1
|
Martin CA, Radhakrishnan S, Ribelles JLG, Trentz O, Eak N, Reddy MS, Rela M, Subbaraya NK. Adipose tissue derived stromal cells in a gelatin based 3D matrix with exclusive ascorbic acid signalling emerged as a novel neural tissue engineering construct – An innovative prototype for soft tissue. Regen Biomater 2022; 9:rbac031. [PMID: 35702348 PMCID: PMC9188297 DOI: 10.1093/rb/rbac031] [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: 12/11/2021] [Revised: 03/30/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
The current study investigated a triad, which comprises of adipose tissue derived stem cells isolated from infrapatellar fat pad and gelatin/polyvinyl alcohol (PVA)-based matrix with exclusive ascorbic acid signalling. Though, the bio-mechanical properties of the gelatin–PVA blended scaffolds in wet condition are equivalent to the ECM of soft tissues in general, in this study, the triad was tested as a model for neural tissue engineering. Apart from being cytocompatible and biocompatible, the porosity of the scaffold has been designed in such a manner that it facilitates the cell signalling and enables the exchange of nutrients and gases. The highly proliferative stem cells from Passage 2 were characterized using both, mesenchymal and embryonic stem cell markers. As an initial exploration the mesenchymal stem cells at Passage 4 were exposed to ascorbic acid and basic fibroblast growth factor signalling for neuronal differentiation in 2D environment independently. The MSCs successfully differentiated and acquired neuron specific markers related to cytoskeleton and synapses. Subsequently, three phases of experiments have been conducted on the 3D gelatin/PVA matrix to prove their efficacy, the growth of stem cells, growth of differentiated neurons and the in situ growth and differentiation of MSCs. The scaffold was conducive and directed MSCs to neuronal lineage under specific signalling. Overall, this organotypic model triad could open a new avenue in the field of soft tissue engineering as a simple and effective tissue construct.
Collapse
Affiliation(s)
- Catherine Ann Martin
- Crystal Growth Centre, Anna University, Chennai-600025, India
- Cell Laboratory, National Foundation for Liver Research, Chrompet, Chennai-600044, India
| | - Subathra Radhakrishnan
- Cell Laboratory, National Foundation for Liver Research, Chrompet, Chennai-600044, India
| | - Jose Luis Gómez Ribelles
- Center for Biomaterials and Tissue Engineering (CBIT), Universitat Politècnica de València, Camino de Vera s/n., 46022, Valencia, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - Omana Trentz
- MIOT Institute of Research, MIOT Hospitals, Chennai-600089, India
| | - Nivethaa Eak
- Crystal Growth Centre, Anna University, Chennai-600025, India
| | - Mettu Srinivas Reddy
- Cell Laboratory, National Foundation for Liver Research, Chrompet, Chennai-600044, India
| | - Mohamed Rela
- Cell Laboratory, National Foundation for Liver Research, Chrompet, Chennai-600044, India
| | | |
Collapse
|
2
|
Nanan KK, Sturgill DM, Prigge MF, Thenoz M, Dillman AA, Mandler MD, Oberdoerffer S. TET-Catalyzed 5-Carboxylcytosine Promotes CTCF Binding to Suboptimal Sequences Genome-wide. iScience 2019; 19:326-339. [PMID: 31404833 PMCID: PMC6699469 DOI: 10.1016/j.isci.2019.07.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/23/2019] [Accepted: 07/25/2019] [Indexed: 01/01/2023] Open
Abstract
The mechanisms supporting dynamic regulation of CTCF-binding sites remain poorly understood. Here we describe the TET-catalyzed 5-methylcytosine derivative, 5-carboxylcytosine (5caC), as a factor driving new CTCF binding within genomic DNA. Through a combination of in vivo and in vitro approaches, we reveal that 5caC generally strengthens CTCF association with DNA and facilitates binding to suboptimal sequences. Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ~13,000 new CTCF sites. The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength. As CTCF has multiple roles in gene expression, these findings have wide-reaching implications and point to induced 5caC as a potential mechanism to achieve differential CTCF binding in cells.
Collapse
Affiliation(s)
- Kyster K Nanan
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David M Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria F Prigge
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Morgan Thenoz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allissa A Dillman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
3
|
Roy AR, Ahmed A, DiStefano PV, Chi L, Khyzha N, Galjart N, Wilson MD, Fish JE, Delgado-Olguín P. The transcriptional regulator CCCTC-binding factor limits oxidative stress in endothelial cells. J Biol Chem 2018; 293:8449-8461. [PMID: 29610276 PMCID: PMC5986204 DOI: 10.1074/jbc.m117.814699] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 03/28/2018] [Indexed: 12/22/2022] Open
Abstract
The CCCTC-binding factor (CTCF) is a versatile transcriptional regulator required for embryogenesis, but its function in vascular development or in diseases with a vascular component is poorly understood. Here, we found that endothelial Ctcf is essential for mouse vascular development and limits accumulation of reactive oxygen species (ROS). Conditional knockout of Ctcf in endothelial progenitors and their descendants affected embryonic growth, and caused lethality at embryonic day 10.5 because of defective yolk sac and placental vascular development. Analysis of global gene expression revealed Frataxin (Fxn), the gene mutated in Friedreich's ataxia (FRDA), as the most strongly down-regulated gene in Ctcf-deficient placental endothelial cells. Moreover, in vitro reporter assays showed that Ctcf activates the Fxn promoter in endothelial cells. ROS are known to accumulate in the endothelium of FRDA patients. Importantly, Ctcf deficiency induced ROS-mediated DNA damage in endothelial cells in vitro, and in placental endothelium in vivo Taken together, our findings indicate that Ctcf promotes vascular development and limits oxidative stress in endothelial cells. These results reveal a function for Ctcf in vascular development, and suggest a potential mechanism for endothelial dysfunction in FRDA.
Collapse
Affiliation(s)
- Anna R Roy
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Abdalla Ahmed
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter V DiStefano
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Lijun Chi
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Nadiya Khyzha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Genetics and Genome Biology Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Jason E Fish
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario M5G 2C4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and
- Heart and Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Ontario M5S 3H2, Canada
| | - Paul Delgado-Olguín
- From the Translational Medicine Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada,
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Heart and Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Ontario M5S 3H2, Canada
| |
Collapse
|
4
|
Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue. Proc Natl Acad Sci U S A 2018; 115:E5096-E5105. [PMID: 29760084 DOI: 10.1073/pnas.1802611115] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Obesity is characterized by an accumulation of macrophages in adipose, some of which form distinct crown-like structures (CLS) around fat cells. While multiple discrete adipose tissue macrophage (ATM) subsets are thought to exist, their respective effects on adipose tissue, and the transcriptional mechanisms that underlie the functional differences between ATM subsets, are not well understood. We report that obese fat tissue of mice and humans contain multiple distinct populations of ATMs with unique tissue distributions, transcriptomes, chromatin landscapes, and functions. Mouse Ly6c ATMs reside outside of CLS and are adipogenic, while CD9 ATMs reside within CLS, are lipid-laden, and are proinflammatory. Adoptive transfer of Ly6c ATMs into lean mice activates gene programs typical of normal adipocyte physiology. By contrast, adoptive transfer of CD9 ATMs drives gene expression that is characteristic of obesity. Importantly, human adipose tissue contains similar ATM populations, including lipid-laden CD9 ATMs that increase with body mass. These results provide a higher resolution of the cellular and functional heterogeneity within ATMs and provide a framework within which to develop new immune-directed therapies for the treatment of obesity and related sequela.
Collapse
|
5
|
Marshall AD, Bailey CG, Rasko JEJ. CTCF and BORIS in genome regulation and cancer. Curr Opin Genet Dev 2013; 24:8-15. [PMID: 24657531 DOI: 10.1016/j.gde.2013.10.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 10/25/2022]
Abstract
CTCF plays a vital role in chromatin structure and function. CTCF is ubiquitously expressed and plays diverse roles in gene regulation, imprinting, insulation, intra/interchromosomal interactions, nuclear compartmentalisation, and alternative splicing. CTCF has a single paralogue, the testes-specific CTCF-like gene (CTCFL)/BORIS. CTCF and BORIS can be deregulated in cancer. The tumour suppressor gene CTCF can be mutated or deleted in cancer, or CTCF DNA binding can be altered by epigenetic changes. BORIS is aberrantly expressed frequently in cancer, leading some to propose a pro-tumourigenic role for BORIS. However, BORIS can inhibit cell proliferation, and is mutated in cancer similarly to CTCF suggesting BORIS activation in cancer may be due to global genetic or epigenetic changes typical of malignant transformation.
Collapse
Affiliation(s)
- Amy D Marshall
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia; Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, NSW, Australia.
| |
Collapse
|
6
|
Huang K, Jia J, Wu C, Yao M, Li M, Jin J, Jiang C, Cai Y, Pei D, Pan G, Yao H. Ribosomal RNA gene transcription mediated by the master genome regulator protein CCCTC-binding factor (CTCF) is negatively regulated by the condensin complex. J Biol Chem 2013; 288:26067-26077. [PMID: 23884423 DOI: 10.1074/jbc.m113.486175] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CCCTC-binding factor (CTCF) is a ubiquitously expressed "master weaver" and plays multiple functions in the genome, including transcriptional activation/repression, chromatin insulation, imprinting, X chromosome inactivation, and high-order chromatin organization. It has been shown that CTCF facilitates the recruitment of the upstream binding factor onto ribosomal DNA (rDNA) and regulates the local epigenetic state of rDNA repeats. However, the mechanism by which CTCF modulates rRNA gene transcription has not been well understood. Here we found that wild-type CTCF augments the pre-rRNA level, cell size, and cell growth in cervical cancer cells. In contrast, RNA interference-mediated knockdown of CTCF reduced pre-rRNA transcription. CTCF positively regulates rRNA gene transcription in a RNA polymerase I-dependent manner. We identified an RRGR motif as a putative nucleolar localization sequence in the C-terminal region of CTCF that is required for activating rRNA gene transcription. Using mass spectrometry, we identified SMC2 and SMC4, two subunits of condensin complexes that interact with CTCF. Condensin negatively regulates CTCF-mediated rRNA gene transcription. Knockdown of SMC2 expression significantly facilitates the loading of CTCF and the upstream binding factor onto the rDNA locus and increases histone acetylation across the rDNA locus. Taken together, our study suggests that condensin competes with CTCF in binding to a specific rDNA locus and negatively regulates CTCF-mediated rRNA gene transcription.
Collapse
Affiliation(s)
- Kaimeng Huang
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the College of Life Science, Jilin University, Changchun, Jilin 130012, China, and
| | - Jinping Jia
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wu
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Mingze Yao
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Min Li
- the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jingji Jin
- the College of Life Science, Jilin University, Changchun, Jilin 130012, China, and
| | - Cizhong Jiang
- the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yong Cai
- the College of Life Science, Jilin University, Changchun, Jilin 130012, China, and
| | - Duanqing Pei
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Guangjin Pan
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,.
| | - Hongjie Yao
- From the Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,.
| |
Collapse
|
7
|
Paredes SH, Melgar MF, Sethupathy P. Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index. ACTA ACUST UNITED AC 2012; 29:1485-7. [PMID: 23047559 DOI: 10.1093/bioinformatics/bts596] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION It has been known for more than 2 decades that after RNA polymerase II (RNAPII) initiates transcription, it can enter into a paused or stalled state immediately downstream of the transcription start site before productive elongation. Recent advances in high-throughput genomic technologies facilitated the discovery that RNAPII pausing at promoters is a widespread physiologically regulated phenomenon. The molecular underpinnings of pausing are incompletely understood. The CCCTC-factor (CTCF) is a ubiquitous nuclear factor that has diverse regulatory functions, including a recently discovered role in promoting RNAPII pausing at splice sites. RESULTS In this study, we analyzed CTCF binding sites and nascent transcriptomic data from three different cell types, and found that promoter-proximal CTCF binding is significantly associated with RNAPII pausing.
Collapse
Affiliation(s)
- Sur Herrera Paredes
- Curriculum in Bioinformatics and Computational Biology, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | |
Collapse
|