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Nussinov R, Yavuz BR, Jang H. Single cell spatial biology over developmental time can decipher pediatric brain pathologies. Neurobiol Dis 2024; 199:106597. [PMID: 38992777 DOI: 10.1016/j.nbd.2024.106597] [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: 03/27/2024] [Revised: 06/18/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024] Open
Abstract
Pediatric low grade brain tumors and neurodevelopmental disorders share proteins, signaling pathways, and networks. They also share germline mutations and an impaired prenatal differentiation origin. They may differ in the timing of the events and proliferation. We suggest that their pivotal distinct, albeit partially overlapping, outcomes relate to the cell states, which depend on their spatial location, and timing of gene expression during brain development. These attributes are crucial as the brain develops sequentially, and single-cell spatial organization influences cell state, thus function. Our underlying premise is that the root cause in neurodevelopmental disorders and pediatric tumors is impaired prenatal differentiation. Data related to pediatric brain tumors, neurodevelopmental disorders, brain cell (sub)types, locations, and timing of expression in the developing brain are scant. However, emerging single cell technologies, including transcriptomic, spatial biology, spatial high-resolution imaging performed over the brain developmental time, could be transformational in deciphering brain pathologies thereby pharmacology.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Bengi Ruken Yavuz
- Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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2
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Chiew MY, Wang E, Lan KC, Lin YR, Hsueh YH, Tu YK, Liu CF, Chen PC, Lu HE, Chen WL. Improving iPSC Differentiation Using a Nanodot Platform. ACS APPLIED MATERIALS & INTERFACES 2024; 16:36030-36046. [PMID: 38951110 PMCID: PMC11261571 DOI: 10.1021/acsami.4c04451] [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: 03/18/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]
Abstract
Differentiation of induced pluripotent stem cells (iPSCs) is an extremely complex process that has proven difficult to study. In this research, we utilized nanotopography to elucidate details regarding iPSC differentiation by developing a nanodot platform consisting of nanodot arrays of increasing diameter. Subjecting iPSCs cultured on the nanodot platform to a cardiomyocyte (CM) differentiation protocol revealed several significant gene expression profiles that were associated with poor differentiation. The observed expression trends were used to select existing small-molecule drugs capable of modulating differentiation efficiency. BRD K98 was repurposed to inhibit CM differentiation, while iPSCs treated with NSC-663284, carmofur, and KPT-330 all exhibited significant increases in not only CM marker expression but also spontaneous beating, suggesting improved CM differentiation. In addition, quantitative polymerase chain reaction was performed to determine the gene regulation responsible for modulating differentiation efficiency. Multiple genes involved in extracellular matrix remodeling were correlated with a CM differentiation efficiency, while genes involved in the cell cycle exhibited contrasting expression trends that warrant further studies. The results suggest that expression profiles determined via short time-series expression miner analysis of nanodot-cultured iPSC differentiation can not only reveal drugs capable of enhancing differentiation efficiency but also highlight crucial sets of genes related to processes such as extracellular matrix remodeling and the cell cycle that can be targeted for further investigation. Our findings confirm that the nanodot platform can be used to reveal complex mechanisms behind iPSC differentiation and could be an indispensable tool for optimizing iPSC technology for clinical applications.
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Affiliation(s)
- Men Yee Chiew
- Center
for Regenerative Medicine and Cellular Therapy, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan, ROC
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 300, Taiwan, ROC
| | - Erick Wang
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 300, Taiwan, ROC
- College
of Biological Science and Technology Industrial Ph. D. Program, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan, ROC
| | - Kuan-Chun Lan
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8397, Japan
| | - Yan-Ren Lin
- Department
of Emergency and Critical Care Medicine, Changhua Christian Hospital, Changhua 500, Taiwan, ROC
- Department
of Post Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan, ROC
- School
of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, ROC
- School
of Medicine, Chung Shan Medical University, Taichung 402, Taiwan, ROC
| | - Yu-Huan Hsueh
- College
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 300, Taiwan, ROC
- Department
of Orthopedic Surgery, E-Da Hospital, I-Shou
University, Kaohsiung 824, Taiwan
| | - Yuan-Kun Tu
- Department
of Orthopedic Surgery, E-Da Hospital, I-Shou
University, Kaohsiung 824, Taiwan
| | - Chu-Feng Liu
- Emergency Medicine Department, Kaohsiung
Chang Gung Memorial Hospital, Kaohsiung, 833, Taiwan,
ROC
- Ph. D. Degree Program of Biomedical Science
and Engineering, National Yang Ming Chiao
Tung University, Hsinchu 300, Taiwan, ROC
| | - Po-Chun Chen
- Institute of Materials Science and Engineering, National Taipei University of Technology, Taipei 106, Taiwan, ROC
| | - Huai-En Lu
- Center
for Regenerative Medicine and Cellular Therapy, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan, ROC
- Institute of Biochemistry and Molecular
Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan, ROC
- Bioresource
Collection and Research Center, Food Industry Research
and Development Institute, Hsinchu
City 300, Taiwan, ROC
| | - Wen Liang Chen
- Center
for Regenerative Medicine and Cellular Therapy, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan, ROC
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 300, Taiwan, ROC
- College
of Biological Science and Technology Industrial Ph. D. Program, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan, ROC
- Bioresource
Collection and Research Center, Food Industry Research
and Development Institute, Hsinchu
City 300, Taiwan, ROC
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Nussinov R, Yavuz BR, Demirel HC, Arici MK, Jang H, Tuncbag N. Review: Cancer and neurodevelopmental disorders: multi-scale reasoning and computational guide. Front Cell Dev Biol 2024; 12:1376639. [PMID: 39015651 PMCID: PMC11249571 DOI: 10.3389/fcell.2024.1376639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
The connection and causality between cancer and neurodevelopmental disorders have been puzzling. How can the same cellular pathways, proteins, and mutations lead to pathologies with vastly different clinical presentations? And why do individuals with neurodevelopmental disorders, such as autism and schizophrenia, face higher chances of cancer emerging throughout their lifetime? Our broad review emphasizes the multi-scale aspect of this type of reasoning. As these examples demonstrate, rather than focusing on a specific organ system or disease, we aim at the new understanding that can be gained. Within this framework, our review calls attention to computational strategies which can be powerful in discovering connections, causalities, predicting clinical outcomes, and are vital for drug discovery. Thus, rather than centering on the clinical features, we draw on the rapidly increasing data on the molecular level, including mutations, isoforms, three-dimensional structures, and expression levels of the respective disease-associated genes. Their integrated analysis, together with chromatin states, can delineate how, despite being connected, neurodevelopmental disorders and cancer differ, and how the same mutations can lead to different clinical symptoms. Here, we seek to uncover the emerging connection between cancer, including pediatric tumors, and neurodevelopmental disorders, and the tantalizing questions that this connection raises.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Bengi Ruken Yavuz
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
| | | | - M. Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara, Türkiye
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Nurcan Tuncbag
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Türkiye
- School of Medicine, Koc University, Istanbul, Türkiye
- Koc University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
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Zhang L, Kwack KH, Thiyagarajan R, Mullaney KK, Lamb NA, Bard JE, Sohn J, Seldeen KL, Arao Y, Blackshear PJ, Abrams SI, Troen BR, Kirkwood KL. Tristetraprolin regulates the skeletal phenotype and osteoclastogenic potential through monocytic myeloid-derived suppressor cells. FASEB J 2024; 38:e23338. [PMID: 38038723 PMCID: PMC11128769 DOI: 10.1096/fj.202301703r] [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: 08/23/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023]
Abstract
Tristetraprolin (TTP; also known as NUP475, GOS24, or TIS11), encoded by Zfp36, is an RNA-binding protein that regulates target gene expression by promoting mRNA decay and preventing translation. Although previous studies have indicated that TTP deficiency is associated with systemic inflammation and a catabolic-like skeletal phenotype, the mechanistic underpinnings remain unclear. Here, using both TTP-deficient (TTPKO) and myeloid-specific TTPKO (cTTPKO) mice, we reveal that global absence or loss of TTP in the myeloid compartment results in a reduced bone microarchitecture, whereas gain-of-function TTP knock-in (TTPKI) mice exhibit no significant loss of bone microarchitecture. Flow cytometry analysis revealed a significant immunosuppressive immune cell phenotype with increased monocytic myeloid-derived suppressor cells (M-MDSCs) in TTPKO and cTTPKO mice, whereas no significant changes were observed in TTPKI mice. Single-cell transcriptomic analyses of bone marrow myeloid progenitor cell populations indicated a dramatic increase in early MDSC marker genes for both cTTPKO and TTPKO bone marrow populations. Consistent with these phenotypic and transcriptomic data, in vitro osteoclastogenesis analysis of bone marrow M-MDSCs from cTTPKO and TTPKO displayed enhanced osteoclast differentiation and functional capacity. Focused transcriptomic analyses of differentiated M-MDSCs showed increased osteoclast-specific transcription factors and cell fusion gene expression. Finally, functional data showed that M-MDSCs from TTP loss-of-function mice were capable of osteoclastogenesis and bone resorption in a context-dependent manner. Collectively, these findings indicate that TTP plays a central role in regulating osteoclastogenesis through multiple mechanisms, including induction of M-MDSCs that appear to regulate skeletal phenotype.
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Affiliation(s)
| | - Kyu Hwan Kwack
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul, Republic of Korea
| | - Ramkumar Thiyagarajan
- Departments of Medicine, University at Buffalo, Buffalo, NY, USA
- Division of Geriatrics and Palliative Medicine, University at Buffalo, Buffalo, NY, USA
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, USA
| | - Kylie K. Mullaney
- Departments of Oral Biology, University at Buffalo, Buffalo, NY, USA
| | - Natalie A. Lamb
- Departments of Biochemistry, University at Buffalo, Buffalo, NY, USA
- Genomics and Bioinformatics Core, New York State Center of Excellence for Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Jonathan E. Bard
- Departments of Biochemistry, University at Buffalo, Buffalo, NY, USA
- Genomics and Bioinformatics Core, New York State Center of Excellence for Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Jiho Sohn
- Departments of Oral Biology, University at Buffalo, Buffalo, NY, USA
- Departments of Medicine, University at Buffalo, Buffalo, NY, USA
| | - Kenneth L. Seldeen
- Departments of Medicine, University at Buffalo, Buffalo, NY, USA
- Division of Geriatrics and Palliative Medicine, University at Buffalo, Buffalo, NY, USA
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, USA
| | - Yukitomo Arao
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Perry J. Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Departments of Biochemistry & Medicine, Duke University Medical Center, Durham, NC, USA
| | - Scott I. Abrams
- Departments of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Bruce R. Troen
- Departments of Medicine, University at Buffalo, Buffalo, NY, USA
- Departments of Biochemistry, University at Buffalo, Buffalo, NY, USA
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, USA
| | - Keith L. Kirkwood
- Departments of Oral Biology, University at Buffalo, Buffalo, NY, USA
- Head & Neck/Plastic & Reconstructive Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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Devilée LA, Miller JM, Reid JD, Salama ABM, Ou Q, Jamal M, Nong Y, Andres D, Satin J, Mohamed TMA, Hudson JE, Abouleisa RRE. Pharmacological or genetic inhibition of LTCC promotes cardiomyocyte proliferation through inhibition of calcineurin activity. RESEARCH SQUARE 2023:rs.3.rs-3552794. [PMID: 38076903 PMCID: PMC10705701 DOI: 10.21203/rs.3.rs-3552794/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Cardiomyocytes (CMs) lost during ischemic cardiac injury cannot be replaced due to their limited proliferative capacity, which leads to progressive heart failure. Calcium (Ca2+) is an important signal transducer that regulates key cellular processes, but its role in regulating CM proliferation is incompletely understood. A drug screen targeting proteins involved in CM calcium cycling in human embryonic stem cell-derived cardiac organoids (hCOs) revealed that only the inhibition of L-Type Calcium Channel (LTCC), but not other Ca2+ regulatory proteins (SERCA or RYR), induced the CM cell cycle. Furthermore, overexpression of Ras-related associated with Diabetes (RRAD), an endogenous inhibitor of LTCC, induced CM cell cycle activity in vitro, in human cardiac slices, and in vivo. Mechanistically, LTCC inhibition by RRAD induces the cell cycle in CMs by modulating calcineurin activity and translocating Hoxb13 to the CM nucleus. Together, this represents a robust pathway for regenerative strategies.
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Affiliation(s)
- Lynn A.C. Devilée
- QIMR Berghofer Medical Research Institute, Cardiac Bioengineering Laboratory, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jessica M. Miller
- Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY, U.S.A
- Surgery Department, Baylor College of Medicine, Houston, TX, U.S.A
| | - Janice D. Reid
- QIMR Berghofer Medical Research Institute, Cardiac Bioengineering Laboratory, Brisbane, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Abou Bakr M. Salama
- Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY, U.S.A
- Surgery Department, Baylor College of Medicine, Houston, TX, U.S.A
- Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Qinghui Ou
- Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY, U.S.A
| | - Madiha Jamal
- Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY, U.S.A
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Yibing Nong
- Center for Cardiometabolic Science, Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, KY, U.S.A
| | - Douglas Andres
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, U.S.A
| | - Jonathan Satin
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, U.S.A
| | - Tamer M. A. Mohamed
- Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY, U.S.A
- Surgery Department, Baylor College of Medicine, Houston, TX, U.S.A
| | - James E. Hudson
- QIMR Berghofer Medical Research Institute, Cardiac Bioengineering Laboratory, Brisbane, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Riham R. E. Abouleisa
- Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY, U.S.A
- Surgery Department, Baylor College of Medicine, Houston, TX, U.S.A
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Zion E, Chen X. Studying histone inheritance in different systems using imaging-based methods and perspectives. Biochem Soc Trans 2023; 51:1035-1046. [PMID: 37171077 PMCID: PMC10317187 DOI: 10.1042/bst20220983] [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: 03/07/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/13/2023]
Abstract
Understanding cell identity is critically important in the fields of cell and developmental biology. During cell division, a mother cell duplicates the genetic material and cellular components to give rise to two daughter cells. While both cells receive the same genetic information, they can take on similar or different cell fates, resulting from a symmetric or asymmetric division. These fates can be modulated by epigenetic mechanisms that can alter gene expression without changing genetic information. Histone proteins, which wrap DNA into fundamental units of chromatin, are major carriers of epigenetic information and can directly influence gene expression and other cellular functions through their interactions with DNA. While it has been well studied how the genetic information is duplicated and segregated, how epigenetic information, such as histones, are inherited through cell division is still an area of investigation. Since canonical histone proteins are incorporated into chromatin during DNA replication and can be modified over time, it is important to study their inheritance within the context of the cell cycle. Here, we outline the biological basis of histone inheritance as well as the imaging-based experimental design that can be used to study this process. Furthermore, we discuss various studies that have investigated this phenomenon with the focus on asymmetrically dividing cells in different systems. This synopsis provides insight into histone inheritance within the context of the cell cycle, along with the technical methods and considerations that must be taken when studying this process in vivo.
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Affiliation(s)
- Emily Zion
- Department of Biology, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, U.S.A
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, U.S.A
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, U.S.A
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Nussinov R, Yavuz BR, Arici MK, Demirel HC, Zhang M, Liu Y, Tsai CJ, Jang H, Tuncbag N. Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK. Biophys Rev 2023; 15:163-181. [PMID: 37124926 PMCID: PMC10133437 DOI: 10.1007/s12551-023-01054-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
AbstractNeurodevelopmental disorders (NDDs) and cancer share proteins, pathways, and mutations. Their clinical symptoms are different. However, individuals with NDDs have higher probabilities of eventually developing cancer. Here, we review the literature and ask how the shared features can lead to different medical conditions and why having an NDD first can increase the chances of malignancy. To explore these vital questions, we focus on dysregulated PI3K/mTOR, a major brain cell growth pathway in differentiation, and MAPK, a critical pathway in proliferation, a hallmark of cancer. Differentiation is governed by chromatin organization, making aberrant chromatin remodelers highly likely agents in NDDs. Dysregulated chromatin organization and accessibility influence the lineage of specific cell brain types at specific embryonic development stages. PAK1, with pivotal roles in brain development and in cancer, also regulates MAPK. We review, clarify, and connect dysregulated pathways with dysregulated proliferation and differentiation in cancer and NDDs and highlight PAK1 role in brain development and MAPK regulation. Exactly how PAK1 activation controls brain development, and why specific chromatin remodeler components, e.g., BAF170 encoded by SMARCC2 in autism, await clarification.
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Bayraktar M, Durmuş M, Al-Shuhaib MBS. Identification of two novel SNPs in the myocyte enhancer factor 2B (MEF2B) gene and its association with growth traits in two breeds of Turkish sheep. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Promoting Immortalized Adipose-Derived Stem Cell Transdifferentiation and Proliferation into Neuronal-Like Cells through Consecutive 525 nm and 825 nm Photobiomodulation. Stem Cells Int 2022; 2022:2744789. [PMID: 36106176 PMCID: PMC9467736 DOI: 10.1155/2022/2744789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Neuronal cells can be generated from adipose-derived stem cells (ADSCs) through biological or chemical inducers. Research has shown that this process may be optimized by the introduction of laser irradiation in the form of photobiomodulation (PBM) to cells. This in vitro study is aimed at generating neuronal-like cells with inducers, chemical or biological, and at furthermore treating these transdifferentiating cells with consecutive PBM of a 525 nm green (G) laser and 825 nm near-infrared (NIR) laser light with a fluence of 10 J/cm2. Cells were exposed to induction type 1 (IT1): 3-isobutyl-1-methylxanthine (IBMX) (0.5 mM)+indomethacin (200 μM)+insulin (5 μg/ml) for 14 days, preinduced with β-mercaptoethanol (BME) (1 mM) for two days, and then incubated with IT2: β-hydroxyanisole (BHA) (100 μM)+retinoic acid (RA) (10-6 M)+epidermal growth factor (EGF) (10 ng/ml)+basic fibroblast growth factor (bFGF) (10 ng/ml) for 14 days and preinduced with β-mercaptoethanol (BME) (1 mM) for two days and then incubated with indomethacin (200 μM)+RA (1 μM)+forskolin (10 μM) for 14 days. The results were evaluated through morphological observations, viability, proliferation, and migration studies, 24 h, 48 h, and 7 days post-PBM. The protein detection of an early neuronal marker, neuron-specific enolase (NSE), and late, ciliary neurotrophic factor (CNTF), was determined with enzyme-linked immunosorbent assays (ELISAs). The genetic expression was also explored through real-time PCR. Results indicated differentiation in all experimental groups; however, cells that were preinduced showed higher proliferation and a higher differentiation rate than the group that was not preinduced. Within the preinduced groups, results indicated that cells treated with IT2 and consecutive PBM upregulated differentiation the most morphologically and physiologically.
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Supervised dimensionality reduction for exploration of single-cell data by HSS-LDA. PATTERNS 2022; 3:100536. [PMID: 36033591 PMCID: PMC9403402 DOI: 10.1016/j.patter.2022.100536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/01/2022] [Accepted: 06/03/2022] [Indexed: 01/23/2023]
Abstract
Single-cell technologies generate large, high-dimensional datasets encompassing a diversity of omics. Dimensionality reduction captures the structure and heterogeneity of the original dataset, creating low-dimensional visualizations that contribute to the human understanding of data. Existing algorithms are typically unsupervised, using measured features to generate manifolds, disregarding known biological labels such as cell type or experimental time point. We repurpose the classification algorithm, linear discriminant analysis (LDA), for supervised dimensionality reduction of single-cell data. LDA identifies linear combinations of predictors that optimally separate a priori classes, enabling the study of specific aspects of cellular heterogeneity. We implement feature selection by hybrid subset selection (HSS) and demonstrate that this computationally efficient approach generates non-stochastic, interpretable axes amenable to diverse biological processes such as differentiation over time and cell cycle. We benchmark HSS-LDA against several popular dimensionality-reduction algorithms and illustrate its utility and versatility for the exploration of single-cell mass cytometry, transcriptomics, and chromatin accessibility data.
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Ayaz G, Yan H, Malik N, Huang J. An Updated View of the Roles of p53 in Embryonic Stem Cells. Stem Cells 2022; 40:883-891. [PMID: 35904997 PMCID: PMC9585900 DOI: 10.1093/stmcls/sxac051] [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: 01/26/2022] [Accepted: 07/14/2022] [Indexed: 11/12/2022]
Abstract
The TP53 gene is unarguably one of the most studied human genes. Its encoded protein, p53, is a tumor suppressor and is often called the "guardian of the genome" due to its pivotal role in maintaining genome stability. Historically, most studies of p53 have focused on its roles in somatic cells and tissues, but in the last two decades, its functions in embryonic stem cells (ESCs) and induced pluripotent stem cells have attracted increasing attention. Recent studies have identified p53 as a critical regulator of pluripotency, self-renewal, differentiation, proliferation, and genome stability in mouse and human embryonic stem cells. In this article, we systematically review the studies on the functions of p53 in ESCs, provide an updated overview, attempt to reconcile controversial results described in the literature, and discuss the relevance of these cellular functions of p53 to its roles in tumor suppression.
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Affiliation(s)
- Gamze Ayaz
- Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hualong Yan
- Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Navdeep Malik
- Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jing Huang
- Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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12
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An S, Yao D, Zhang W, Sun H, Yu T, Jia R, Yang Y. WDR36 Safeguards Self-Renewal and Pluripotency of Human Extended Pluripotent Stem Cells. Front Genet 2022; 13:905395. [PMID: 35937980 PMCID: PMC9353684 DOI: 10.3389/fgene.2022.905395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Extended pluripotent stem cells (EPS cells) have unlimited self-renewal ability and the potential to differentiate into mesodermal, ectodermal, and endodermal cells. Notably, in addition to developing the embryonic (Em) lineages, it can also make an effective contribution to extraembryonic (ExEm) lineages both in vitro and in vivo. However, multiple mysteries still remain about the underlying molecular mechanism of EPS cells’ maintenance and developmental potential. WDR36 (WD Repeat Domain 36), a protein of 105 kDa with 14 WD40 repeats, which may fold into two β-propellers, participates in 18sRNA synthesis and P53 stress response. Though WDR36 safeguards mouse early embryonic development, that is, homozygous knockout of WDR36 can result in embryonic lethality, what role does WDR36 plays in self-renewal and differentiation developmental potential of human EPS cells is still a subject of concern. Here, our findings suggested that the expression of WDR36 was downregulated during human hEPS cells lost self-renewal. Through constructing inducible knockdown or overexpressing WDR36-human EPS cell lines, we found that WDR36 knockdown disrupted self-renewal but promoted the mesodermal differentiation of human EPS cells; however, overexpressing of WDR36 had little effect. Additionally, P53 inhibition could reverse the effects of WDR36 knockdown, on both self-renewal maintenance and differentiation potential of human EPS cells. These data implied that WDR36 safeguards self-renewal and pluripotency of human EPS cells, which would extend our understanding of the molecular mechanisms of human EPS cells’ self-renewal and differentiation.
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Affiliation(s)
- Shiyu An
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Dan Yao
- Department of Obstetrics, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Institute, Nanjing, China
- Fourth Clinical Medicine College, Nanjing Medical University, Nanjing, China
| | - Wenyi Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Hao Sun
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Tianyi Yu
- Department of Gynecology and Obstetrics, Affiliated Zhongda Hospital, Medical School, Southeast University, Nanjing, China
| | - Ruizhe Jia
- Department of Obstetrics, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Institute, Nanjing, China
- *Correspondence: Yang Yang, ; Ruizhe Jia,
| | - Yang Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Yang Yang, ; Ruizhe Jia,
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13
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Basic Fibroblast Growth Factor Induces Cholinergic Differentiation of Tonsil-Derived Mesenchymal Stem Cells. Tissue Eng Regen Med 2022; 19:1063-1075. [PMID: 35857260 DOI: 10.1007/s13770-022-00474-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022] Open
Abstract
BACKGROUND Mesenchymal stem cells (MSCs) are considered a potential tool for regenerating damaged tissues due to their great multipotency into various cell types. Here, we attempted to find the appropriate conditions for neuronal differentiation of tonsil-derived MSCs (TMSCs) and expand the potential application of TMSCs for treating neurological diseases. METHODS The TMSCs were differentiated in DMEM/F-12 (Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12) supplemented with various neurotrophic factors for 7-28 days to determine the optimal neuronal differentiation condition for the TMSCs. The morphologies as well as the levels of the neural markers and neurotransmitters were assessed to determine neuronal differentiation potentials and the neuronal lineages of the differentiated TMSCs. RESULTS Our initial study demonstrated that DMEM/F12 supplemented with 50 ng/mL basic fibroblast growth factor with 10 μM forskolin was the optimal condition for neuronal differentiation for the TMSCs. TMSCs had higher protein expression of neuronal markers, including neuron-specific enolase (NSE), GAP43, postsynaptic density protein 95 (PSD95), and synaptosomal-associated protein of 25 kDa (SNAP25) compared to the undifferentiated TMSCs. Immunofluorescence staining also validated the increased mature neuron markers, NeuN and synaptophysin, in the differentiated TMSCs. The expression of glial fibrillar acidic protein and ionized calcium-binding adaptor molecule 1 the markers of astrocytes and microglia, were also slightly increased. Additionally, the differentiated TMSCs released a significantly higher level of acetylcholine, the cholinergic neurotransmitter, as analyzed by the liquid chromatography-tandem mass spectrometry and showed an enhanced choline acetyltransferase immunoreactivity compared to the undifferentiated cells. CONCLUSION Our study suggests that the optimized condition favors the TMSCs to differentiate into cholinergic neuron-like phenotype, which could be used as a possible therapeutic tool in treating certain neurological disorders such as Alzheimer's disease.
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14
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Timilsina S, Kirsch-Mangu T, Werth S, Shepard B, Ma T, Villa-Diaz LG. Enhanced self-renewal of human pluripotent stem cells by simulated microgravity. NPJ Microgravity 2022; 8:22. [PMID: 35787634 PMCID: PMC9253108 DOI: 10.1038/s41526-022-00209-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/22/2022] [Indexed: 11/19/2022] Open
Abstract
A systematic study on the biological effects of simulated microgravity (sµg) on human pluripotent stem cells (hPSC) is still lacking. Here, we used a fast-rotating 2-D clinostat to investigate the sµg effect on proliferation, self-renewal, and cell cycle regulation of hPSCs. We observed significant upregulation of protein translation of pluripotent transcription factors in hPSC cultured in sµg compared to cells cultured in 1g conditions. In addition to a significant increase in expression of telomere elongation genes. Differentiation experiments showed that hPSC cultured in sµg condition were less susceptible to differentiation compared to cells in 1g conditions. These results suggest that sµg enhances hPSC self-renewal. Our study revealed that sµg enhanced the cell proliferation of hPSCs by regulating the expression of cell cycle-associated kinases. RNA-seq analysis indicated that in sµg condition the expression of differentiation and development pathways are downregulated, while multiple components of the ubiquitin proteasome system are upregulated, contributing to an enhanced self-renewal of hPSCs. These effects of sµg were not replicated in human fibroblasts. Taken together, our results highlight pathways and mechanisms in hPSCs vulnerable to microgravity that imposes significant impacts on human health and performance, physiology, and cellular and molecular processes.
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Affiliation(s)
- S Timilsina
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA
| | - T Kirsch-Mangu
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA
| | - S Werth
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA
| | - B Shepard
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA
| | - T Ma
- Department of Computer Science, Engineering, Oakland University, Rochester, MI, 48309, USA
| | - L G Villa-Diaz
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA. .,Department of Bioengineering, Oakland University, Rochester, MI, 48309, USA.
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15
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Zhu W, Sun J, Bishop SP, Sadek H, Zhang J. Turning back the clock: A concise viewpoint of cardiomyocyte cell cycle activation for myocardial regeneration and repair. J Mol Cell Cardiol 2022; 170:15-21. [PMID: 35660800 PMCID: PMC9391298 DOI: 10.1016/j.yjmcc.2022.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/18/2022] [Accepted: 05/14/2022] [Indexed: 11/25/2022]
Abstract
Patients with acute myocardial infarction (MI) could progress to end-stage congestive heart failure, which is one of the most significant problems in public health. From the molecular and cellular perspective, heart failure often results from the loss of cardiomyocytes-the fundamental contractile unit of the heart-and the damage caused by myocardial injury in adult mammals cannot be repaired, in part because mammalian cardiomyocytes undergo cell-cycle arrest during the early perinatal period. However, recent studies in the hearts of neonatal small and large mammals suggest that the onset of cardiomyocyte cell-cycle arrest can be reversed, which may lead to the development of entirely new strategies for the treatment of heart failure. In this Viewpoint, we summarize these and other provocative findings about the cellular and molecular mechanisms that regulate cardiomyocyte proliferation and how they may be targeted to turn back the clock of cardiomyocyte cell-cycle arrest and improve recovery from cardiac injury and disease.
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Affiliation(s)
- Wuqiang Zhu
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center for Regenerative Medicine, Mayo Clinic, Scottsdale, AZ 85259, United States of America
| | - Jiacheng Sun
- Department of Biomedical Engineering, School of Medicine and School of Engineering, the University of Alabama at Birmingham, Birmingham, AL 35294, United States of America
| | - Sanford P Bishop
- Department of Biomedical Engineering, School of Medicine and School of Engineering, the University of Alabama at Birmingham, Birmingham, AL 35294, United States of America
| | - Hesham Sadek
- Division of Cardiovascular Diseases, UT Southwestern Medical Center, United States of America
| | - Jianyi Zhang
- Department of Biomedical Engineering, School of Medicine and School of Engineering, the University of Alabama at Birmingham, Birmingham, AL 35294, United States of America; Department of Medicine, Division of Cardiovascular Diseases, School of Medicine, the University of Alabama at Birmingham, Birmingham, AL 35294, United States of America.
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16
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Ranjan R, Snedeker J, Wooten M, Chu C, Bracero S, Mouton T, Chen X. Differential condensation of sister chromatids acts with Cdc6 to ensure asynchronous S-phase entry in Drosophila male germline stem cell lineage. Dev Cell 2022; 57:1102-1118.e7. [PMID: 35483360 PMCID: PMC9134767 DOI: 10.1016/j.devcel.2022.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/16/2022] [Accepted: 04/05/2022] [Indexed: 01/06/2023]
Abstract
During Drosophila melanogaster male germline stem cell (GSC) asymmetric division, preexisting old versus newly synthesized histones H3 and H4 are asymmetrically inherited. However, the biological outcomes of this phenomenon have remained unclear. Here, we tracked old and new histones throughout the GSC cell cycle through the use of high spatial and temporal resolution microscopy. We found unique features that differ between old and new histone-enriched sister chromatids, including differences in nucleosome density, chromosomal condensation, and H3 Ser10 phosphorylation. These distinct chromosomal features lead to their differential association with Cdc6, a pre-replication complex component, and subsequent asynchronous DNA replication initiation in the resulting daughter cells. Disruption of asymmetric histone inheritance abolishes differential Cdc6 association and asynchronous S-phase entry, demonstrating that histone asymmetry acts upstream of these critical cell-cycle progression events. Furthermore, disruption of these GSC-specific chromatin features leads to GSC defects, indicating a connection between histone inheritance, cell-cycle progression, and cell fate determination.
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Affiliation(s)
- Rajesh Ranjan
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Carolina Chu
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sabrina Bracero
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Taylar Mouton
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xin Chen
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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17
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Liu J, Yang M, Zhao W, Zhou X. CCPE: cell cycle pseudotime estimation for single cell RNA-seq data. Nucleic Acids Res 2022; 50:704-716. [PMID: 34931240 PMCID: PMC8789092 DOI: 10.1093/nar/gkab1236] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/22/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Pseudotime analysis from scRNA-seq data enables to characterize the continuous progression of various biological processes, such as the cell cycle. Cell cycle plays an important role in cell fate decisions and differentiation and is often regarded as a confounder in scRNA-seq data analysis when analyzing the role of other factors. Therefore, accurate prediction of cell cycle pseudotime and identification of cell cycle stages are important steps for characterizing the development-related biological processes. Here, we develop CCPE, a novel cell cycle pseudotime estimation method to characterize cell cycle timing and identify cell cycle phases from scRNA-seq data. CCPE uses a discriminative helix to characterize the circular process of the cell cycle and estimates each cell's pseudotime along the cell cycle. We evaluated the performance of CCPE based on a variety of simulated and real scRNA-seq datasets. Our results indicate that CCPE is an effective method for cell cycle estimation and competitive in various applications compared with other existing methods. CCPE successfully identified cell cycle marker genes and is robust to dropout events in scRNA-seq data. Accurate prediction of the cell cycle using CCPE can also effectively facilitate the removal of cell cycle effects across cell types or conditions.
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Affiliation(s)
- Jiajia Liu
- College of Electronic and Information Engineering, Tongji University, Shanghai, Shanghai 201804, China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Mengyuan Yang
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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18
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Abouleisa RR, Salama ABM, Ou Q, Tang XL, Solanki M, Guo Y, Nong Y, McNally L, Lorkiewicz PK, Kassem KM, Ahern BM, Choudhary K, Thomas R, Huang Y, Juhardeen HR, Siddique A, Ifthikar Z, Hammad SK, El-Baz AS, Ivey KN, Conklin DJ, Satin J, Hill BG, Srivastava D, Bolli R, Mohamed TM. Transient Cell Cycle Induction in Cardiomyocytes to Treat Subacute Ischemic Heart Failure. Circulation 2022; 145:1339-1355. [PMID: 35061545 PMCID: PMC9038650 DOI: 10.1161/circulationaha.121.057641] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
The regenerative capacity of the heart after myocardial infarction (MI) is limited. Our previous study showed that ectopic introduction of Cdk1/CyclinB1 and Cdk4/CyclinD1 complexes (4F) promotes cardiomyocyte proliferation in 15-20% of infected cardiomyocytes
in vitro
and
in vivo
and improves cardiac function after MI in mice.
Methods:
Here, using temporal single-cell RNAseq we aimed to identify the necessary reprogramming stages during the forced cardiomyocyte proliferation with 4F on a single cell basis. Also, using rat and pig models of ischemic heart failure, we aimed to start the first preclinical testing to introduce 4F gene therapy as a candidate for the treatment of ischemia-induced heart failure.
Results:
Temporal bulk and single-cell RNAseq and further biochemical validations of mature hiPS-CMs treated with either LacZ or 4F adenoviruses revealed full cell cycle reprogramming in 15% of the cardiomyocyte population at 48 h post-infection with 4F, which was mainly associated with sarcomere disassembly and metabolic reprogramming (n=3/timepoint/group). Transient overexpression of 4F, specifically in cardiomyocytes, was achieved using a polycistronic non-integrating lentivirus (NIL) encoding the 4F; each is driven by a TNNT2 promoter (TNNT2-4Fpolycistronic-NIL). TNNT2-4Fpolycistronic-NIL or control virus was injected intramyocardially one week after MI in rats (n=10/group) or pigs (n=6-7/group). Four weeks post-injection, TNNT2-4Fpolycistronic-NIL treated animals showed significant improvement in left ventricular ejection fraction and scar size compared with the control virus treated animals. At four months after treatment, rats that received TNNT2-4Fpolycistronic-NIL still showed a sustained improvement in cardiac function and no obvious development of cardiac arrhythmias or systemic tumorigenesis (n=10/group).
Conclusions:
This study provides mechanistic insights into the process of forced cardiomyocyte proliferation and advances the clinical feasibility of this approach by minimizing the oncogenic potential of the cell cycle factors thanks to the use of a novel transient and cardiomyocyte-specific viral construct.
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Affiliation(s)
- Riham R.E. Abouleisa
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY
| | - Abou Bakr M. Salama
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY; Faculty of Medicine, Zagazig University, Egypt
| | - Qinghui Ou
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY
| | - Xian-Liang Tang
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY
| | - Mitesh Solanki
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY
| | - Yiru Guo
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY
| | - Yibing Nong
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY
| | - Lindsey McNally
- Envirome Institute, Diabetes and Obesity Center, Department of Medicine, University of Louisville, KY
| | - Pawel K. Lorkiewicz
- Envirome Institute, Diabetes and Obesity Center, Department of Medicine, University of Louisville, KY
| | - Kamal M. Kassem
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY
| | | | | | | | - Yu Huang
- Gladstone Institute, San Francisco, CA
| | | | - Aisha Siddique
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Zainab Ifthikar
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Sally K. Hammad
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY; Department of Biochemistry Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Ayman S. El-Baz
- Department of Bioengineering, Speed School of Engineering, University of Louisville, KY
| | | | - Daniel J. Conklin
- Envirome Institute, Diabetes and Obesity Center, Department of Medicine, University of Louisville, KY
| | | | - Bradford G. Hill
- Envirome Institute, Diabetes and Obesity Center, Department of Medicine, University of Louisville, KY
| | | | - Roberto Bolli
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY
| | - Tamer M.A. Mohamed
- From the Institute of Molecular Cardiology, Department of Medicine, University of Louisville, KY; Envirome Institute, Diabetes and Obesity Center, Department of Medicine, University of Louisville, KY; Department of Bioengineering, Speed School of Engineering, University of Louisville, KY; Department of Pharmacology and Toxicology, University of Louisville, KY; Institute of Cardiovascular Sciences, University of Manchester, U.K
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19
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Ge Y, Smits AM, Liu J, Zhang J, van Brakel TJ, Goumans MJTH, Jongbloed MRM, de Vries AAF. Generation, Characterization, and Application of Inducible Proliferative Adult Human Epicardium-Derived Cells. Cells 2021; 10:2064. [PMID: 34440833 PMCID: PMC8391799 DOI: 10.3390/cells10082064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 12/20/2022] Open
Abstract
RATIONALE In recent decades, the great potential of human epicardium-derived cells (EPDCs) as an endogenous cell source for cardiac regeneration has been recognized. The limited availability and low proliferation capacity of primary human EPDCs and phenotypic differences between EPDCs obtained from different individuals hampers their reproducible use for experimental studies. AIM To generate and characterize inducible proliferative adult human EPDCs for use in fundamental and applied research. METHODS AND RESULTS Inducible proliferation of human EPDCs was achieved by doxycycline-controlled expression of simian virus 40 large T antigen (LT) with a repressor-based lentiviral Tet-On system. In the presence of doxycycline, these inducible EPDCs (iEPDCs) displayed high and long-term proliferation capacity. After doxycycline removal, LT expression ceased and the iEPDCs regained their cuboidal epithelial morphology. Similar to primary EPDCs, iEPDCs underwent an epithelial-to-mesenchymal transition (EMT) after stimulation with transforming growth factor β3. This was confirmed by reverse transcription-quantitative polymerase chain reaction analysis of epithelial and mesenchymal marker gene expression and (immuno) cytochemical staining. Collagen gel-based cell invasion assays demonstrated that mesenchymal iEPDCs, like primary EPDCs, possess increased invasion and migration capacities as compared to their epithelial counterparts. Mesenchymal iEPDCs co-cultured with sympathetic ganglia stimulated neurite outgrowth similarly to primary EPDCs. CONCLUSION Using an inducible LT expression system, inducible proliferative adult human EPDCs were generated displaying high proliferative capacity in the presence of doxycycline. These iEPDCs maintain essential epicardial characteristics with respect to morphology, EMT ability, and paracrine signaling following doxycycline removal. This renders iEPDCs a highly useful new in vitro model for studying human epicardial properties.
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Affiliation(s)
- Yang Ge
- Department of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands; (Y.G.); (M.R.M.J.)
- Department of Cardiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (J.L.); (J.Z.); (A.A.F.d.V.)
| | - Anke M. Smits
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands;
| | - Jia Liu
- Department of Cardiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (J.L.); (J.Z.); (A.A.F.d.V.)
- Central Laboratory, Longgang District People’s Hospital of Shenzhen & The Third Affiliated Hospital of The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Juan Zhang
- Department of Cardiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (J.L.); (J.Z.); (A.A.F.d.V.)
| | - Thomas J. van Brakel
- Department of Cardiothoracic Surgery, Leiden University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands;
| | - Marie José T. H. Goumans
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands;
| | - Monique R. M. Jongbloed
- Department of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands; (Y.G.); (M.R.M.J.)
- Department of Cardiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (J.L.); (J.Z.); (A.A.F.d.V.)
| | - Antoine A. F. de Vries
- Department of Cardiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (J.L.); (J.Z.); (A.A.F.d.V.)
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20
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Kommalapati VK, Kumar D, Tangutur AD. Quisinostat mediated autophagy is associated with differentiation in neuroblastoma SK-N-SH cells. Mol Biol Rep 2021; 48:4973-4979. [PMID: 34125328 DOI: 10.1007/s11033-021-06481-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/05/2021] [Indexed: 01/18/2023]
Abstract
Neuroblastoma (NB) is the most common childhood cancer that arises from the sympathetic nervous system. NB is characterized by poor prognosis. One of the strategies to control NB is activating the differentiation process in undifferentiated NB cells. Many differentiating agents including 13-cis-retinoic acid (RA) led to disappointing results. In the current study, we investigated the effect of Quisinostat/JNJ-26481585(JNJ) on NB SK-N-SH cells differentiation. The SK-N-SH cell differentiation was observed by morphology and neurite length measurement. The cell cycle arrest was determined by FACS analysis. The relative levels of autophagy marker LC3-II, neuronal markers βIII-tubulin and Eno-2, cell cycle related proteins cyclin D1 and CDK 4 were detected by western blotting. JNJ induces differentiation in SK-N-SH cells, as evident by the morphological features and expression of neuronal markers, βIII-tubulin and Eno-2. Cell cycle arrest at G1 phase was confirmed by a decrease in the expression of cyclin D1 and CDK 4. Furthermore, we also observed that autophagy plays an important role in JNJ induced cell differentiation of SK-N-SH cells. We demonstrated that autophagy is induced upon JNJ treatment and is important for the neuronal differentiation of human SK-N-SH cells.
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Affiliation(s)
- Vamsi Krishna Kommalapati
- Department of Applied Biology, CSIR- Indian Institute of Chemical Technology, Hyderabad, 500007, Telangana, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India
| | - Dinesh Kumar
- Department of Applied Biology, CSIR- Indian Institute of Chemical Technology, Hyderabad, 500007, Telangana, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India
| | - Anjana Devi Tangutur
- Department of Applied Biology, CSIR- Indian Institute of Chemical Technology, Hyderabad, 500007, Telangana, India.
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India.
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21
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Mhamdi-Ghodbani M, Starzonek C, Degenhardt S, Bender M, Said M, Greinert R, Volkmer B. UVB damage response of dermal stem cells as melanocyte precursors compared to keratinocytes, melanocytes, and fibroblasts from human foreskin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 220:112216. [PMID: 34023595 DOI: 10.1016/j.jphotobiol.2021.112216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/21/2021] [Accepted: 05/14/2021] [Indexed: 02/09/2023]
Abstract
Ultraviolet B (UVB) radiation induces mutagenic DNA photolesions in skin cells especially in form of cyclobutane pyrimidine dimers (CPDs). Protection mechanisms as DNA repair and apoptosis are of great importance in order to prevent skin carcinogenesis. In human skin, neural crest-derived precursors of melanocytes, the dermal stem cells (DSCs), are discussed to be at the origin of melanoma. Although they are constantly exposed to solar UV radiation, it is still not investigated how DSCs cope with UV-induced DNA damage. Here, we report a comparative study of the DNA damage response after irradiation with a physiological relevant UVB dose in DSCs in comparison to fibroblasts, melanocytes and keratinocytes isolated from human foreskin. Within our experimental settings, DSCs were able to repair DNA photolesions as efficient as the other skin cell types with solely keratinocytes repairing significantly faster. Interestingly, only fibroblasts showed significant alterations in cell cycle distribution in terms of a transient S phase arrest following irradiation. Moreover, with the applied UVB dose none of the examined cell types was prone to UVB-induced apoptosis. This may cause persistent genomic alterations and in case of DSCs it may have severe consequences for their daughter cells, the differentiated melanocytes. Altogether, this is the first study demonstrating a similar UV response in dermal stem cells compared to differentiated skin cells.
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Affiliation(s)
- Mouna Mhamdi-Ghodbani
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Christin Starzonek
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Sarah Degenhardt
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Marc Bender
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | | | - Rüdiger Greinert
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Beate Volkmer
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany.
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Terzi Cizmecioglu N, Huang J, Keskin EG, Wang X, Esen I, Chen F, Orkin SH. ARID4B is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit. J Biol Chem 2021; 295:17738-17751. [PMID: 33454011 DOI: 10.1074/jbc.ra120.015534] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/13/2020] [Indexed: 11/06/2022] Open
Abstract
Distinct cell types emerge from embryonic stem cells through a precise and coordinated execution of gene expression programs during lineage commitment. This is established by the action of lineage specific transcription factors along with chromatin complexes. Numerous studies have focused on epigenetic factors that affect embryonic stem cells (ESC) self-renewal and pluripotency. However, the contribution of chromatin to lineage decisions at the exit from pluripotency has not been as extensively studied. Using a pooled epigenetic shRNA screen strategy, we identified chromatin-related factors critical for differentiation toward mesodermal and endodermal lineages. Here we reveal a critical role for the chromatin protein, ARID4B. Arid4b-deficient mESCs are similar to WT mESCs in the expression of pluripotency factors and their self-renewal. However, ARID4B loss results in defects in up-regulation of the meso/endodermal gene expression program. It was previously shown that Arid4b resides in a complex with SIN3A and HDACS 1 and 2. We identified a physical and functional interaction of ARID4B with HDAC1 rather than HDAC2, suggesting functionally distinct Sin3a subcomplexes might regulate cell fate decisions Finally, we observed that ARID4B deficiency leads to increased H3K27me3 and a reduced H3K27Ac level in key developmental gene loci, whereas a subset of genomic regions gain H3K27Ac marks. Our results demonstrate that epigenetic control through ARID4B plays a key role in the execution of lineage-specific gene expression programs at pluripotency exit.
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Affiliation(s)
- Nihal Terzi Cizmecioglu
- Department of Biological Sciences, Faculty of Arts and Sciences, Middle East Technical University, Ankara, Turkey.
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian China
| | - Ezgi G Keskin
- Department of Biological Sciences, Faculty of Arts and Sciences, Middle East Technical University, Ankara, Turkey
| | - Xiaofeng Wang
- Geisel School of Medicine, Dartmouth University, Hanover, New Hampshire USA
| | - Idil Esen
- Howard Hughes Medical Institute, Dana Farber/Boston Children's Cancer and Blood Disorders Center, Dept. of Pediatrics, Harvard Medical School, Boston, Massachusetts USA
| | - Fei Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian China
| | - Stuart H Orkin
- Howard Hughes Medical Institute, Dana Farber/Boston Children's Cancer and Blood Disorders Center, Dept. of Pediatrics, Harvard Medical School, Boston, Massachusetts USA.
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23
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Anticancer effects of an extract from a local planarian species on human acute myeloid leukemia HL-60 cells in vitro. Biomed Pharmacother 2020; 130:110549. [DOI: 10.1016/j.biopha.2020.110549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
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24
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Zhang D, Fan R, Lei L, Lei L, Wang Y, Lv N, Chen P, Williamson RA, Wang B, Hu J. Cell cycle exit during bortezomib-induced osteogenic differentiation of mesenchymal stem cells was mediated by Xbp1s-upregulated p21 Cip1 and p27 Kip1. J Cell Mol Med 2020; 24:9428-9438. [PMID: 32628811 PMCID: PMC7417721 DOI: 10.1111/jcmm.15605] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/10/2020] [Accepted: 06/21/2020] [Indexed: 01/19/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are multipotent cells capable of differentiating into a variety of cell types. Bortezomib, the first approved proteasome inhibitor used for the treatment of multiple myeloma (MM), has been shown to induce osteoblast differentiation, making it beneficial for myeloma bone disease. In the present study, we aimed to investigate the effects and underlying mechanisms of bortezomib on the cell cycle during osteogenic differentiation. We confirmed that low doses of bortezomib can induce MSCs towards osteogenic differentiation, but high doses are toxic. In the course of bortezomib-induced osteogenic differentiation, we observed cell cycle exit characterized by G0 /G1 phase cell cycle arrest with a significant reduction in cell proliferation. Additionally, we found that the cell cycle exit was tightly related to the induction of the cyclin-dependent kinase inhibitors p21Cip1 and p27Kip1 . Notably, we further demonstrated that the up-regulation of p21Cip1 and p27Kip1 is transcriptionally dependent on the bortezomib-activated ER stress signalling branch Ire1α/Xbp1s. Taken together, these findings reveal an intracellular pathway that integrates proteasome inhibition, osteogenic differentiation and the cell cycle through activation of the ER stress signalling branch Ire1α/Xbp1s.
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Affiliation(s)
- Dan Zhang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Rong Fan
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Li Lei
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Lei Lei
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yanmeng Wang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Nan Lv
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Ping Chen
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Ramone A Williamson
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Baiyan Wang
- Department of Clinical Hematology, Second Affiliated Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jinsong Hu
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
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25
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Katebi A, Kohar V, Lu M. Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle. iScience 2020; 23:101150. [PMID: 32450514 PMCID: PMC7251928 DOI: 10.1016/j.isci.2020.101150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/05/2020] [Accepted: 05/05/2020] [Indexed: 02/03/2023] Open
Abstract
Many biological processes involve precise cellular state transitions controlled by complex gene regulation. Here, we use budding yeast cell cycle as a model system and explore how a gene regulatory circuit encodes essential information of state transitions. We present a generalized random circuit perturbation method for circuits containing heterogeneous regulation types and its usage to analyze both steady and oscillatory states from an ensemble of circuit models with random kinetic parameters. The stable steady states form robust clusters with a circular structure that are associated with cell cycle phases. This circular structure in the clusters is consistent with single-cell RNA sequencing data. The oscillatory states specify the irreversible state transitions along cell cycle progression. Furthermore, we identify possible mechanisms to understand the irreversible state transitions from the steady states. We expect this approach to be robust and generally applicable to unbiasedly predict dynamical transitions of a gene regulatory circuit.
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Affiliation(s)
- Ataur Katebi
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Vivek Kohar
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Mingyang Lu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA.
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26
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An SY, Lee HJ, Lee SC, Heo JS. Supplement of nitric oxide through calcium carbonate-based nanoparticles contributes osteogenic differentiation of mouse embryonic stem cells. Tissue Cell 2020; 66:101390. [PMID: 32933713 DOI: 10.1016/j.tice.2020.101390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/16/2022]
Abstract
This study investigated the delivery of S-nitrosothiol (GSNO) as a nitric oxide (NO) donor loaded into calcium carbonate-based mineralized nanoparticles (GSNO-MNPs) to regulate cell signaling pathways for the osteogenic differentiation of mouse embryonic stem cells (ESCs). GSNO-MNPs were prepared by an anionic block copolymer template-mediated calcium carbonate (CaCO3) mineralization process in the presence of GSNO. GSNO-MNPs were spherical and had a narrow size distribution. GSNO was stably loaded within the MNPs without denaturation. TEM analysis also demonstrated the localization of GSNO-MNPs within membrane-bound structures in the cell, indicating the successful introduction of GSNO-MNPs into the cytosol of ESCs. Intracellular levels of NO and cGMP were significantly increased upon treatment with GSNO-MNPs, compared with the control group. When cells were exposed to GSNO-MNPs, the effects of nanoparticles on cell viability were not statistically significant. GSNO-MNPs treatment increased ALP activity assay and intracellular calcium levels. Real-time RT-PCR also revealed highly increased expression levels of the osteogenic target genes ALP, osteocalcin (OCN), and osterix (OSX) in GSNO-MNP-treated ESCs. The protein levels of OSX and Runt-related transcription factor 2 (RUNX2) showed similar patterns of expression based on real-time RT-PCR. These results indicate that GSNO-MNPs influenced the osteogenic differentiation of ESCs. Transcriptome profiling identified several significantly enriched and involved biological networks, such as RAP1, RAS, PI3K-AKT, and MAPK signaling pathways. These findings suggest that GSNO-MNPs can modulate osteogenic differentiation in ESCs via complex molecular pathways.
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Affiliation(s)
- Seong Yeong An
- Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, School of Dentistry, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Hong Jae Lee
- Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, School of Dentistry, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Sang Cheon Lee
- Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, School of Dentistry, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
| | - Jung Sun Heo
- Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, School of Dentistry, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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James CD, Morgan IM, Bristol ML. The Relationship between Estrogen-Related Signaling and Human Papillomavirus Positive Cancers. Pathogens 2020; 9:E403. [PMID: 32455952 PMCID: PMC7281727 DOI: 10.3390/pathogens9050403] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/15/2022] Open
Abstract
High risk-human papillomaviruses (HPVs) are known carcinogens. Numerous reports have linked the steroid hormone estrogen, and the expression of estrogen receptors (ERs), to HPV-related cancers, although the exact nature of the interactions remains to be fully elucidated. Here we will focus on estrogen signaling and describe both pro and potentially anti-cancer effects of this hormone in HPV-positive cancers. This review will summarize: (1) cell culture-related evidence, (2) animal model evidence, and (3) clinical evidence demonstrating an interaction between estrogen and HPV-positive cancers. This comprehensive review provides insights into the potential relationship between estrogen and HPV. We suggest that estrogen may provide a potential therapeutic for HPV-related cancers, however additional studies are necessary.
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Affiliation(s)
- Claire D. James
- School of Dentistry, Philips Institute for Oral Health Research, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA;
| | - Iain M. Morgan
- School of Dentistry, Philips Institute for Oral Health Research, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA;
- VCU Massey Cancer Center, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
| | - Molly L. Bristol
- School of Dentistry, Philips Institute for Oral Health Research, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA;
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28
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Life in the (Pluripotent) Fast Lane: Cdk1 Preserves the Epigenome to Maintain Pluripotency. Mol Cell 2020; 78:374-375. [PMID: 32386539 DOI: 10.1016/j.molcel.2020.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Michowski and colleagues (2020) engineered analog-sensitive Cdk1 knockin mice to identify Cdk1 targets in embryonic stem cells, which led them to discover a novel function for Cdk1 in shaping the epigenetic landscape by direct regulation of epigenetic modulators.
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29
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Abstract
Thymus regenerative therapy implementation is severely obstructed by the limited number and expansion capacity in vitro of tissue-specific thymic epithelial stem cells (TESC). Current solutions are mostly based on growth factors that can drive differentiation of pluripotent stem cells toward tissue-specific TESC. Target-specific small chemical compounds represent an alternative solution that could induce and support the clonal expansion of TESC and reversibly block their differentiation into mature cells. These compounds could be used both in the composition of culture media designed for TESC expansion in vitro, and in drugs development for thymic regeneration in vivo. It should allow reaching the ultimate objective - autologous thymic tissue regeneration in paediatric patients who had their thymus removed in the course of cardiac surgery.
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30
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Uribe-Etxebarria V, García-Gallastegui P, Pérez-Garrastachu M, Casado-Andrés M, Irastorza I, Unda F, Ibarretxe G, Subirán N. Wnt-3a Induces Epigenetic Remodeling in Human Dental Pulp Stem Cells. Cells 2020; 9:cells9030652. [PMID: 32156036 PMCID: PMC7140622 DOI: 10.3390/cells9030652] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/13/2022] Open
Abstract
Dental pulp stem cells (DPSCs) from adult teeth show the expression of a very complete repertoire of stem pluripotency core factors and a high plasticity for cell reprogramming. Canonical Wnt and Notch signaling pathways regulate stemness and the expression of pluripotency core factors in DPSCs, and even very short-term (48 h) activations of the Wnt pathway induce a profound remodeling of DPSCs at the physiologic and metabolic levels. In this work, DPSC cultures were exposed to treatments modulating Notch and Wnt signaling, and also induced to differentiate to osteo/adipocytes. DNA methylation, histone acetylation, histone methylation, and core factor expression levels where assessed by mass spectroscopy, Western blot, and qPCR. A short-term activation of Wnt signaling by WNT-3A induced a genomic DNA demethylation, and increased histone acetylation and histone methylation in DPSCs. The efficiency of cell reprogramming methods relies on the ability to surpass the epigenetic barrier, which determines cell lineage specificity. This study brings important information about the regulation of the epigenetic barrier by Wnt signaling in DPSCs, which could contribute to the development of safer and less aggressive reprogramming methodologies with a view to cell therapy.
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Affiliation(s)
- Verónica Uribe-Etxebarria
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, 48940 Leioa, Spain; (V.U.-E.); (P.G.-G.); (M.P.-G.); (M.C.-A.); (I.I.); (F.U.)
- Pathology Department, New York University, 550 1st Avenue, New York, NY 10016, USA
| | - Patricia García-Gallastegui
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, 48940 Leioa, Spain; (V.U.-E.); (P.G.-G.); (M.P.-G.); (M.C.-A.); (I.I.); (F.U.)
| | - Miguel Pérez-Garrastachu
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, 48940 Leioa, Spain; (V.U.-E.); (P.G.-G.); (M.P.-G.); (M.C.-A.); (I.I.); (F.U.)
| | - María Casado-Andrés
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, 48940 Leioa, Spain; (V.U.-E.); (P.G.-G.); (M.P.-G.); (M.C.-A.); (I.I.); (F.U.)
- Unité Mixte de Recherche UMR1029. INSERM-Université de Bordeaux, 33000 Bordeaux, France
| | - Igor Irastorza
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, 48940 Leioa, Spain; (V.U.-E.); (P.G.-G.); (M.P.-G.); (M.C.-A.); (I.I.); (F.U.)
| | - Fernando Unda
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, 48940 Leioa, Spain; (V.U.-E.); (P.G.-G.); (M.P.-G.); (M.C.-A.); (I.I.); (F.U.)
| | - Gaskon Ibarretxe
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, 48940 Leioa, Spain; (V.U.-E.); (P.G.-G.); (M.P.-G.); (M.C.-A.); (I.I.); (F.U.)
- Correspondence: ; Tel.: +34-94-601-3218
| | - Nerea Subirán
- Physiology Department, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, 48940 Leioa, Spain;
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Alksne M, Kalvaityte M, Simoliunas E, Rinkunaite I, Gendviliene I, Locs J, Rutkunas V, Bukelskiene V. In vitro comparison of 3D printed polylactic acid/hydroxyapatite and polylactic acid/bioglass composite scaffolds: Insights into materials for bone regeneration. J Mech Behav Biomed Mater 2020; 104:103641. [PMID: 32174399 DOI: 10.1016/j.jmbbm.2020.103641] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
3D printing of polylactic acid (PLA) and hydroxyapatite (HA) or bioglass (BG) bioceramics composites is the most promising technique for artificial bone construction. However, HA and BG have different chemical composition as well as different bone regeneration inducing mechanisms. Thus, it is important to compare differentiation processes induced by 3D printed PLA + HA and PLA + BG scaffolds in order to evaluate the strongest osteoconductive and osteoinductive properties possessing bioceramics. In this study, we analysed porous PLA + HA (10%) and PLA + BG (10%) composites' effect on rat's dental pulp stem cells fate in vitro. Obtained results indicated, that PLA + BG scaffolds lead to weaker cell adhesion and proliferation than PLA + HA. Nevertheless, osteoinductive and other biofriendly properties were more pronounced by PLA + BG composites. Overall, the results showed a strong advantage of bioceramic BG against HA, thus, 3D printed PLA + BG composite scaffolds could be a perspective component for patient-specific, cheaper and faster artificial bone tissue production.
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Affiliation(s)
- Milda Alksne
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT-10257, Vilnius, Lithuania.
| | - Migle Kalvaityte
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT-10257, Vilnius, Lithuania
| | - Egidijus Simoliunas
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT-10257, Vilnius, Lithuania
| | - Ieva Rinkunaite
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT-10257, Vilnius, Lithuania
| | - Ieva Gendviliene
- Institute of Odontology, Faculty of Medicine, Vilnius University, Zalgirio Str. 115, LT-08217, Vilnius, Lithuania
| | - Janis Locs
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU, Institute of General Chemical Engineering, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Pulka 3, Riga, LV-1007, Latvia
| | - Vygandas Rutkunas
- Institute of Odontology, Faculty of Medicine, Vilnius University, Zalgirio Str. 115, LT-08217, Vilnius, Lithuania
| | - Virginija Bukelskiene
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, LT-10257, Vilnius, Lithuania
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Zhang K, Wang J. Exploring the underlying mechanisms of the coupling between cell differentiation and cell cycle. J Phys Chem B 2019; 123:3490-3498. [PMID: 30933510 DOI: 10.1021/acs.jpcb.9b00509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Differentiation and replication are the two major fates of the cells. They are the fundamental processes for completing the cellular functions. Although the underlying biological processes have been considerably explored for each of these processes and significant progresses have been made, global quantification and physical understanding are still challenging, especially for the relationship among them. In this study, we developed a theoretical framework for both the cell cycle and cell differentiation by exploring the associated global dynamics and their underlying relationship. We found that the dynamics of the cell cycle and cell differentiation is governed by both the landscape gradient and rotational curl flux. While landscape attracts the system down to the stable state basins, the curl flux drives the stable oscillation flow. We uncovered the irregular sombrero-shaped landscapes of the cell cycle at different developmental stages. We studied how the cells develop from undifferentiated cells to differentiated cells and how the cell cycle proceeds at different developmental stages. We investigated how the cell differentiation can influence the cell cycle where more progressive differentiation can lead to the changes of the cell cycle oscillations. In contrast, we can also quantitatively illustrate how the cell cycle can influence the cell differentiation where cell cycle regulation can lead to the changes of the differentiation processes. Through the landscape and flux analysis, we uncovered the key regulatory elements controlling the progression of the cell differentiation and cell cycle. This can help to design an effective strategy for drug discovery against associated diseases.
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Affiliation(s)
- Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun , Jilin 130022 , P.R.China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun , Jilin 130022 , P.R.China.,Department of Chemistry and of Physics and Astronomy , Stony Brook University , Stony Brook , New York 11794-3400 , United States
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MacKenzie RK, Sankar PR, Bendall AJ. Dlx5 and Dlx6 can antagonize cell division at the G 1/S checkpoint. BMC Mol Cell Biol 2019; 20:8. [PMID: 31041891 PMCID: PMC6460778 DOI: 10.1186/s12860-019-0191-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 04/02/2019] [Indexed: 11/17/2022] Open
Abstract
Background Dlx5 and Dlx6 stimulate differentiation of diverse progenitors during embryonic development. Their actions as pro-differentiation transcription factors includes the up-regulation of differentiation markers but the extent to which differentiation may also be stimulated by regulation of the cell cycle has not been addressed. Results We document that expression of Dlx5 and Dlx6 antagonizes cell proliferation in a variety of cell types without inducing apoptosis or promoting cell cycle exit. Rather, a variety of evidence indicates that elevated Dlx5 and Dlx6 expression reduces the proportion of cells in S phase and affects the length of the cell cycle. Conclusions Antagonism of S-phase entry by Dlx5 and Dlx6 proteins likely represents a lineage-independent function to effect Dlx-mediated differentiation in multiple progenitor cell types.
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Affiliation(s)
- Rachel K MacKenzie
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd East, Guelph, Ontario, N1G 2W1, Canada
| | - Parvathy Ravi Sankar
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd East, Guelph, Ontario, N1G 2W1, Canada
| | - Andrew J Bendall
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd East, Guelph, Ontario, N1G 2W1, Canada.
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Li J, Narayanan C, Bian J, Sambo D, Brickler T, Zhang W, Chetty S. A transient DMSO treatment increases the differentiation potential of human pluripotent stem cells through the Rb family. PLoS One 2018; 13:e0208110. [PMID: 30540809 PMCID: PMC6291069 DOI: 10.1371/journal.pone.0208110] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/12/2018] [Indexed: 01/01/2023] Open
Abstract
The propensity for differentiation varies substantially across human pluripotent stem cell (hPSC) lines, greatly restricting the use of hPSCs for cell replacement therapy or disease modeling. Here, we investigate the underlying mechanisms and demonstrate that activation of the retinoblastoma (Rb) pathway in a transient manner is important for differentiation. In prior work, we demonstrated that pre-treating hPSCs with dimethylsulfoxide (DMSO) before directed differentiation enhanced differentiation potential across all three germ layers. Here, we show that exposure to DMSO improves the efficiency of hPSC differentiation through Rb and by repressing downstream E2F-target genes. While transient inactivation of the Rb family members (including Rb, p107, and p130) suppresses DMSO’s capacity to enhance differentiation across all germ layers, transient expression of a constitutively active (non-phosphorylatable) form of Rb increases the differentiation efficiency similar to DMSO. Inhibition of downstream targets of Rb, such as E2F signaling, also promotes differentiation of hPSCs. More generally, we demonstrate that the duration of Rb activation plays an important role in regulating differentiation capacity.
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Affiliation(s)
- Jingling Li
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
| | - Cyndhavi Narayanan
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jing Bian
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
| | - Danielle Sambo
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
| | - Thomas Brickler
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
| | - Wancong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sundari Chetty
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, United States of America
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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35
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Li P, Wu M, Lin Q, Wang S, Chen T, Jiang H. Key genes and integrated modules in hematopoietic differentiation of human embryonic stem cells: a comprehensive bioinformatic analysis. Stem Cell Res Ther 2018; 9:301. [PMID: 30409225 PMCID: PMC6225692 DOI: 10.1186/s13287-018-1050-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/07/2018] [Accepted: 10/16/2018] [Indexed: 12/30/2022] Open
Abstract
Background The generation of hematopoietic stem cells (HSCs) and blood cells from human embryonic stem cells (hESCs) is a major goal for regenerative medicine; however, the differentiation mechanisms are largely undefined. Here, we aimed to identify the regulated genes and functional modules related to the early differentiation of the endothelial-to-hematopoietic transition (EHT) using comprehensive bioinformatics analyses. Methods Undifferentiated hESCs (hESC-H9), CD34+ cells from 10-day differentiated hESC-H9 cells, and CD34+ cells from umbilical cord cells were isolated and collected. Cells from these three groups were subjected to RNA extraction and microarray analysis by which differentially expressed genes (DEGs) and time-series profiles were analyzed by significance analysis of microarray (SAM) and short time-series expression miner (STEM) algorithms. Gene enrichment analysis was performed by ClusterProfiler Package in Rstudio, while a protein-protein interaction (PPI) network was constructed by search tool for the retrieval of interacting genes (STRING) and visualized in Cytoscape. Hub genes were further identified with the MCODE algorithm in Cytoscape. Results In the present study, we identified 11,262 DEGs and 16 time-series profiles that were enriched in biological processes of chromosome segregation, cell cycle, and leukocyte activation and differentiation, as well as hematopoiesis. Analysis using the MCODE algorithm further identified six integrated modules that might play an important role in the EHT process, including mitosis/cell cycle, mitochondrial process, splicing, ubiquitination, ribosome, and apoptosis. Conclusions The study identified potential genes and integrated functional modules associated with the hematopoietic and endothelial differentiation of human ESCs. Electronic supplementary material The online version of this article (10.1186/s13287-018-1050-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Li
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Mengyao Wu
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Qiwang Lin
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Shu Wang
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Hua Jiang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China.
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36
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Gruenheit N, Parkinson K, Brimson CA, Kuwana S, Johnson EJ, Nagayama K, Llewellyn J, Salvidge WM, Stewart B, Keller T, van Zon W, Cotter SL, Thompson CRL. Cell Cycle Heterogeneity Can Generate Robust Cell Type Proportioning. Dev Cell 2018; 47:494-508.e4. [PMID: 30473004 PMCID: PMC6251973 DOI: 10.1016/j.devcel.2018.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 07/27/2018] [Accepted: 09/26/2018] [Indexed: 01/01/2023]
Abstract
Cell-cell heterogeneity can facilitate lineage choice during embryonic development because it primes cells to respond to differentiation cues. However, remarkably little is known about the origin of heterogeneity or whether intrinsic and extrinsic variation can be controlled to generate reproducible cell type proportioning seen in vivo. Here, we use experimentation and modeling in D. discoideum to demonstrate that population-level cell cycle heterogeneity can be optimized to generate robust cell fate proportioning. First, cell cycle position is quantitatively linked to responsiveness to differentiation-inducing signals. Second, intrinsic variation in cell cycle length ensures cells are randomly distributed throughout the cell cycle at the onset of multicellular development. Finally, extrinsic perturbation of optimal cell cycle heterogeneity is buffered by compensatory changes in global signal responsiveness. These studies thus illustrate key regulatory principles underlying cell-cell heterogeneity optimization and the generation of robust and reproducible fate choice in development. Dictyostelium cells break symmetry in a stochastic salt and pepper fashion Cell cycle position affects responsiveness to differentiation inducing signals Cell cycle length variation ensures cells are distributed in different cycle phases Perturbation of cell cycle dynamics is buffered by changes in signal responsiveness
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Affiliation(s)
- Nicole Gruenheit
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK; Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Katie Parkinson
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Christopher A Brimson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Satoshi Kuwana
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Edward J Johnson
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Koki Nagayama
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Jack Llewellyn
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK; School of Mathematics, Faculty of Science and Engineering, The University of Manchester, Alan Turing Building, Manchester M13 9PL, UK
| | - William M Salvidge
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Balint Stewart
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK; Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Thomas Keller
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Wouter van Zon
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Simon L Cotter
- School of Mathematics, Faculty of Science and Engineering, The University of Manchester, Alan Turing Building, Manchester M13 9PL, UK
| | - Christopher R L Thompson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK; Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
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37
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Jin L, Chang C, Pawlik KM, Datta A, Johnson LM, Vu T, Napoli JL, Datta PK. Serine Threonine Kinase Receptor-Associated Protein Deficiency Impairs Mouse Embryonic Stem Cells Lineage Commitment Through CYP26A1-Mediated Retinoic Acid Homeostasis. Stem Cells 2018; 36:1368-1379. [PMID: 29781215 DOI: 10.1002/stem.2854] [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: 01/09/2018] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 01/07/2023]
Abstract
Retinoic acid (RA) signaling is essential for the differentiation of embryonic stem cells (ESCs) and vertebrate development. RA biosynthesis and metabolism are controlled by a series of enzymes, but the molecular regulators of these enzymes remain largely obscure. In this study, we investigated the functional role of the WD-domain protein STRAP (serine threonine kinase receptor-associated protein) in the pluripotency and lineage commitment of murine ESCs. We generated Strap knockout (KO) mouse ESCs and subjected them to spontaneous differentiation. We observed that, despite the unchanged characteristics of ESCs, Strap KO ESCs exhibited defects for lineage differentiation. Signature gene expression analyses revealed that Strap deletion attenuated intracellular RA signaling in embryoid bodies (EBs), and exogenous RA significantly rescued this deficiency. Moreover, loss of Strap selectively induced Cyp26A1 expression in mouse EBs, suggesting a potential role of STRAP in RA signaling. Mechanistically, we identified putative Krüppel-like factor 9 (KLF9) binding motifs to be critical in the enhancement of non-canonical RA-induced transactivation of Cyp26A1. Increased KLF9 expression in the absence of STRAP is partially responsible for Cyp26A1 induction. Interestingly, STRAP knockdown in Xenopus embryos influenced anterior-posterior neural patterning and impaired the body axis and eye development during early Xenopus embryogenesis. Taken together, our study reveals an intrinsic role for STRAP in the regulation of RA signaling and provides new molecular insights for ESC fate determination. Stem Cells 2018;36:1368-1379.
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Affiliation(s)
- Lin Jin
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, Birmingham, Alabama, USA.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, USA
| | - Chenbei Chang
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kevin M Pawlik
- Department of Biochemistry & Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Arunima Datta
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, Birmingham, Alabama, USA.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, USA
| | - Larry M Johnson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Trung Vu
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, Birmingham, Alabama, USA
| | - Joseph L Napoli
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA
| | - Pran K Datta
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, Birmingham, Alabama, USA.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, USA
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38
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Wu DR, Gu KL, Yu JC, Fu X, Wang XW, Guo WT, Liao LQ, Zhu H, Zhang XS, Hui J, Wang Y. Opposing roles of miR-294 and MBNL1/2 in shaping the gene regulatory network of embryonic stem cells. EMBO Rep 2018; 19:embr.201745657. [PMID: 29735517 DOI: 10.15252/embr.201745657] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 01/25/2023] Open
Abstract
Alternative pre-mRNA splicing plays important roles in regulating self-renewal and differentiation of embryonic stem cells (ESCs). However, how specific alternative splicing programs are established in ESCs remains elusive. Here, we show that a subset of alternative splicing events in ESCs is dependent on miR-294 expression. Remarkably, roughly 60% of these splicing events are affected by the depletion of Muscleblind-Like Splicing Regulator 1 and 2 (Mbnl1/2). Distinct from canonical miRNA function, miR-294 represses Mbnl1/2 through both posttranscriptional and epigenetic mechanisms. Furthermore, we uncover non-canonical functions of MBNL proteins that bind and promote the expression of miR-294 targets, including Cdkn1a and Tgfbr2, thereby opposing the role of miR-294 in regulating cell proliferation, apoptosis, and epithelial-mesenchymal transition (EMT). Our study reveals extensive interactions between miRNAs and splicing factors, highlighting their roles in regulating cell type-specific alternative splicing and defining gene expression programs during development and cellular differentiation.
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Affiliation(s)
- Da-Ren Wu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Kai-Li Gu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jian-Cheng Yu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xi-Wen Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Wen-Ting Guo
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Le-Qi Liao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Hong Zhu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Shan Zhang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
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39
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Mohamed TMA, Ang YS, Radzinsky E, Zhou P, Huang Y, Elfenbein A, Foley A, Magnitsky S, Srivastava D. Regulation of Cell Cycle to Stimulate Adult Cardiomyocyte Proliferation and Cardiac Regeneration. Cell 2018; 173:104-116.e12. [PMID: 29502971 PMCID: PMC5973786 DOI: 10.1016/j.cell.2018.02.014] [Citation(s) in RCA: 368] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/02/2018] [Accepted: 02/06/2018] [Indexed: 01/01/2023]
Abstract
Human diseases are often caused by loss of somatic cells that are incapable of re-entering the cell cycle for regenerative repair. Here, we report a combination of cell-cycle regulators that induce stable cytokinesis in adult post-mitotic cells. We screened cell-cycle regulators expressed in proliferating fetal cardiomyocytes and found that overexpression of cyclin-dependent kinase 1 (CDK1), CDK4, cyclin B1, and cyclin D1 efficiently induced cell division in post-mitotic mouse, rat, and human cardiomyocytes. Overexpression of the cell-cycle regulators was self-limiting through proteasome-mediated degradation of the protein products. In vivo lineage tracing revealed that 15%-20% of adult cardiomyocytes expressing the four factors underwent stable cell division, with significant improvement in cardiac function after acute or subacute myocardial infarction. Chemical inhibition of Tgf-β and Wee1 made CDK1 and cyclin B dispensable. These findings reveal a discrete combination of genes that can efficiently unlock the proliferative potential in cells that have terminally exited the cell cycle.
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Affiliation(s)
- Tamer M A Mohamed
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, San Francisco, CA 94158, USA; Institute of Cardiovascular Sciences, University of Manchester, Manchester M13 9PT, UK; Faculty of Pharmacy, Zagazig University, Al Sharqia Governorate, Egypt; Tenaya Therapeutics, South San Francisco, CA 94080, USA
| | - Yen-Sin Ang
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, San Francisco, CA 94158, USA
| | - Ethan Radzinsky
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, San Francisco, CA 94158, USA
| | - Ping Zhou
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, San Francisco, CA 94158, USA
| | - Yu Huang
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, San Francisco, CA 94158, USA
| | - Arye Elfenbein
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, San Francisco, CA 94158, USA
| | - Amy Foley
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, San Francisco, CA 94158, USA
| | - Sergey Magnitsky
- Department of Radiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, San Francisco, CA 94158, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.
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40
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Abstract
OBJECTIVES N-myc downstream-regulated gene-1 (NDRG1) is a hypoxia-inducible and differentiation-related protein and candidate biomarker in pancreatic cancer. As NDRG1 expression is lost in high-grade tumors, the effects of the differentiating histone deacetylase inhibitor trichostatin A (TSA) were examined in human pancreatic cancer cell lines representing different tumor grades. METHODS PANC-1 (poorly differentiated) and Capan-1 (moderately to well-differentiated) cells were treated with TSA. Effects were assessed in vitro by microscopic analysis, colorimetric assays, cell counts, real-time polymerase chain reaction, and Western blotting. RESULTS Treatment of PANC-1 cells over 4 days with 0.5 μM TSA restored cellular differentiation, inhibited proliferation, and enhanced p21 protein expression. Trichostatin A upregulated NDRG1 mRNA and protein levels under normoxia from day 1 and by 6-fold by day 4 (P < 0.01 at all time points). After 24 hours under hypoxia, NDRG1 expression was further increased in differentiated cells (P < 0.01). Favorable changes were identified in the expression of other hypoxia-regulated genes. CONCLUSIONS Histone deacetylase inhibitors offer a potential novel epidrug approach for pancreatic cancer by reversing the undifferentiated phenotype and allowing patients to overcome resistance and better respond to conventional cytotoxic treatments.
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41
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Briggs JA, Li VC, Lee S, Woolf CJ, Klein A, Kirschner MW. Mouse embryonic stem cells can differentiate via multiple paths to the same state. eLife 2017; 6:26945. [PMID: 28990928 PMCID: PMC5648529 DOI: 10.7554/elife.26945] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023] Open
Abstract
In embryonic development, cells differentiate through stereotypical sequences of intermediate states to generate particular mature fates. By contrast, driving differentiation by ectopically expressing terminal transcription factors (direct programming) can generate similar fates by alternative routes. How differentiation in direct programming relates to embryonic differentiation is unclear. We applied single-cell RNA sequencing to compare two motor neuron differentiation protocols: a standard protocol approximating the embryonic lineage, and a direct programming method. Both initially undergo similar early neural commitment. Later, the direct programming path diverges into a novel transitional state rather than following the expected embryonic spinal intermediates. The novel state in direct programming has specific and uncharacteristic gene expression. It forms a loop in gene expression space that converges separately onto the same final motor neuron state as the standard path. Despite their different developmental histories, motor neurons from both protocols structurally, functionally, and transcriptionally resemble motor neurons isolated from embryos.
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Affiliation(s)
| | - Victor C Li
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Seungkyu Lee
- Department of Neurobiology, Harvard Medical School, Boston, United States.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Clifford J Woolf
- Department of Neurobiology, Harvard Medical School, Boston, United States.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Allon Klein
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, United States
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42
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Zhang ZR, Leung WN, Li G, Kong SK, Lu X, Wong YM, Chan CW. Osthole Enhances Osteogenesis in Osteoblasts by Elevating Transcription Factor Osterix via cAMP/CREB Signaling In Vitro and In Vivo. Nutrients 2017; 9:E588. [PMID: 28629115 PMCID: PMC5490567 DOI: 10.3390/nu9060588] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/28/2017] [Accepted: 06/05/2017] [Indexed: 12/24/2022] Open
Abstract
Anabolic anti-osteoporotic agents are desirable for treatment and prevention of osteoporosis and fragility fractures. Osthole is a coumarin derivative extracted from the medicinal herbs Cnidium monnieri (L.) Cusson and Angelica pubescens Maxim.f. Osthole has been reported with osteogenic and anti-osteoporotic properties, whereas the underlying mechanism of its benefit still remains unclear. The objective of the present study was to investigate the osteopromotive action of osthole on mouse osteoblastic MC3T3-E1 cells and on mouse femoral fracture repair, and to explore the interaction between osthole-induced osteopromotive effect and cyclic adenosine monophosphate (cAMP) elevating effect. Osthole treatment promoted osteogenesis in osteoblasts by enhancing alkaline phosphatase (ALP) activity and mineralization. Oral gavage of osthole enhanced fracture repair and increased bone strength. Mechanistic study showed osthole triggered the cAMP/CREB pathway through the elevation of the intracellular cAMP level and activation of the phosphorylation of the cAMP response element-binding protein (CREB). Blockage of cAMP/CREB downstream signals with protein kinase A (PKA) inhibitor KT5720 partially suppressed osthole-mediated osteogenesis by inhibiting the elevation of transcription factor, osterix. In conclusion, osthole shows osteopromotive effect on osteoblasts in vitro and in vivo. Osthole-mediated osteogenesis is related to activation of the cAMP/CREB signaling pathway and downstream osterix expression.
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Affiliation(s)
- Zhong-Rong Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Wing Nang Leung
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Gang Li
- Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Siu Kai Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Xiong Lu
- Key Lab of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Yin Mei Wong
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Chun Wai Chan
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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43
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Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Nucleic Acids Res 2017; 45:1281-1296. [PMID: 28003475 PMCID: PMC5388401 DOI: 10.1093/nar/gkw1214] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
Molecular changes underlying stem cell differentiation are of fundamental interest. scRNA-seq on murine hematopoietic stem cells (HSC) and their progeny MPP1 separated the cells into 3 main clusters with distinct features: active, quiescent, and an un-characterized cluster. Induction of anemia resulted in mobilization of the quiescent to the active cluster and of the early to later stage of cell cycle, with marked increase in expression of certain transcription factors (TFs) while maintaining expression of interferon response genes. Cells with surface markers of long term HSC increased the expression of a group of TFs expressed highly in normal cycling MPP1 cells. However, at least Id1 and Hes1 were significantly activated in both HSC and MPP1 cells in anemic mice. Lineage-specific genes were differently expressed between cells, and correlated with the cell cycle stages with a specific augmentation of erythroid related genes in the G2/M phase. Most lineage specific TFs were stochastically expressed in the early precursor cells, but a few, such as Klf1, were detected only at very low levels in few precursor cells. The activation of these factors may correlate with stages of differentiation. This study reveals effects of cell cycle progression on the expression of lineage specific genes in precursor cells, and suggests that hematopoietic stress changes the balance of renewal and differentiation in these homeostatic cells.
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Affiliation(s)
- Jennifer Yang
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Yoshiaki Tanaka
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Montrell Seay
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Zhen Li
- Department of Neurobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jiaqi Jin
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Lana Xia Garmire
- Epidemiology Program, University of Hawaii Cancer Center, HI, USA
| | - Xun Zhu
- Epidemiology Program, University of Hawaii Cancer Center, HI, USA
| | - Ashley Taylor
- Hematology, Yale Comprehensive Cancer Center and Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Weidong Li
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,JiangXi Key Laboratory of Systems Biomedicine, Jiujiang University, Jiangxi, PR China
| | - Ghia Euskirchen
- Department of Genetics, Stanford University, Palo, Alto, CA, USA
| | - Stephanie Halene
- Hematology, Yale Comprehensive Cancer Center and Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Palo, Alto, CA, USA
| | - In-Hyun Park
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Xinghua Pan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Key Laboratory of Biochip Technology, Southern Medical University, Guangzhou, Guangdong, PR China
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44
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D’Arrigo D, Bottagisio M, Lopa S, Moretti M, B. Lovati A. Tissue engineering approaches to develop decellularized tendon matrices functionalized with progenitor cells cultured under undifferentiated and tenogenic conditions. AIMS BIOENGINEERING 2017. [DOI: 10.3934/bioeng.2017.4.431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Cannoodt R, Saelens W, Saeys Y. Computational methods for trajectory inference from single-cell transcriptomics. Eur J Immunol 2016; 46:2496-2506. [DOI: 10.1002/eji.201646347] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/30/2016] [Accepted: 09/26/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Robrecht Cannoodt
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
- Center for Medical Genetics; Ghent University; Ghent Belgium
- Cancer Research Institute Ghent (CRIG); Ghent Belgium
| | - Wouter Saelens
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine group; VIB Inflammation Research Center; Ghent Belgium
- Department of Internal Medicine; Ghent University; Ghent Belgium
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46
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Kwon M, Kim JM, Lee K, Park SY, Lim HS, Kim T, Jeong D. Synchronized Cell Cycle Arrest Promotes Osteoclast Differentiation. Int J Mol Sci 2016; 17:ijms17081292. [PMID: 27517906 PMCID: PMC5000689 DOI: 10.3390/ijms17081292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 01/26/2023] Open
Abstract
Osteoclast progenitors undergo cell cycle arrest before differentiation into osteoclasts, induced by exposure to macrophage colony-stimulating factor (M-CSF) and receptor activator of nuclear factor-κB ligand (RANKL). The role of such cell cycle arrest in osteoclast differentiation has remained unclear, however. We here examined the effect of synchronized cell cycle arrest on osteoclast formation. Osteoclast progenitors deprived of M-CSF in culture adopted a uniform morphology and exhibited cell cycle arrest at the G0–G1 phase in association with both down-regulation of cyclins A and D1 as well as up-regulation of the cyclin-dependent kinase inhibitor p27Kip1. Such M-CSF deprivation also promoted the differentiation of osteoclast progenitors into multinucleated osteoclasts expressing high levels of osteoclast marker proteins such as NFATc1, c-Fos, Atp6v0d2, cathepsin K, and integrin β3 on subsequent exposure to M-CSF and RANKL. Our results suggest that synchronized arrest and reprogramming of osteoclast progenitors renders them poised to respond to inducers of osteoclast formation. Further characterization of such effects may facilitate induction of the differentiation of heterogeneous and multipotent cells into desired cell lineages.
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Affiliation(s)
- Minsuk Kwon
- Laboratory of Bone Metabolism and Control, Department of Microbiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
| | - Jin-Man Kim
- Laboratory of Bone Metabolism and Control, Department of Microbiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
| | - Kyunghee Lee
- Laboratory of Bone Metabolism and Control, Department of Microbiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
| | - So-Young Park
- Department of Physiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
| | - Hyun-Sook Lim
- Department of Public Health Administration, Hanyang Women's University, Seoul 04763, Korea.
| | - Taesoo Kim
- Clinical Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Korea.
| | - Daewon Jeong
- Laboratory of Bone Metabolism and Control, Department of Microbiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
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47
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Narula J, Fujita M, Igoshin OA. Functional requirements of cellular differentiation: lessons from Bacillus subtilis. Curr Opin Microbiol 2016; 34:38-46. [PMID: 27501460 DOI: 10.1016/j.mib.2016.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/11/2016] [Indexed: 01/09/2023]
Abstract
Successful execution of differentiation programs requires cells to assess multitudes of internal and external cues and respond with appropriate gene expression programs. Here, we review how Bacillus subtilis sporulation network deals with these tasks focusing on the lessons generalizable to other systems. With feedforward loops controlling both production and activation of downstream transcriptional regulators, cells achieve ultrasensitive threshold-like responses. The arrangement of sporulation network genes on the chromosome and transcriptional feedback loops allow coordination of sporulation decision with DNA-replication. Furthermore, to assess the starvation conditions without sensing specific metabolites, cells respond to changes in their growth rates with increased activity of sporulation master regulator. These design features of the sporulation network enable cells to robustly decide between vegetative growth and sporulation.
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Affiliation(s)
- Jatin Narula
- Department of Bioengineering and Center for Theoretical Biological Physics, Rice University, United States
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, United States
| | - Oleg A Igoshin
- Department of Bioengineering and Center for Theoretical Biological Physics, Rice University, United States.
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48
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Abstract
Current efforts in cellular disease modeling and regenerative medicine are limited by the paucity of cell types that can be generated in the laboratory. A new study introduces a computational framework, Mogrify, that uses network biology to predict combinations of transcription factors necessary for direct conversion between human cell types to ameliorate this issue.
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49
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Ko CI, Fan Y, de Gannes M, Wang Q, Xia Y, Puga A. Repression of the Aryl Hydrocarbon Receptor Is Required to Maintain Mitotic Progression and Prevent Loss of Pluripotency of Embryonic Stem Cells. Stem Cells 2016; 34:2825-2839. [DOI: 10.1002/stem.2456] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Chia-I Ko
- Department of Environmental Health and Center for Environmental Genetics; University of Cincinnati College of Medicine; Cincinnati Ohio USA
| | - Yunxia Fan
- Department of Environmental Health and Center for Environmental Genetics; University of Cincinnati College of Medicine; Cincinnati Ohio USA
| | - Matthew de Gannes
- Department of Environmental Health and Center for Environmental Genetics; University of Cincinnati College of Medicine; Cincinnati Ohio USA
| | - Qin Wang
- Department of Environmental Health and Center for Environmental Genetics; University of Cincinnati College of Medicine; Cincinnati Ohio USA
| | - Ying Xia
- Department of Environmental Health and Center for Environmental Genetics; University of Cincinnati College of Medicine; Cincinnati Ohio USA
| | - Alvaro Puga
- Department of Environmental Health and Center for Environmental Genetics; University of Cincinnati College of Medicine; Cincinnati Ohio USA
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50
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Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells. Sci Rep 2016; 6:28112. [PMID: 27346849 PMCID: PMC4921813 DOI: 10.1038/srep28112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/31/2016] [Indexed: 11/08/2022] Open
Abstract
The high proliferation rate of embryonic stem cells (ESCs) is thought to arise partly from very low expression of p21. However, how p21 is suppressed in ESCs has been unclear. We found that p53 binds to the p21 promoter in human ESCs (hESCs) as efficiently as in differentiated human mesenchymal stem cells, however it does not promote p21 transcription in hESCs. We observed an enrichment for both the repressive histone H3K27me3 and activating histone H3K4me3 chromatin marks at the p21 locus in hESCs, suggesting it is a suppressed, bivalent domain which overrides activation by p53. Reducing H3K27me3 methylation in hESCs rescued p21 expression, and ectopic expression of p21 in hESCs triggered their differentiation. Further, we uncovered a subset of bivalent promoters bound by p53 in hESCs that are similarly induced upon differentiation in a p53-dependent manner, whereas p53 promotes the transcription of other target genes which do not show an enrichment of H3K27me3 in ESCs. Our studies reveal a unique epigenetic strategy used by ESCs to poise undesired p53 target genes, thus balancing the maintenance of pluripotency in the undifferentiated state with a robust response to differentiation signals, while utilizing p53 activity to maintain genomic stability and homeostasis in ESCs.
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