1
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Roy B, Pekec T, Yuan L, Shivashankar GV. Implanting mechanically reprogrammed fibroblasts for aged tissue regeneration and wound healing. Aging Cell 2024; 23:e14032. [PMID: 38010905 PMCID: PMC10861198 DOI: 10.1111/acel.14032] [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: 04/23/2023] [Revised: 08/22/2023] [Accepted: 10/05/2023] [Indexed: 11/29/2023] Open
Abstract
Cell-based therapies are essential for tissue regeneration and wound healing during aging. Autologous transplantation of aging cells is ineffective due to their increased senescence and reduced tissue remodeling capabilities. Alternatively, implanting reprogrammed aged cells provides unique opportunities. In this paper, we demonstrate the implantation of partially reprogrammed aged human dermal fibroblasts into in vitro aged skin models for tissue regeneration and wound healing. The partially reprogrammed cells were obtained using our previously reported, highly efficient mechanical approach. Implanted cells showed enhanced expression of extracellular matrix proteins in the large area of aged tissue. In addition, the implanted cells at wound sites showed increased extracellular matrix protein synthesis and matrix alignment. Transcriptome analysis, combined with chromatin biomarkers, revealed these implanted cells upregulated tissue regeneration and wound healing pathways. Collectively our results provide a novel, nongenetic, partial reprogramming of aged cells for cell-based therapies in regenerative medicine.
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Affiliation(s)
- Bibhas Roy
- Division of Biology and ChemistryPaul Scherrer InstituteVilligenSwitzerland
| | - Tina Pekec
- Division of Biology and ChemistryPaul Scherrer InstituteVilligenSwitzerland
| | - Luezhen Yuan
- Division of Biology and ChemistryPaul Scherrer InstituteVilligenSwitzerland
- Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
| | - G. V. Shivashankar
- Division of Biology and ChemistryPaul Scherrer InstituteVilligenSwitzerland
- Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
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2
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Natesan R, Gowrishankar K, Kuttippurathu L, Kumar PBS, Rao M. Active Remodeling of Chromatin and Implications for In Vivo Folding. J Phys Chem B 2021; 126:100-109. [DOI: 10.1021/acs.jpcb.1c08655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ramakrishnan Natesan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Lakshmi Kuttippurathu
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - P. B. Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 668557, Kerala, India
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
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3
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Lee JH, Kim DH, Lee HH, Kim HW. Role of nuclear mechanosensitivity in determining cellular responses to forces and biomaterials. Biomaterials 2019; 197:60-71. [PMID: 30641265 DOI: 10.1016/j.biomaterials.2019.01.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/25/2018] [Accepted: 01/05/2019] [Indexed: 01/17/2023]
Abstract
Tissue engineers use biomaterials or apply forces to alter cell behaviors and cure damaged/diseased tissues. The external physical cues perceived by cells are transduced intracellularly along the mechanosensitive machineries, including subcellular adhesion molecules and cytoskeletons. The signals are further channeled to a nucleus through the physical links of nucleoskeleton and cytoskeleton or the biochemical translocation of transcription factors. Thus, the external cues are thought to affect directly or indirectly the nucleus and the genetic transcriptional process, ultimately determining cell fate. Here we communicate the importance of such mechanotransductory processes in cell and tissue engineering where external forces- or biomaterials-related physical cues essentially regulate cellular behaviors, with an emphasis on the mechanosensing and signaling along the road to a nucleus.
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Affiliation(s)
- Jung-Hwan Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Republic of Korea; UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea
| | - Dong-Hwee Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 20841, South Korea
| | - Hae-Hyoung Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Republic of Korea; UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Republic of Korea; Department of Nanobiomedical Science & BK21 PLUS Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Republic of Korea; UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea.
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4
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Bernheim-Groswasser A, Gov NS, Safran SA, Tzlil S. Living Matter: Mesoscopic Active Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707028. [PMID: 30256463 DOI: 10.1002/adma.201707028] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/27/2018] [Indexed: 06/08/2023]
Abstract
An introduction to the physical properties of living active matter at the mesoscopic scale (tens of nanometers to micrometers) and their unique features compared with "dead," nonactive matter is presented. This field of research is increasingly denoted as "biological physics" where physics includes chemical physics, soft matter physics, hydrodynamics, mechanics, and the related engineering sciences. The focus is on the emergent properties of these systems and their collective behavior, which results in active self-organization and how they relate to cellular-level biological function. These include locomotion (cell motility and migration) forces that give rise to cell division, the growth and form of cellular assemblies in development, the beating of heart cells, and the effects of mechanical perturbations such as shear flow (in the bloodstream) or adhesion to other cells or tissues. An introduction to the fundamental concepts and theory with selected experimental examples related to the authors' own research is presented, including red-blood-cell membrane fluctuations, motion of the nucleus within an egg cell, self-contracting acto-myosin gels, and structure and beating of heart cells (cardiomyocytes), including how they can be driven by an oscillating, mechanical probe.
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Affiliation(s)
- Anne Bernheim-Groswasser
- Department of Chemical Engineering and Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Nir S Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Samuel A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shelly Tzlil
- Department of Mechanical Engineering, Technion, Haifa, 3200003, Israel
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5
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Uhler C, Shivashankar GV. Nuclear Mechanopathology and Cancer Diagnosis. Trends Cancer 2018; 4:320-331. [PMID: 29606315 DOI: 10.1016/j.trecan.2018.02.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 11/29/2022]
Abstract
Abnormalities in nuclear and chromatin organization are hallmarks of many diseases including cancer. In this review, we highlight our understanding of how the cellular microenvironment regulates nuclear morphology and, with it, the spatial organization of chromosomes and genes, resulting in cell type-specific genomic programs. We also discuss the molecular basis for maintaining nuclear and genomic integrity and how alterations in nuclear mechanotransduction pathways result in various diseases. Finally, we highlight the importance of digital pathology based on nuclear morphometric features combined with single-cell genomics for early cancer diagnostics.
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Affiliation(s)
- Caroline Uhler
- Department of Electrical Engineering & Computer Science, Institute for Data, Systems & Society, MIT, Cambridge, MA, USA
| | - G V Shivashankar
- Mechanobiology Institute, National University of Singapore, Singapore; FIRC Institute of Molecular Oncology (IFOM), Milan, Italy.
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6
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Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription. Proc Natl Acad Sci U S A 2017; 114:13714-13719. [PMID: 29229825 PMCID: PMC5748172 DOI: 10.1073/pnas.1708028115] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We develop a network analysis approach for identifying clusters of interactions between chromosomes, which we validate experimentally. Our method integrates 1D features of the genome, such as epigenetic marks, with 3D interactions, allowing us to study spatially colocalized regions between chromosomes that are functionally relevant. We observe that clusters of interchromosomal regions fall into active and inactive categories. We find that active clusters share transcription factors and are enriched for transcriptional machinery, suggesting that chromosome intermingling regions play a key role in genome regulation. Our method provides a unique quantitative framework that can be broadly applied to study the principles of genome organization and regulation during processes such as cell differentiation and reprogramming. The 3D structure of the genome plays a key role in regulatory control of the cell. Experimental methods such as high-throughput chromosome conformation capture (Hi-C) have been developed to probe the 3D structure of the genome. However, it remains a challenge to deduce from these data chromosome regions that are colocalized and coregulated. Here, we present an integrative approach that leverages 1D functional genomic features (e.g., epigenetic marks) with 3D interactions from Hi-C data to identify functional interchromosomal interactions. We construct a weighted network with 250-kb genomic regions as nodes and Hi-C interactions as edges, where the edge weights are given by the correlation between 1D genomic features. Individual interacting clusters are determined using weighted correlation clustering on the network. We show that intermingling regions generally fall into either active or inactive clusters based on the enrichment for RNA polymerase II (RNAPII) and H3K9me3, respectively. We show that active clusters are hotspots for transcription factor binding sites. We also validate our predictions experimentally by 3D fluorescence in situ hybridization (FISH) experiments and show that active RNAPII is enriched in predicted active clusters. Our method provides a general quantitative framework that couples 1D genomic features with 3D interactions from Hi-C to probe the guiding principles that link the spatial organization of the genome with regulatory control.
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7
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Chromosome Intermingling: Mechanical Hotspots for Genome Regulation. Trends Cell Biol 2017; 27:810-819. [DOI: 10.1016/j.tcb.2017.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/20/2017] [Accepted: 06/20/2017] [Indexed: 11/20/2022]
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8
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Uhler C, Shivashankar GV. Regulation of genome organization and gene expression by nuclear mechanotransduction. Nat Rev Mol Cell Biol 2017; 18:717-727. [PMID: 29044247 DOI: 10.1038/nrm.2017.101] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is well established that cells sense chemical signals from their local microenvironment and transduce them to the nucleus to regulate gene expression programmes. Although a number of experiments have shown that mechanical cues can also modulate gene expression, the underlying mechanisms are far from clear. Nevertheless, we are now beginning to understand how mechanical cues are transduced to the nucleus and how they influence nuclear mechanics, genome organization and transcription. In particular, recent progress in super-resolution imaging, in genome-wide application of RNA sequencing, chromatin immunoprecipitation and chromosome conformation capture and in theoretical modelling of 3D genome organization enables the exploration of the relationship between cell mechanics, 3D chromatin configurations and transcription, thereby shedding new light on how mechanical forces regulate gene expression.
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Affiliation(s)
- Caroline Uhler
- Department of Electrical Engineering and Computer Science, Laboratory of Information and Decision Systems, Institute for Data, Systems and Society, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - G V Shivashankar
- Mechanobiology Institute, National University of Singapore, 119077 Singapore.,Italian Foundation for Cancer Research (FIRC) Institute of Molecular Oncology (IFOM), Milan 20139, Italy
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9
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Wang Y, Nagarajan M, Uhler C, Shivashankar GV. Orientation and repositioning of chromosomes correlate with cell geometry-dependent gene expression. Mol Biol Cell 2017; 28:1997-2009. [PMID: 28615317 PMCID: PMC5541849 DOI: 10.1091/mbc.e16-12-0825] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 12/13/2022] Open
Abstract
Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases.
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Affiliation(s)
- Yejun Wang
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore
| | - Mallika Nagarajan
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore
| | - Caroline Uhler
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore
- FIRC Institute for Molecular Oncology, 20139 Milan, Italy
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10
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Wang Y, Jain N, Nagarajan M, Maharana S, Iyer KV, Talwar S, Shivashankar GV. Coupling between chromosome intermingling and gene regulation during cellular differentiation. Methods 2017; 123:66-75. [PMID: 28554525 DOI: 10.1016/j.ymeth.2017.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/04/2017] [Accepted: 05/24/2017] [Indexed: 11/19/2022] Open
Abstract
In this article, we summarize current findings for the emergence of biophysical properties such as nuclear stiffness, chromatin compaction, chromosome positioning, and chromosome intermingling during stem cell differentiation, which eventually correlated with the changes of gene expression profiles during cellular differentiation. An overview is first provided to link stem cell differentiation with alterations in nuclear architecture, chromatin compaction, along with nuclear and chromatin dynamics. Further, we highlight the recent biophysical and molecular approaches, imaging methods and computational developments in characterizing transcription-related chromosome organization especially chromosome intermingling and nano-scale chromosomal contacts. Finally, the article ends with an outlook towards the emergence of a functional roadmap in setting up chromosome positioning and intermingling in a cell type specific manner during cellular differentiation.
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Affiliation(s)
- Yejun Wang
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Nikhil Jain
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Mallika Nagarajan
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Shovamayee Maharana
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - K Venkatesan Iyer
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Shefali Talwar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore; FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy.
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11
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Superresolution imaging of nanoscale chromosome contacts. Sci Rep 2017; 7:42422. [PMID: 28186153 PMCID: PMC5301241 DOI: 10.1038/srep42422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/09/2017] [Indexed: 12/29/2022] Open
Abstract
Co-expression of a specific group of genes requires physical associations among these genes, which form functional chromosomal contacts. While DNA fluorescence in situ hybridization (FISH) pinpoints the localization of genes within the 3D nuclear architecture, direct evidence of physical chromosomal contacts is still lacking. Here, we report a method for the direct visualization of transcription-dependent chromosomal contacts formed in two distinct mechanical states of cells. We prepared open chromatin spreads from isolated nuclei, ensuring 2D rendering of chromosome organization. Superresolution imaging of these chromatin spreads resolved the nanoscale organization of genome contacts. We optimized our imaging method using chromatin spreads from serum+/− cells. We then showed direct visualization of functional gene clusters targeted by YAP (Yes-associated protein) and SRF (Serum response factor) transcription factors. In addition, we showed the association of NF-κB bound gene clusters induced by TNF-α addition. Furthermore, EpiTect ChIP qPCR results showed that these nanoscale clusters were enriched with corresponding transcription factors. Taken together, our method provides a robust platform to directly visualize and study specific genome-wide chromosomal contacts.
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12
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Kim JJ, Bennett NK, Devita MS, Chahar S, Viswanath S, Lee EA, Jung G, Shao PP, Childers EP, Liu S, Kulesa A, Garcia BA, Becker ML, Hwang NS, Madabhushi A, Verzi MP, Moghe PV. Optical High Content Nanoscopy of Epigenetic Marks Decodes Phenotypic Divergence in Stem Cells. Sci Rep 2017; 7:39406. [PMID: 28051095 PMCID: PMC5209743 DOI: 10.1038/srep39406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022] Open
Abstract
While distinct stem cell phenotypes follow global changes in chromatin marks, single-cell chromatin technologies are unable to resolve or predict stem cell fates. We propose the first such use of optical high content nanoscopy of histone epigenetic marks (epi-marks) in stem cells to classify emergent cell states. By combining nanoscopy with epi-mark textural image informatics, we developed a novel approach, termed EDICTS (Epi-mark Descriptor Imaging of Cell Transitional States), to discern chromatin organizational changes, demarcate lineage gradations across a range of stem cell types and robustly track lineage restriction kinetics. We demonstrate the utility of EDICTS by predicting the lineage progression of stem cells cultured on biomaterial substrates with graded nanotopographies and mechanical stiffness, thus parsing the role of specific biophysical cues as sensitive epigenetic drivers. We also demonstrate the unique power of EDICTS to resolve cellular states based on epi-marks that cannot be detected via mass spectrometry based methods for quantifying the abundance of histone post-translational modifications. Overall, EDICTS represents a powerful new methodology to predict single cell lineage decisions by integrating high content super-resolution nanoscopy and imaging informatics of the nuclear organization of epi-marks.
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Affiliation(s)
- Joseph J. Kim
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Neal K. Bennett
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Mitchel S. Devita
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Sanjay Chahar
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Satish Viswanath
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Eunjee A. Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Giyoung Jung
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
- Division of Heath Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul P. Shao
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Erin P. Childers
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
| | - Shichong Liu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anthony Kulesa
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benjamin A. Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew L. Becker
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
| | - Nathaniel S. Hwang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Prabhas V. Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey, USA
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13
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Uhler C, Shivashankar G. Geometric control and modeling of genome reprogramming. BIOARCHITECTURE 2016; 6:76-84. [PMID: 27434579 PMCID: PMC6085119 DOI: 10.1080/19490992.2016.1201620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 12/29/2022]
Abstract
Cell geometry is tightly coupled to gene expression patterns within the tissue microenvironment. This perspective synthesizes evidence that the 3D organization of chromosomes is a critical intermediate for geometric control of genomic programs. Using a combination of experiments and modeling we outline approaches to decipher the mechano-genomic code that governs cellular homeostasis and reprogramming.
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Affiliation(s)
- Caroline Uhler
- Department of Electrical Engineering & Computer Science, and Institute for Data, Systems and Society, MIT, Cambridge, MA, USA
| | - G.V. Shivashankar
- Mechanobiology Institute National University of Singapore, Singapore
- FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
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14
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Maharana S, Iyer KV, Jain N, Nagarajan M, Wang Y, Shivashankar GV. Chromosome intermingling-the physical basis of chromosome organization in differentiated cells. Nucleic Acids Res 2016; 44:5148-60. [PMID: 26939888 PMCID: PMC5603959 DOI: 10.1093/nar/gkw131] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 02/19/2016] [Indexed: 12/16/2022] Open
Abstract
Chromosome territories (CTs) in higher eukaryotes occupy tissue-specific non-random three-dimensional positions in the interphase nucleus. To understand the mechanisms underlying CT organization, we mapped CT position and transcriptional changes in undifferentiated embryonic stem (ES) cells, during early onset of mouse ES cell differentiation and in terminally differentiated NIH3T3 cells. We found chromosome intermingling volume to be a reliable CT surface property, which can be used to define CT organization. Our results show a correlation between the transcriptional activity of chromosomes and heterologous chromosome intermingling volumes during differentiation. Furthermore, these regions were enriched in active RNA polymerase and other histone modifications in the differentiated states. These findings suggest a correlation between the evolution of transcription program in modifying CT architecture in undifferentiated stem cells. This leads to the formation of functional CT surfaces, which then interact to define the three-dimensional CT organization during differentiation.
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Affiliation(s)
| | - K Venkatesan Iyer
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Nikhil Jain
- Mechanobiology Institute, National University of Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore
| | - Mallika Nagarajan
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Yejun Wang
- Mechanobiology Institute, National University of Singapore, Singapore
| | - G V Shivashankar
- Mechanobiology Institute, National University of Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore
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15
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Diament A, Pinter RY, Tuller T. Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function. Nat Commun 2014; 5:5876. [PMID: 25510862 DOI: 10.1038/ncomms6876] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 11/17/2014] [Indexed: 01/08/2023] Open
Abstract
It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of three-dimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.
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Affiliation(s)
- Alon Diament
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ron Y Pinter
- Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Tamir Tuller
- 1] Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel [2] The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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16
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Swift J, Discher DE. The nuclear lamina is mechano-responsive to ECM elasticity in mature tissue. J Cell Sci 2014; 127:3005-15. [PMID: 24963133 DOI: 10.1242/jcs.149203] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How cells respond to physical cues in order to meet and withstand the physical demands of their immediate surroundings has been of great interest for many years, with current research efforts focused on mechanisms that transduce signals into gene expression. Pathways that mechano-regulate the entry of transcription factors into the cell nucleus are emerging, and our most recent studies show that the mechanical properties of the nucleus itself are actively controlled in response to the elasticity of the extracellular matrix (ECM) in both mature and developing tissue. In this Commentary, we review the mechano-responsive properties of nuclei as determined by the intermediate filament lamin proteins that line the inside of the nuclear envelope and that also impact upon transcription factor entry and broader epigenetic mechanisms. We summarize the signaling pathways that regulate lamin levels and cell-fate decisions in response to a combination of ECM mechanics and molecular cues. We will also discuss recent work that highlights the importance of nuclear mechanics in niche anchorage and cell motility during development, hematopoietic differentiation and cancer metastasis, as well as emphasizing a role for nuclear mechanics in protecting chromatin from stress-induced damage.
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Affiliation(s)
- Joe Swift
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dennis E Discher
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
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Ganai N, Sengupta S, Menon GI. Chromosome positioning from activity-based segregation. Nucleic Acids Res 2014; 42:4145-59. [PMID: 24459132 PMCID: PMC3985638 DOI: 10.1093/nar/gkt1417] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chromosomes within eukaryotic cell nuclei at interphase are not positioned at random, since gene-rich chromosomes are predominantly found towards the interior of the cell nucleus across a number of cell types. The physical mechanisms that could drive and maintain the spatial segregation of chromosomes based on gene density are unknown. Here, we identify a mechanism for such segregation, showing that the territorial organization of chromosomes, another central feature of nuclear organization, emerges naturally from our model. Our computer simulations indicate that gene density-dependent radial segregation of chromosomes arises as a robust consequence of differences in non-equilibrium activity across chromosomes. Arguing that such differences originate in the inhomogeneous distribution of ATP-dependent chromatin remodeling and transcription machinery on each chromosome, we show that a variety of non-random positional distributions emerge through the interplay of such activity, nuclear shape and specific interactions of chromosomes with the nuclear envelope. Results from our model are in reasonable agreement with experimental data and we make a number of predictions that can be tested in experiments.
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Affiliation(s)
- Nirmalendu Ganai
- Department of Physics, Nabadwip Vidyasagar College, Nabadwip, Nadia 741302, India, TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500075, India, Centre for Advanced Materials, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India, The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600 113, India, Mechanobiology Institute, National University of Singapore, T-Lab, #10-01, 5A Engineering Drive 1, Singapore 117411, Singapore and Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
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Turner LA, J. Dalby M. Nanotopography – potential relevance in the stem cell niche. Biomater Sci 2014; 2:1574-1594. [DOI: 10.1039/c4bm00155a] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanotopographical cues observed in vivo (such as in the sinusoid and bone) closely resemble nanotopographies that in vitro have been shown to promote niche relevant stem cells behaviours; specifically, retention of multipotency and osteogenic differentiation on ordered and disordered nano-pits respectively. These and other observations highlight a potential role for nano topography in the stem cell niche.
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Affiliation(s)
- Lesley-Anne Turner
- Centre for Cell Engineering
- Institute of Molecular
- Cell and Systems Biology
- College of Medical
- Veterinary and Life Sciences
| | - Matthew J. Dalby
- Centre for Cell Engineering
- Institute of Molecular
- Cell and Systems Biology
- College of Medical
- Veterinary and Life Sciences
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Jahed Z, Shams H, Mehrbod M, Mofrad MRK. Mechanotransduction pathways linking the extracellular matrix to the nucleus. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 310:171-220. [PMID: 24725427 DOI: 10.1016/b978-0-12-800180-6.00005-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cells contain several mechanosensing components that transduce mechanical signals into biochemical cascades. During cell-ECM adhesion, a complex network of molecules mechanically couples the extracellular matrix (ECM), cytoskeleton, and nucleoskeleton. The network comprises transmembrane receptor proteins and focal adhesions, which link the ECM and cytoskeleton. Additionally, recently identified protein complexes extend this linkage to the nucleus by linking the cytoskeleton and the nucleoskeleton. Despite numerous studies in this field, due to the complexity of this network, our knowledge of the mechanisms of cell-ECM adhesion at the molecular level remains remarkably incomplete. Herein, we present a review of the structures of key molecules involved in cell-ECM adhesion, along with an evaluation of their predicted roles in mechanical sensing. Additionally, specific binding events prompted by force-induced conformational changes of each molecule are discussed. Finally, we propose a model for the biomechanical events prominent in cell-ECM adhesion.
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Affiliation(s)
- Zeinab Jahed
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California at Berkeley, Berkeley, California, USA
| | - Hengameh Shams
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California at Berkeley, Berkeley, California, USA
| | - Mehrdad Mehrbod
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California at Berkeley, Berkeley, California, USA
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California at Berkeley, Berkeley, California, USA.
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Mehta IS, Kulashreshtha M, Chakraborty S, Kolthur-Seetharam U, Rao BJ. Chromosome territories reposition during DNA damage-repair response. Genome Biol 2013; 14:R135. [PMID: 24330859 PMCID: PMC4062845 DOI: 10.1186/gb-2013-14-12-r135] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 12/13/2013] [Indexed: 01/02/2023] Open
Abstract
Background Local higher-order chromatin structure, dynamics and composition of the DNA are known to determine double-strand break frequencies and the efficiency of repair. However, how DNA damage response affects the spatial organization of chromosome territories is still unexplored. Results Our report investigates the effect of DNA damage on the spatial organization of chromosome territories within interphase nuclei of human cells. We show that DNA damage induces a large-scale spatial repositioning of chromosome territories that are relatively gene dense. This response is dose dependent, and involves territories moving from the nuclear interior to the periphery and vice versa. Furthermore, we have found that chromosome territory repositioning is contingent upon double-strand break recognition and damage sensing. Importantly, our results suggest that this is a reversible process where, following repair, chromosome territories re-occupy positions similar to those in undamaged control cells. Conclusions Thus, our report for the first time highlights DNA damage-dependent spatial reorganization of whole chromosomes, which might be an integral aspect of cellular damage response.
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Shin JW, Swift J, Ivanovska I, Spinler KR, Buxboim A, Discher DE. Mechanobiology of bone marrow stem cells: from myosin-II forces to compliance of matrix and nucleus in cell forms and fates. Differentiation 2013; 86:77-86. [PMID: 23790394 PMCID: PMC3964600 DOI: 10.1016/j.diff.2013.05.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/22/2022]
Abstract
Adult stem cells and progenitors are of great interest for their clinical application as well as their potential to reveal deep sensitivities to microenvironmental factors. The bone marrow is a niche for at least two types of stem cells, and the prototype is the hematopoietic stem cell/progenitors (HSC/Ps), which have saved many thousands of patients for several decades now. In bone marrow, HSC/Ps interact functionally with marrow stromal cells that are often referred to as mesenchymal stem cells (MSCs) or derivatives thereof. Myosin and matrix elasticity greatly affect MSC function, and these mechanobiological factors are now being explored with HSC/Ps both in vitro and in vivo. Also emerging is a role for the nucleus as a mechanically sensitive organelle that is semi-permeable to transcription factors which are modified for nuclear entry by cytoplasmic mechanobiological pathways. Since therapies envisioned with induced pluripotent stem cells and embryonic stem cells generally involve in vitro commitment to an adult stem cell or progenitor, a very deep understanding of stem cell mechanobiology is essential to progress with these multi-potent cells.
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Affiliation(s)
- Jae-Won Shin
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA
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