. Studying protein-peptide interactions (PpIs) is challenging due to their dynamic and transient nature. Here we developed improved docking methods (3SD and 3SD-RR) to predict the PpI poses, ensuring constant quality in most targets and also addressing issues like intrinsically disordered regions (IDRs) and artificial intelligence-predicted structures. Our study provides an improved solution to the challenges in studying PpIs through computational docking and has the potential to contribute to PPIs-targeted drug discovery.
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Affiliation(s)
- Sungwoo Choi
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Seung Han Son
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Min Young Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Insung Na
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida; Tampa, FL 33612, USA.
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; CGK Biopharma Co. Ltd., 222 Wangshipri-ro, Sungdong-gu, Seoul 04763, Republic of Korea.
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4
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Son SH, Kim MY, Choi S, Kim JS, Lee YS, Lee S, Lee YJ, Lee JY, Lee SE, Lim YS, Ha DH, Oh E, Won YB, Ji CJ, Park MA, Kim B, Byun KT, Chung MS, Jeong J, Choi D, Baek EJ, Cho EH, Kim SB, Je AR, Kweon HS, Park HS, Park D, Bae JS, Jang SJ, Yun CO, Chae JH, Lee JW, Lee SJ, Kim CG, Kang HC, Uversky VN, Kim CG. A Cell-Penetrant Peptide Disrupting the Transcription Factor CP2c Complexes Induces Cancer-Specific Synthetic Lethality. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2305096. [PMID: 37845006 PMCID: PMC10667816 DOI: 10.1002/advs.202305096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/23/2023] [Indexed: 10/18/2023]
Abstract
Despite advances in precision oncology, cancer remains a global public health issue. In this report, proof-of-principle evidence is presented that a cell-penetrable peptide (ACP52C) dissociates transcription factor CP2c complexes and induces apoptosis in most CP2c oncogene-addicted cancer cells through transcription activity-independent mechanisms. CP2cs dissociated from complexes directly interact with and degrade YY1, leading to apoptosis via the MDM2-p53 pathway. The liberated CP2cs also inhibit TDP2, causing intrinsic genome-wide DNA strand breaks and subsequent catastrophic DNA damage responses. These two mechanisms are independent of cancer driver mutations but are hindered by high MDM2 p60 expression. However, resistance to ACP52C mediated by MDM2 p60 can be sensitized by CASP2 inhibition. Additionally, derivatives of ACP52C conjugated with fatty acid alone or with a CASP2 inhibiting peptide show improved pharmacokinetics and reduced cancer burden, even in ACP52C-resistant cancers. This study enhances the understanding of ACP52C-induced cancer-specific apoptosis induction and supports the use of ACP52C in anticancer drug development.
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Affiliation(s)
- Seung Han Son
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Min Young Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Sungwoo Choi
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Ji Sook Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
- Department of Pathology, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Yong Sang Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Sangwon Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Yeon Ju Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jin Youn Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Seol Eui Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Young Su Lim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Dae Hyun Ha
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Eonju Oh
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Young-Bin Won
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Chang-Jun Ji
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Mi Ae Park
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Boram Kim
- Department of Biotechnology and Research Institute for Biomedical and Health Science, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, 27478, South Korea
| | - Kyu Tae Byun
- Department of Biotechnology and Research Institute for Biomedical and Health Science, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, 27478, South Korea
| | - Min Sung Chung
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Eun Jung Baek
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, 04763, South Korea
| | - Eung-Ho Cho
- Department of Surgery, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, South Korea
| | - Sang-Bum Kim
- Department of Surgery, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, South Korea
| | - A Reum Je
- Center for Research Equipment, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Hee-Seok Kweon
- Center for Research Equipment, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | | | - Dongsun Park
- Department of Biology Education, Korea National University of Education, Cheongju, Chungbuk, 29173, South Korea
| | - June Sung Bae
- Department of Research and Development, OncoClew Co. Ltd, Seoul, 04778, South Korea
| | - Se Jin Jang
- Department of Research and Development, OncoClew Co. Ltd, Seoul, 04778, South Korea
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, South Korea
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, 05505, South Korea
| | - Chae-Ok Yun
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Ji Hyung Chae
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Su-Jae Lee
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Chan Gil Kim
- Department of Biotechnology and Research Institute for Biomedical and Health Science, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk, 27478, South Korea
| | - Ho Chul Kang
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer`s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
- CGK Biopharma Co. Ltd., Seoul, 04763, South Korea
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5
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Structural and Functional Insights into CP2c Transcription Factor Complexes. Int J Mol Sci 2022; 23:ijms23126369. [PMID: 35742810 PMCID: PMC9223585 DOI: 10.3390/ijms23126369] [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: 05/09/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023] Open
Abstract
CP2c, also known as TFCP2, α-CP2, LSF, and LBP-1c, is a prototypic member of the transcription factor (TF) CP2 subfamily involved in diverse ubiquitous and tissue/stage-specific cellular processes and in human malignancies including cancer. Despite its importance, many fundamental regulatory mechanisms of CP2c are still unclear. Here, we uncover unprecedented structural and functional aspects of CP2c using DSP crosslinking and Western blot in addition to conventional methods. We found that a monomeric form of a CP2c homotetramer (tCP2c; [C4]) binds to the known CP2c-binding DNA motif (CNRG-N(5~6)-CNRG), whereas a dimeric form of a CP2c, CP2b, and PIAS1 heterohexamer ([C2B2P2]2) binds to the three consecutive CP2c half-sites or two staggered CP2c binding motifs, where the [C4] exerts a pioneering function for recruiting the [C2B2P2]2 to the target. All CP2c exists as a [C4], or as a [C2B2P2]2 or [C2B2P2]4 in the nucleus. Importantly, one additional cytosolic heterotetrameric CP2c and CP2a complex, ([C2A2]), exerts some homeostatic regulation of the nuclear complexes. These data indicate that these findings are essential for the transcriptional regulation of CP2c in cells within relevant timescales, providing clues not only for the transcriptional regulation mechanism by CP2c but also for future therapeutics targeting CP2c function.
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Zhang Q, Zhang Y, Zhang J, Zhang D, Li M, Yan H, Zhang H, Song L, Wang J, Hou Z, Yang Y, Zou X. p66α Suppresses Breast Cancer Cell Growth and Migration by Acting as Co-Activator of p53. Cells 2021; 10:3593. [PMID: 34944103 PMCID: PMC8700327 DOI: 10.3390/cells10123593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/03/2021] [Accepted: 12/16/2021] [Indexed: 01/31/2023] Open
Abstract
p66α is a GATA zinc finger domain-containing transcription factor that has been shown to be essential for gene silencing by participating in the NuRD complex. Several studies have suggested that p66α is a risk gene for a wide spectrum of diseases such as diabetes, schizophrenia, and breast cancer; however, its biological role has not been defined. Here, we report that p66α functions as a tumor suppressor to inhibit breast cancer cell growth and migration, evidenced by the fact that the depletion of p66α results in accelerated tumor growth and migration of breast cancer cells. Mechanistically, immunoprecipitation assays identify p66α as a p53-interacting protein that binds the DNA-binding domain of p53 molecule predominantly via its CR2 domain. Depletion of p66α in multiple breast cells results in decreased expression of p53 target genes, while over-expression of p66α results in increased expression of these target genes. Moreover, p66α promotes the transactivity of p53 by enhancing p53 binding at target promoters. Together, these findings demonstrate that p66α is a tumor suppressor by functioning as a co-activator of p53.
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Affiliation(s)
- Qun Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yihong Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Jie Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Dan Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Mengying Li
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Han Yan
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Hui Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Liwei Song
- Shanghai Pulmonary Tumor Medical Center, Shanghai Chest Hospital, Shanghai 200025, China;
- Naruiboen Biomedical Technology Corporation Limited, Linyi 277700, China
| | - Jiamin Wang
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Zhaoyuan Hou
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yunhai Yang
- Shanghai Pulmonary Tumor Medical Center, Shanghai Chest Hospital, Shanghai 200025, China;
| | - Xiuqun Zou
- Hongqiao International Institute of Medicine, Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; (Q.Z.); (Y.Z.); (J.Z.); (D.Z.); (M.L.); (H.Y.); (H.Z.); (J.W.); (Z.H.)
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry & Molecular Cellular Biology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
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7
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Cheon YP, Choi D, Lee SH, Kim CG. YY1 and CP2c in Unidirectional Spermatogenesis and Stemness. Dev Reprod 2021; 24:249-262. [PMID: 33537512 PMCID: PMC7837418 DOI: 10.12717/dr.2020.24.4.249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/21/2020] [Accepted: 12/29/2020] [Indexed: 11/17/2022]
Abstract
Spermatogonial stem cells (SSCs) have stemness characteristics, including germ cell-specific imprints that allow them to form gametes. Spermatogenesis involves changes in gene expression such as a transition from expression of somatic to germ cell-specific genes, global repression of gene expression, meiotic sex chromosome inactivation, highly condensed packing of the nucleus with protamines, and morphogenesis. These step-by-step processes finally generate spermatozoa that are fertilization competent. Dynamic epigenetic modifications also confer totipotency to germ cells after fertilization. Primordial germ cells (PGCs) in embryos do not enter meiosis, remain in the proliferative stage, and are referred to as gonocytes, before entering quiescence. Gonocytes develop into SSCs at about 6 days after birth in rodents. Although chromatin structural modification by Polycomb is essential for gene silencing in mammals, and epigenetic changes are critical in spermatogenesis, a comprehensive understanding of transcriptional regulation is lacking. Recently, we evaluated the expression profiles of Yin Yang 1 (YY1) and CP2c in the gonads of E14.5 and 12-week-old mice. YY1 localizes at the nucleus and/or cytoplasm at specific stages of spermatogenesis, possibly by interaction with CP2c and YY1-interacting transcription factor. In the present article, we discuss the possible roles of YY1 and CP2c in spermatogenesis and stemness based on our results and a review of the relevant literature.
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Affiliation(s)
- Yong-Pil Cheon
- Division of Developmental Biology and Physiology, Institute for Basic Sciences, Sungshin University, Seoul 02844, Korea
| | - Donchan Choi
- Department of Life Science, College of Environmental Sciences, Yong-In University, Yongin 17092, Korea
| | - Sung-Ho Lee
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
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8
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Regulating the Regulators: The Role of Histone Deacetylase 1 (HDAC1) in Erythropoiesis. Int J Mol Sci 2020; 21:ijms21228460. [PMID: 33187090 PMCID: PMC7696854 DOI: 10.3390/ijms21228460] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in transcriptional regulation in eukaryotic cells. Class I deacetylase HDAC1/2 often associates with repressor complexes, such as Sin3 (Switch Independent 3), NuRD (Nucleosome remodeling and deacetylase) and CoREST (Corepressor of RE1 silencing transcription factor) complexes. It has been shown that HDAC1 interacts with and modulates all essential transcription factors for erythropoiesis. During erythropoiesis, histone deacetylase activity is dramatically reduced. Consistently, inhibition of HDAC activity promotes erythroid differentiation. The reduction of HDAC activity not only results in the activation of transcription activators such as GATA-1 (GATA-binding factor 1), TAL1 (TAL BHLH Transcription Factor 1) and KLF1 (Krüpple-like factor 1), but also represses transcription repressors such as PU.1 (Putative oncogene Spi-1). The reduction of histone deacetylase activity is mainly through HDAC1 acetylation that attenuates HDAC1 activity and trans-repress HDAC2 activity through dimerization with HDAC1. Therefore, the acetylation of HDAC1 can convert the corepressor complex to an activator complex for gene activation. HDAC1 also can deacetylate non-histone proteins that play a role on erythropoiesis, therefore adds another layer of gene regulation through HDAC1. Clinically, it has been shown HDACi can reactivate fetal globin in adult erythroid cells. This review will cover the up to date research on the role of HDAC1 in modulating key transcription factors for erythropoiesis and its clinical relevance.
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MMTR/Dmap1 Sets the Stage for Early Lineage Commitment of Embryonic Stem Cells by Crosstalk with PcG Proteins. Cells 2020; 9:cells9051190. [PMID: 32403252 PMCID: PMC7290897 DOI: 10.3390/cells9051190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/05/2020] [Accepted: 05/08/2020] [Indexed: 01/13/2023] Open
Abstract
Chromatin remodeling, including histone modification, chromatin (un)folding, and nucleosome remodeling, is a significant transcriptional regulation mechanism. By these epigenetic modifications, transcription factors and their regulators are recruited to the promoters of target genes, and thus gene expression is controlled through either transcriptional activation or repression. The Mat1-mediated transcriptional repressor (MMTR)/DNA methyltransferase 1 (DNMT1)-associated protein (Dmap1) is a transcription corepressor involved in chromatin remodeling, cell cycle regulation, DNA double-strand break repair, and tumor suppression. The Tip60-p400 complex proteins, including MMTR/Dmap1, interact with the oncogene Myc in embryonic stem cells (ESCs). These proteins interplay with the stem cell-related proteome networks and regulate gene expressions. However, the detailed mechanisms of their functions are unknown. Here, we show that MMTR/Dmap1, along with other Tip60-p400 complex proteins, bind the promoters of differentiation commitment genes in mouse ESCs. Hence, MMTR/Dmap1 controls gene expression alterations during differentiation. Furthermore, we propose a novel mechanism of MMTR/Dmap1 function in early stage lineage commitment of mouse ESCs by crosstalk with the polycomb group (PcG) proteins. The complex controls histone mark bivalency and transcriptional poising of commitment genes. Taken together, our comprehensive findings will help better understand the MMTR/Dmap1-mediated transcriptional regulation in ESCs and other cell types.
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Kim MY, Na I, Kim JS, Son SH, Choi S, Lee SE, Kim JH, Jang K, Alterovitz G, Chen Y, van der Vaart A, Won HS, Uversky VN, Kim CG. Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2. SCIENCE ADVANCES 2019; 5:eaav9810. [PMID: 31799386 PMCID: PMC6867884 DOI: 10.1126/sciadv.aav9810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Although intrinsically disordered protein regions (IDPRs) are commonly engaged in promiscuous protein-protein interactions (PPIs), using them as drug targets is challenging due to their extreme structural flexibility. We report a rational discovery of inhibitors targeting an IDPR of MBD2 that undergoes disorder-to-order transition upon PPI and is critical for the regulation of the Mi-2/NuRD chromatin remodeling complex (CRC). Computational biology was essential for identifying target site, searching for promising leads, and assessing their binding feasibility and off-target probability. Molecular action of selected leads inhibiting the targeted PPI of MBD2 was validated in vitro and in cell, followed by confirming their inhibitory effects on the epithelial-mesenchymal transition of various cancer cells. Identified lead compounds appeared to potently inhibit cancer metastasis in a murine xenograft tumor model. These results constitute a pioneering example of rationally discovered IDPR-targeting agents and suggest Mi-2/NuRD CRC and/or MBD2 as a promising target for treating cancer metastasis.
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Affiliation(s)
- Min Young Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Insung Na
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ji Sook Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Department of Pathology, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Seung Han Son
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Sungwoo Choi
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Seol Eui Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 28160, Korea
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Gil Alterovitz
- Boston Children's Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Hyung-Sik Won
- Department of Biotechnology, Konkuk University, Chungju, Chungbuk 27478, Korea
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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Kim MY, Choi S, Lee SE, Kim JS, Son SH, Lim YS, Kim BJ, Ryu BY, Uversky VN, Lee YJ, Kim CG. Development of a MEL Cell-Derived Allograft Mouse Model for Cancer Research. Cancers (Basel) 2019; 11:cancers11111707. [PMID: 31683958 PMCID: PMC6895914 DOI: 10.3390/cancers11111707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/26/2019] [Accepted: 10/30/2019] [Indexed: 11/22/2022] Open
Abstract
Murine erythroleukemia (MEL) cells are often employed as a model to dissect mechanisms of erythropoiesis and erythroleukemia in vitro. Here, an allograft model using MEL cells resulting in splenomegaly was established to develop a diagnostic model for isolation/quantification of metastatic cells, anti-cancer drug screening, and evaluation of the tumorigenic or metastatic potentials of molecules in vivo. In this animal model, circulating MEL cells from the blood stream were successfully isolated and quantified with an additional in vitro cultivation step. In terms of the molecular-pathological analysis, we were able to successfully evaluate the functional discrimination between methyl-CpG-binding domain 2 (Mbd2) and p66α in erythroid differentiation, and tumorigenic potential in spleen and blood stream of allograft model mice. In addition, we found that the number of circulating MEL cells in anti-cancer drug-treated mice was dose-dependently decreased. Our data demonstrate that the newly established allograft model is useful to dissect erythroleukemia pathologies and non-invasively provides valuable means for isolation of metastatic cells, screening of anti-cancer drugs, and evaluation of the tumorigenic potentials.
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Affiliation(s)
- Min Young Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Sungwoo Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Seol Eui Lee
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Ji Sook Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.
- Department of Clinical Pathology, Hanyang University Seoul Hospital, Seoul 04763, Korea.
| | - Seung Han Son
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Young Soo Lim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Bang-Jin Kim
- Department of Animal Science & Technology, Chung-Ang University, Ansung, Gyeonggi-do 17546, Korea.
| | - Buom-Yong Ryu
- Department of Animal Science & Technology, Chung-Ang University, Ansung, Gyeonggi-do 17546, Korea.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Moscow Region, Russia.
| | - Young Jin Lee
- Institute of Pharmaceutical Science and Technology, Department of Pharmacy, Hanyang University, Ansan, Gyeonggi-do 15588, Korea.
| | - Chul Geun Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea.
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King AJ, Higgs DR. Potential new approaches to the management of the Hb Bart's hydrops fetalis syndrome: the most severe form of α-thalassemia. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2018; 2018:353-360. [PMID: 30504332 PMCID: PMC6246003 DOI: 10.1182/asheducation-2018.1.353] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The α-thalassemia trait, associated with deletions removing both α-globin genes from 1 chromosome (genotype ζ αα/ζ--), is common throughout Southeast Asia. Consequently, many pregnancies in couples of Southeast Asian origin carry a 1 in 4 risk of producing a fetus inheriting no functional α-globin genes (ζ--/ζ--), leading to hemoglobin (Hb) Bart's hydrops fetalis syndrome (BHFS). Expression of the embryonic α-globin genes (ζ-globin) is normally limited to the early stages of primitive erythropoiesis, and so when the ζ-globin genes are silenced, at ∼6 weeks of gestation, there should be no α-like globin chains to pair with the fetal γ-globin chains of Hb, which consequently form nonfunctional tetramers (γ4) known as Hb Bart's. When deletions leave the ζ-globin gene intact, a low level of ζ-globin gene expression continues in definitive erythroid cells, producing small amounts of Hb Portland (ζ2γ2), a functional form of Hb that allows the fetus to survive up to the second or third trimester. Untreated, all affected individuals die at these stages of development. Prevention is therefore of paramount importance. With improvements in early diagnosis, intrauterine transfusion, and advanced perinatal care, there are now a small number of individuals with BHFS who have survived, with variable outcomes. A deeper understanding of the mechanism underlying the switch from ζ- to α-globin expression could enable persistence or reactivation of embryonic globin synthesis in definitive cells, thereby providing new therapeutic options for such patients.
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Affiliation(s)
- Andrew J King
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Douglas R Higgs
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
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