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Xie G, Zhang L, Usman OH, Kumar S, Modak C, Patel D, Kavanaugh M, Mallory X, Wang YJ, Irianto J. Phenotypic, genomic, and transcriptomic heterogeneity in a pancreatic cancer cell line. Pancreas 2024:00006676-990000000-00169. [PMID: 38710020 DOI: 10.1097/mpa.0000000000002371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
OBJECTIVES To evaluate the suitability of the MIA PaCa-2 cell line for studying pancreatic cancer intratumor heterogeneity, we aim to further characterize the nature of MIA PaCa-2 cells' phenotypic, genomic, and transcriptomic heterogeneity. METHODS MIA PaCa-2 single-cell clones were established through flow cytometry. For the phenotypic study, we quantified the cellular morphology, proliferation rate, migration potential, and drug sensitivity of the clones. The chromosome copy number and transcriptomic profiles were quantified using SNPa and RNA-seq, respectively. RESULTS Four MIA PaCa-2 clones showed distinctive phenotypes, with differences in cellular morphology, proliferation rate, migration potential, and drug sensitivity. We also observed a degree of genomic variations between these clones in form of chromosome copy number alterations and single nucleotide variations, suggesting the genomic heterogeneity of the population, and the intrinsic genomic instability of MIA PaCa-2 cells. Lastly, transcriptomic analysis of the clones also revealed gene expression profile differences between the clones, including the uniquely regulated ITGAV, which dictates the morphology of MIA PaCa-2 clones. CONCLUSIONS MIA PaCa-2 is comprised of cells with distinctive phenotypes, heterogeneous genomes, and differential transcriptomic profiles, suggesting its suitability as a model to study the underlying mechanisms behind pancreatic cancer heterogeneity.
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Xie G, Toledo MP, Hu X, Yong HJ, Sanchez PS, Liu C, Naji A, Irianto J, Wang YJ. NKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing. BMC Genomics 2024; 25:427. [PMID: 38689254 PMCID: PMC11059690 DOI: 10.1186/s12864-024-10335-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Current approaches to profile the single-cell transcriptomics of human pancreatic endocrine cells almost exclusively rely on freshly isolated islets. However, human islets are limited in availability. Furthermore, the extensive processing steps during islet isolation and subsequent single cell dissolution might alter gene expressions. In this work, we report the development of a single-nucleus RNA sequencing (snRNA-seq) approach with targeted islet cell enrichment for endocrine-population focused transcriptomic profiling using frozen archival pancreatic tissues without islet isolation. RESULTS We cross-compared five nuclei isolation protocols and selected the citric acid method as the best strategy to isolate nuclei with high RNA integrity and low cytoplasmic contamination from frozen archival human pancreata. We innovated fluorescence-activated nuclei sorting based on the positive signal of NKX2-2 antibody to enrich nuclei of the endocrine population from the entire nuclei pool of the pancreas. Our sample preparation procedure generated high-quality single-nucleus gene-expression libraries while preserving the endocrine population diversity. In comparison with single-cell RNA sequencing (scRNA-seq) library generated with live cells from freshly isolated human islets, the snRNA-seq library displayed comparable endocrine cellular composition and cell type signature gene expression. However, between these two types of libraries, differential enrichments of transcripts belonging to different functional classes could be observed. CONCLUSIONS Our work fills a technological gap and helps to unleash frozen archival pancreatic tissues for molecular profiling targeting the endocrine population. This study opens doors to retrospective mappings of endocrine cell dynamics in pancreatic tissues of complex histopathology. We expect that our protocol is applicable to enrich nuclei for transcriptomics studies from various populations in different types of frozen archival tissues.
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Affiliation(s)
- Gengqiang Xie
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Maria Pilar Toledo
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Xue Hu
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Hyo Jeong Yong
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Pamela Sandoval Sanchez
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Chengyang Liu
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ali Naji
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Yue J Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA.
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3
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Usman OH, Kumar S, Walker RR, Xie G, Sumajit HC, Jalil AR, Ramakrishnan S, Dooling LJ, Wang YJ, Irianto J. Differential modulation of cellular phenotype and drug sensitivity by extracellular matrix proteins in primary and metastatic pancreatic cancer cells. Mol Biol Cell 2023; 34:ar130. [PMID: 37903222 PMCID: PMC10848942 DOI: 10.1091/mbc.e23-02-0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/06/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is reported to be the third highest cause of cancer-related deaths in the United States. PDAC is known for its high proportion of stroma, which accounts for 90% of the tumor mass. The stroma is made up of extracellular matrix (ECM) and nonmalignant cells such as inflammatory cells, cancer-associated fibroblasts, and lymphatic and blood vessels. Here, we decoupled the effects of the ECM on PDAC cell lines by culturing cells on surfaces coated with different ECM proteins. Our data show that the primary tumor-derived cell lines have different morphology depending on the ECM proteins on which they are cultured, while metastatic lesion-derived PDAC lines' morphology does not change with respect to the different ECM proteins. Similarly, ECM proteins modulate the proliferation rate and the gemcitabine sensitivity of the primary tumor PDAC cell lines, but not the metastatic PDAC lines. Lastly, transcriptomics analysis of the primary tumor PDAC cells cultured on different ECM proteins reveals the regulation of various pathways, such as cell cycle, cell-adhesion molecules, and focal adhesion, including the regulation of several integrin genes that are essential for ECM recognition.
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Affiliation(s)
- Olalekan H. Usman
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Sampath Kumar
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Reddick R. Walker
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Gengqiang Xie
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Hyeje C. Sumajit
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - AbdelAziz R. Jalil
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104
| | - Subramanian Ramakrishnan
- Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University College of Engineering, Tallahassee, FL 32310
| | - Lawrence J. Dooling
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104
| | - Yue Julia Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
| | - Jerome Irianto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306
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4
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Tobin MP, Pfeifer CR, Zhu PK, Hayes BH, Wang M, Vashisth M, Xia Y, Phan SH, Belt SA, Irianto J, Discher DE. Differences in cell shape, motility, and growth reflect chromosomal number variations that can be visualized with live-cell ChReporters. Mol Biol Cell 2023; 34:br19. [PMID: 37903225 PMCID: PMC10848937 DOI: 10.1091/mbc.e23-06-0207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023] Open
Abstract
Chromosome numbers often change dynamically in tumors and cultured cells, which complicates therapy as well as understanding genotype-mechanotype relationships. Here we use a live-cell "ChReporter" method to identify cells with a single chromosomal loss in efforts to better understand differences in cell shape, motility, and growth. We focus on a standard cancer line and first show clonal populations that retain the ChReporter exhibit large differences in cell and nuclear morphology as well as motility. Phenotype metrics follow simple rules, including migratory persistence scaling with speed, and cytoskeletal differences are evident from drug responses, imaging, and single-cell RNA sequencing. However, mechanotype-genotype relationships between fluorescent ChReporter-positive clones proved complex and motivated comparisons of clones that differ only in loss or retention of a Chromosome-5 ChReporter. When lost, fluorescence-null cells show low expression of Chromosome-5 genes, including a key tumor suppressor APC that regulates microtubules and proliferation. Colonies are compact, nuclei are rounded, and cells proliferate more, with drug results implicating APC, and patient survival data indicating an association in multiple tumor-types. Visual identification of genotype with ChReporters can thus help clarify mechanotype and mechano-evolution.
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Affiliation(s)
- Michael P. Tobin
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | | | | | - Brandon H. Hayes
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Mai Wang
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Manasvita Vashisth
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Yuntao Xia
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Steven H. Phan
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Susanna A. Belt
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Jerome Irianto
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E. Discher
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
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5
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Zhang L, Bass HW, Irianto J, Mallory X. Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data. Genome Res 2023; 33:gr.277249.122. [PMID: 37993137 PMCID: PMC10760445 DOI: 10.1101/gr.277249.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/25/2023] [Indexed: 11/24/2023]
Abstract
Single-cell DNA sequencing enables the construction of evolutionary trees that can reveal how tumors gain mutations and grow. Different whole-genome amplification procedures render genomic materials of different characteristics, often suitable for the detection of either single-nucleotide variation or copy number aberration, but not ideally for both. Consequently, this hinders the inference of a comprehensive phylogenetic tree and limits opportunities to investigate the interplay of SNVs and CNAs. Existing methods such as SCARLET and COMPASS require that the SNVs and CNAs are detected from the same sets of cells, which is technically challenging. Here we present a novel computational tool, SCsnvcna, that places SNVs on a tree inferred from CNA signals, whereas the sets of cells rendering the SNVs and CNAs are independent, offering a more practical solution in terms of the technical challenges. SCsnvcna is a Bayesian probabilistic model using both the genotype constraints on the tree and the cellular prevalence to search the optimal solution. Comprehensive simulations and comparison with seven state-of-the-art methods show that SCsnvcna is robust and accurate in a variety of circumstances. Particularly, SCsnvcna most frequently produces the lowest error rates, with ability to scale to a wide range of numerical values for leaf nodes in the tree, SNVs, and SNV cells. The application of SCsnvcna to two published colorectal cancer data sets shows highly consistent placement of SNV cells and SNVs with the original study while also supporting a refined placement of ATP7B, illustrating SCsnvcna's value in analyzing complex multitumor samples.
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Affiliation(s)
- Liting Zhang
- Department of Computer Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Jerome Irianto
- College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Xian Mallory
- Department of Computer Science, Florida State University, Tallahassee, Florida 32306, USA;
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6
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Dooling LJ, Andrechak JC, Hayes BH, Kadu S, Zhang W, Pan R, Vashisth M, Irianto J, Alvey CM, Ma L, Discher DE. Cooperative phagocytosis of solid tumours by macrophages triggers durable anti-tumour responses. Nat Biomed Eng 2023; 7:1081-1096. [PMID: 37095318 PMCID: PMC10791169 DOI: 10.1038/s41551-023-01031-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/27/2023] [Indexed: 04/26/2023]
Abstract
In solid tumours, the abundance of macrophages is typically associated with a poor prognosis. However, macrophage clusters in tumour-cell nests have been associated with survival in some tumour types. Here, by using tumour organoids comprising macrophages and cancer cells opsonized via a monoclonal antibody, we show that highly ordered clusters of macrophages cooperatively phagocytose cancer cells to suppress tumour growth. In mice with poorly immunogenic tumours, the systemic delivery of macrophages with signal-regulatory protein alpha (SIRPα) genetically knocked out or else with blockade of the CD47-SIRPα macrophage checkpoint was combined with the monoclonal antibody and subsequently triggered the production of endogenous tumour-opsonizing immunoglobulin G, substantially increased the survival of the animals and helped confer durable protection from tumour re-challenge and metastasis. Maximizing phagocytic potency by increasing macrophage numbers, by tumour-cell opsonization and by disrupting the phagocytic checkpoint CD47-SIRPα may lead to durable anti-tumour responses in solid cancers.
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Affiliation(s)
- Lawrence J Dooling
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason C Andrechak
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Brandon H Hayes
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Siddhant Kadu
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA
| | - William Zhang
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruby Pan
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA
| | - Manasvita Vashisth
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Cory M Alvey
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA
| | - Leyuan Ma
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dennis E Discher
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA.
- Physical Sciences-Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA, USA.
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.
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7
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Coscarella IL, Landim-Vieira M, Rastegarpouyani H, Chase PB, Irianto J, Pinto JR. Nucleus Mechanosensing in Cardiomyocytes. Int J Mol Sci 2023; 24:13341. [PMID: 37686151 PMCID: PMC10487505 DOI: 10.3390/ijms241713341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Cardiac muscle contraction is distinct from the contraction of other muscle types. The heart continuously undergoes contraction-relaxation cycles throughout an animal's lifespan. It must respond to constantly varying physical and energetic burdens over the short term on a beat-to-beat basis and relies on different mechanisms over the long term. Muscle contractility is based on actin and myosin interactions that are regulated by cytoplasmic calcium ions. Genetic variants of sarcomeric proteins can lead to the pathophysiological development of cardiac dysfunction. The sarcomere is physically connected to other cytoskeletal components. Actin filaments, microtubules and desmin proteins are responsible for these interactions. Therefore, mechanical as well as biochemical signals from sarcomeric contractions are transmitted to and sensed by other parts of the cardiomyocyte, particularly the nucleus which can respond to these stimuli. Proteins anchored to the nuclear envelope display a broad response which remodels the structure of the nucleus. In this review, we examine the central aspects of mechanotransduction in the cardiomyocyte where the transmission of mechanical signals to the nucleus can result in changes in gene expression and nucleus morphology. The correlation of nucleus sensing and dysfunction of sarcomeric proteins may assist the understanding of a wide range of functional responses in the progress of cardiomyopathic diseases.
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Affiliation(s)
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Hosna Rastegarpouyani
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Prescott Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Jose Renato Pinto
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
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8
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Hayes BH, Zhu PK, Wang M, Pfeifer CR, Xia Y, Phan S, Andrechak JC, Du J, Tobin MP, Anlas A, Dooling LJ, Vashisth M, Irianto J, Lampson MA, Discher DE. Confinement plus Myosin-II suppression maximizes heritable loss of chromosomes, as revealed by live-cell ChReporters. J Cell Sci 2023:308945. [PMID: 37158012 DOI: 10.1242/jcs.260753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
A cell's mechanical environment can have many effects, but whether it impacts a cell's DNA sequence has remained unclear. To investigate this, we developed a live-cell method to measure changes in chromosome numbers. We edited constitutive genes with GFP/RFP-tags on single alleles and discovered that cells that lose Chromosome-reporters (ChReporters) become non-fluorescent. We applied our new tools to confined mitosis and to inhibition of the putative tumor suppressor Myosin-II. We quantified compression of mitotic chromatin in vivo and demonstrated that similar compression in vitro resulted in cell death, but also rare and heritable ChReptorter loss. Myosin-II suppression rescued lethal multipolar divisions and maximized ChReporter loss in 3D-compression and 2D-confinement, but not in standard 2D-culture. ChReporter loss associated with chromosome mis-segregation, rather than just the number of divisions, and loss in vitro and in mice was selected against in subsequent 2D-cultures. Inhibition of the spindle assembly checkpoint (SAC) caused ChReporter loss in 2D, as expected, but not in 3D-compression, suggesting a SAC perturbation. Thus, confinement and myosin-II affect DNA sequence and mechano-evolution, and ChReporters enable diverse studies of viable genetic changes.
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Affiliation(s)
- Brandon H Hayes
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter Kuangzheng Zhu
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mai Wang
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte R Pfeifer
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuntao Xia
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven Phan
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason C Andrechak
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junhong Du
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael P Tobin
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alisya Anlas
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lawrence J Dooling
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manasvita Vashisth
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerome Irianto
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Dennis E Discher
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Andrechak JC, Dooling LJ, Tobin MP, Zhang W, Hayes BH, Lee JY, Jin X, Irianto J, Discher DE. CD47-SIRPα Checkpoint Disruption in Metastases Requires Tumor-Targeting Antibody for Molecular and Engineered Macrophage Therapies. Cancers (Basel) 2022; 14:1930. [PMID: 35454837 PMCID: PMC9026896 DOI: 10.3390/cancers14081930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
The macrophage checkpoint interaction CD47-SIRPα is an emerging target for cancer therapy, but clinical trials of monoclonal anti-CD47 show efficacy only in liquid tumors when combined with tumor-opsonizing IgG. Here, in challenging metastatic solid tumors, CD47 deletion shows no effect on tumor growth unless combined with otherwise ineffective tumor-opsonization, and we likewise show wild-type metastases are suppressed by SIRPα-blocked macrophages plus tumor-opsonization. Lung tumor nodules of syngeneic B16F10 melanoma cells with CD47 deletion show opsonization drives macrophage phagocytosis of B16F10s, consistent with growth versus phagocytosis calculus for exponential suppression of cancer. Wild-type CD47 levels on metastases in lungs of immunocompetent mice and on human metastases in livers of immunodeficient mice show that systemic injection of antibody-engineered macrophages also suppresses growth. Such in vivo functionality can be modulated by particle pre-loading of the macrophages. Thus, even though CD47-SIRPα disruption and tumor-opsonizing IgG are separately ineffective against established metastatic solid tumors, their combination in molecular and cellular therapies prolongs survival.
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Affiliation(s)
- Jason C Andrechak
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lawrence J Dooling
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael P Tobin
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William Zhang
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brandon H Hayes
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Justine Y Lee
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaoling Jin
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerome Irianto
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Dennis E Discher
- Biophysical Engineering Labs, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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10
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Leite Coscarella I, Wang L, Irianto J, Knollmann BC, Chase PB, Pinto JR. Hypertrophic and dilated cardiomyopathy-associatedTNNT2 pathogenic variants induce nucleus remodeling in hiPSC-CM models. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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11
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Wang XF, Yang SA, Gong S, Chang CH, Portilla JM, Chatterjee D, Irianto J, Bao H, Huang YC, Deng WM. Polyploid mitosis and depolyploidization promote chromosomal instability and tumor progression in a Notch-induced tumor model. Dev Cell 2021; 56:1976-1988.e4. [PMID: 34146466 DOI: 10.1016/j.devcel.2021.05.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/18/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023]
Abstract
Ploidy variation is a cancer hallmark and is frequently associated with poor prognosis in high-grade cancers. Using a Drosophila solid-tumor model where oncogenic Notch drives tumorigenesis in a transition-zone microenvironment in the salivary gland imaginal ring, we find that the tumor-initiating cells normally undergo endoreplication to become polyploid. Upregulation of Notch signaling, however, induces these polyploid transition-zone cells to re-enter mitosis and undergo tumorigenesis. Growth and progression of the transition-zone tumor are fueled by a combination of polyploid mitosis, endoreplication, and depolyploidization. Both polyploid mitosis and depolyploidization are error prone, resulting in chromosomal copy-number variation and polyaneuploidy. Comparative RNA-seq and epistasis analysis reveal that the DNA-damage response genes, also active during meiosis, are upregulated in these tumors and are required for the ploidy-reduction division. Together, these findings suggest that polyploidy and associated cell-cycle variants are critical for increased tumor-cell heterogeneity and genome instability during cancer progression.
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Affiliation(s)
- Xian-Feng Wang
- Department of Biochemistry and Molecular Biology, Tulane University Louisiana Center Research Center, New Orleans, LA 70112, USA
| | - Sheng-An Yang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Shangyu Gong
- Department of Biochemistry and Molecular Biology, Tulane University Louisiana Center Research Center, New Orleans, LA 70112, USA
| | - Chih-Hsuan Chang
- Department of Biochemistry and Molecular Biology, Tulane University Louisiana Center Research Center, New Orleans, LA 70112, USA
| | - Juan Martin Portilla
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Deeptiman Chatterjee
- Department of Biochemistry and Molecular Biology, Tulane University Louisiana Center Research Center, New Orleans, LA 70112, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA
| | - Hongcun Bao
- Department of Biochemistry and Molecular Biology, Tulane University Louisiana Center Research Center, New Orleans, LA 70112, USA
| | - Yi-Chun Huang
- Department of Biochemistry and Molecular Biology, Tulane University Louisiana Center Research Center, New Orleans, LA 70112, USA
| | - Wu-Min Deng
- Department of Biochemistry and Molecular Biology, Tulane University Louisiana Center Research Center, New Orleans, LA 70112, USA; Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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12
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Zhu K, Hayes B, Wang M, Tobin MP, Andrechak JC, Xia Y, Dooling LJ, Pfeifer CR, Irianto J, Discher DE, Du J. Live Cell Chromosome Loss Reporter Shows Mechanical Confinement Associates with Chromosome Mis-Segregation. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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13
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Yong HJ, Xie G, Liu C, Wang W, Naji A, Irianto J, Wang YJ. Gene Signatures of NEUROGENIN3+ Endocrine Progenitor Cells in the Human Pancreas. Front Endocrinol (Lausanne) 2021; 12:736286. [PMID: 34566896 PMCID: PMC8456125 DOI: 10.3389/fendo.2021.736286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
NEUROGENIN3+ (NEUROG3+) cells are considered to be pancreatic endocrine progenitors. Our current knowledge on the molecular program of NEUROG3+ cells in humans is largely extrapolated from studies in mice. We hypothesized that single-cell RNA-seq enables in-depth exploration of the rare NEUROG3+ cells directly in humans. We aligned four large single-cell RNA-seq datasets from postnatal human pancreas. Our integrated analysis revealed 10 NEUROG3+ epithelial cells from a total of 11,174 pancreatic cells. Noticeably, human NEUROG3+ cells clustered with mature pancreatic cells and epsilon cells displayed the highest frequency of NEUROG3 positivity. We confirmed the co-expression of NEUROG3 with endocrine markers and the high percentage of NEUROG3+ cells among epsilon cells at the protein level based on immunostaining on pancreatic tissue sections. We further identified unique genetic signatures of the NEUROG3+ cells. Regulatory network inference revealed novel transcription factors including Prospero homeobox protein 1 (PROX1) may act jointly with NEUROG3. As NEUROG3 plays a central role in endocrine differentiation, knowledge gained from our study will accelerate the development of beta cell regeneration therapies to treat diabetes.
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Affiliation(s)
- Hyo Jeong Yong
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, United States
| | - Gengqiang Xie
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, United States
| | - Chengyang Liu
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Wei Wang
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Ali Naji
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Jerome Irianto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, United States
| | - Yue J. Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, United States
- *Correspondence: Yue J. Wang,
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14
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Bijonowski BM, Fu Q, Yuan X, Irianto J, Li Y, Grant SC, Ma T. Aggregation-induced integrated stress response rejuvenates culture-expanded human mesenchymal stem cells. Biotechnol Bioeng 2020; 117:3136-3149. [PMID: 32579299 DOI: 10.1002/bit.27474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/08/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022]
Abstract
Protein homeostasis is critical for cellular function, as loss of homeostasis is attributed to aging and the accumulation of unwanted proteins. Human mesenchymal stem cells (MSCs) have shown promising therapeutic potential due to their impressive abilities to secrete inflammatory modulators, angiogenic, and regenerative cytokines. However, there exists the problem of human MSC expansion with compromised therapeutic quality. Duringin vitro expansion, human MSCs are plated on stiff plastics and undergo culture adaptation, which results in aberrant proliferation, shifts in metabolism, and decreased autophagic activity. It has previously been shown that three-dimensional (3D) aggregation can reverse some of these alterations by heightening autophagy and recovering the metabolic state back to a naïve phenotype. To further understand the proteostasis in human MSC culture, this study investigated the effects of 3D aggregation on the human MSC proteome to determine the specific pathways altered by aggregation. The 3D aggregates and 2D cultures of human MSCs derived from bone marrow (bMSC) and adipose tissue (ASC) were analyzed along with differentiated human dermal fibroblasts (FB). The proteomics analysis showed the elevated eukaryotic initiation factor 2 pathway and the upregulated activity of the integrated stress response (ISR) in 3D aggregates. Specific protein quantification further determined that bMSC and ASC responded to ISR, while FB did not. 3D aggregation significantly increased the ischemic survival of bMSCs and ASCs. Perturbation of ISR with small molecules salubrinal and GSK2606414 resulted in differential responses of bMSC, ASC, and FB. This study indicates that aggregation-based preconditioning culture holds the potential for improving the therapeutic efficacy of expanded human MSCs via the establishment of ISR and homeostasis.
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Affiliation(s)
- Brent M Bijonowski
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida.,University of Münster, Münster, Germany
| | - Qin Fu
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida.,Proteomics Center, Cornell University, Ithaca, New York
| | - Xuegang Yuan
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida.,The National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida
| | - Jerome Irianto
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida
| | - Yan Li
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida
| | - Samuel C Grant
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida.,The National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida
| | - Teng Ma
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida
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15
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Saini K, Tewari M, Cho S, Jalil A, Irianto J, Vashisth M, Pfeifer C, Dooling LJ, Alvey C, Kasznel A, Chenoweth D, Yamamoto K, Discher DE. Heterogeneously Strained Tissue Collagen Resists Collagenase Degradation Where Strains are High. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Zhu K, Xia Y, Irianto J, Andrechak JC, Dooling LJ, Pfeifer CR, Discher DE. Live Cell Monitoring of Chromosome Loss Reporter. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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17
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Abstract
As a cancer cell invades adjacent tissue, penetrates a basement membrane barrier, or squeezes into a blood capillary, its nucleus can be greatly constricted. Here, we examine: (1) the passive and active deformation of the nucleus during 3D migration; (2) the nuclear structures-namely, the lamina and chromatin-that govern nuclear deformability; (3) the effect of large nuclear deformation on DNA and nuclear factors; and (4) the downstream consequences of mechanically stressing the nucleus. We focus especially on recent studies showing that constricted migration causes nuclear envelope rupture and excess DNA damage, leading to cell cycle suppression, possibly cell death, and ultimately it seems to heritable genomic variation. We first review the latest understanding of nuclear dynamics during cell migration, and then explore the functional effects of nuclear deformation, especially in relation to genome integrity and potentially cancerous mutations.
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Affiliation(s)
- Charlotte R Pfeifer
- Biophysical Engineering Labs: Molecular & Cell Biophysics and NanoBio-Polymers, University of Pennsylvania, Philadelphia, PA, USA
| | - Jerome Irianto
- Biophysical Engineering Labs: Molecular & Cell Biophysics and NanoBio-Polymers, University of Pennsylvania, Philadelphia, PA, USA
| | - Dennis E Discher
- Biophysical Engineering Labs: Molecular & Cell Biophysics and NanoBio-Polymers, University of Pennsylvania, Philadelphia, PA, USA.
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18
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Xia Y, Pfeifer CR, Zhu K, Irianto J, Liu D, Pannell K, Chen EJ, Dooling LJ, Tobin MP, Wang M, Ivanovska IL, Smith LR, Greenberg RA, Discher DE. Rescue of DNA damage after constricted migration reveals a mechano-regulated threshold for cell cycle. J Cell Biol 2019; 218:2545-2563. [PMID: 31239284 PMCID: PMC6683732 DOI: 10.1083/jcb.201811100] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/19/2019] [Accepted: 06/04/2019] [Indexed: 12/24/2022] Open
Abstract
Migration through 3D constrictions can cause nuclear rupture and mislocalization of nuclear proteins, but damage to DNA remains uncertain, as does any effect on cell cycle. Here, myosin II inhibition rescues rupture and partially rescues the DNA damage marker γH2AX, but an apparent block in cell cycle appears unaffected. Co-overexpression of multiple DNA repair factors or antioxidant inhibition of break formation also exert partial effects, independently of rupture. Combined treatments completely rescue cell cycle suppression by DNA damage, revealing a sigmoidal dependence of cell cycle on excess DNA damage. Migration through custom-etched pores yields the same damage threshold, with ∼4-µm pores causing intermediate levels of both damage and cell cycle suppression. High curvature imposed rapidly by pores or probes or else by small micronuclei consistently associates nuclear rupture with dilution of stiff lamin-B filaments, loss of repair factors, and entry from cytoplasm of chromatin-binding cGAS (cyclic GMP-AMP synthase). The cell cycle block caused by constricted migration is nonetheless reversible, with a potential for DNA misrepair and genome variation.
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Affiliation(s)
- Yuntao Xia
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Charlotte R. Pfeifer
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA,Department of Physics and Astronomy, Graduate Group, University of Pennsylvania, Philadelphia, PA
| | - Kuangzheng Zhu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Jerome Irianto
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Dazhen Liu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Kalia Pannell
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Emily J. Chen
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Lawrence J. Dooling
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Michael P. Tobin
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Mai Wang
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Irena L. Ivanovska
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Lucas R. Smith
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Roger A. Greenberg
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Dennis E. Discher
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA,Department of Physics and Astronomy, Graduate Group, University of Pennsylvania, Philadelphia, PA,Correspondence to D.E. Discher:
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19
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Abstract
Tissue regeneration at an injured site depends on proliferation, migration, and differentiation of resident stem or progenitor cells, but solid tissues are often sufficiently dense and constricting that nuclei are highly stressed by migration. In this study, constricted migration of myoblastic cell types and mesenchymal stem cells (MSCs) increases nuclear rupture, increases DNA damage, and modulates differentiation. Fewer myoblasts fuse into regenerating muscle in vivo after constricted migration in vitro, and myodifferentiation in vitro is likewise suppressed. Myosin II inhibition rescues rupture and DNA damage, implicating nuclear forces, while mitosis and the cell cycle are suppressed by constricted migration, consistent with a checkpoint. Although perturbed proliferation fails to explain defective differentiation, nuclear rupture mislocalizes differentiation-relevant MyoD and KU80 (a DNA repair factor), with nuclear entry of the DNA-binding factor cGAS. Human MSCs exhibit similar damage, but osteogenesis increases-which is relevant to bone and to calcified fibrotic tissues, including diseased muscle. Tissue repair can thus be modulated up or down by the curvature of pores through which stem cells squeeze.
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Affiliation(s)
- Lucas R. Smith
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104,Department of Neurobiology, Physiology, and Behavior, University of California, Davis, Davis, CA 95616,Department of Physical Medicine and Rehabilitation, University of California, Davis, Sacramento, CA 95817
| | - Jerome Irianto
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Yuntao Xia
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Charlotte R. Pfeifer
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E. Discher
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104,*Address correspondence to: Dennis E. Discher ()
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20
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Xia Y, Pfeifer C, Zhu K, Irianto J, Discher D. Rescue of DNA Damage After Constricted Migration by DNA Repair Factor Overexpression. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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21
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Ivanovska IL, Xia Y, Zhu K, Smith L, Alvey C, Irianto J, Pfeifer C, Ji J, Liu D, Cho S, Bennett R, Liu A, Greenberg RA, Discher DE. Nuclear Rupture at Sites of High Curvature Compromises Retention of DNA Repair Factors. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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22
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Xia Y, Ivanovska IL, Zhu K, Smith L, Irianto J, Pfeifer CR, Alvey CM, Ji J, Liu D, Cho S, Bennett RR, Liu AJ, Greenberg RA, Discher DE. Nuclear rupture at sites of high curvature compromises retention of DNA repair factors. J Cell Biol 2018; 217:3796-3808. [PMID: 30171044 PMCID: PMC6219729 DOI: 10.1083/jcb.201711161] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/24/2018] [Accepted: 08/20/2018] [Indexed: 02/07/2023] Open
Abstract
The nucleus is physically linked to the cytoskeleton, adhesions, and extracellular matrix-all of which sustain forces, but their relationships to DNA damage are obscure. We show that nuclear rupture with cytoplasmic mislocalization of multiple DNA repair factors correlates with high nuclear curvature imposed by an external probe or by cell attachment to either aligned collagen fibers or stiff matrix. Mislocalization is greatly enhanced by lamin A depletion, requires hours for nuclear reentry, and correlates with an increase in pan-nucleoplasmic foci of the DNA damage marker γH2AX. Excess DNA damage is rescued in ruptured nuclei by cooverexpression of multiple DNA repair factors as well as by soft matrix or inhibition of actomyosin tension. Increased contractility has the opposite effect, and stiff tumors with low lamin A indeed exhibit increased nuclear curvature, more frequent nuclear rupture, and excess DNA damage. Additional stresses likely play a role, but the data suggest high curvature promotes nuclear rupture, which compromises retention of DNA repair factors and favors sustained damage.
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Affiliation(s)
- Yuntao Xia
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Irena L. Ivanovska
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Kuangzheng Zhu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Lucas Smith
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Jerome Irianto
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Charlotte R. Pfeifer
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Cory M. Alvey
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA,Graduate Group, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA
| | - Jiazheng Ji
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Dazhen Liu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Sangkyun Cho
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA
| | - Rachel R. Bennett
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Graduate Group, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA
| | - Andrea J. Liu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Graduate Group, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA
| | - Roger A. Greenberg
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Dennis E. Discher
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA ,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA,Graduate Group, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA,Correspondence to Dennis E. Discher:
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23
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Pfeifer CR, Xia Y, Zhu K, Liu D, Irianto J, García VMM, Millán LMS, Niese B, Harding S, Deviri D, Greenberg RA, Discher DE. Constricted migration increases DNA damage and independently represses cell cycle. Mol Biol Cell 2018; 29:1948-1962. [PMID: 29742017 PMCID: PMC6232975 DOI: 10.1091/mbc.e18-02-0079] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cell migration through dense tissues or small capillaries can elongate the nucleus and even damage it, and any impact on cell cycle has the potential to affect various processes including carcinogenesis. Here, nuclear rupture and DNA damage increase with constricted migration in different phases of cell cycle-which we show is partially repressed. We study several cancer lines that are contact inhibited or not and that exhibit diverse frequencies of nuclear lamina rupture after migration through small pores. DNA repair factors invariably mislocalize after migration, and an excess of DNA damage is evident as pan--nucleoplasmic foci of phosphoactivated ATM and γH2AX. Foci counts are suppressed in late cell cycle as expected of mitotic checkpoints, and migration of contact-inhibited cells through large pores into sparse microenvironments leads also as expected to cell-cycle reentry and no effect on a basal level of damage foci. Constricting pores delay such reentry while excess foci occur independent of cell-cycle phase. Knockdown of repair factors increases DNA damage independent of cell cycle, consistent with effects of constricted migration. Because such migration causes DNA damage and impedes proliferation, it illustrates a cancer cell fate choice of "go or grow."
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Affiliation(s)
- Charlotte R. Pfeifer
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104,Graduate Group/Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Yuntao Xia
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Kuangzheng Zhu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Dazhen Liu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Jerome Irianto
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | | | | | - Brandon Niese
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Shane Harding
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104,Basser Center for BRCA, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Dan Deviri
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roger A. Greenberg
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104,Basser Center for BRCA, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E. Discher
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104,Graduate Group/Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA 19104,*Address correspondence to: Dennis E. Discher ()
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24
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Cho S, Abbas A, Irianto J, Ivanovska IL, Xia Y, Tewari M, Discher DE. Progerin phosphorylation in interphase is lower and less mechanosensitive than lamin-A,C in iPS-derived mesenchymal stem cells. Nucleus 2018; 9:230-245. [PMID: 29619860 PMCID: PMC5973135 DOI: 10.1080/19491034.2018.1460185] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Interphase phosphorylation of lamin-A,C depends dynamically on a cell's microenvironment, including the stiffness of extracellular matrix. However, phosphorylation dynamics is poorly understood for diseased forms such as progerin, a permanently farnesylated mutant of LMNA that accelerates aging of stiff and mechanically stressed tissues. Here, fine-excision alignment mass spectrometry (FEA-MS) is developed to quantify progerin and its phosphorylation levels in patient iPS cells differentiated to mesenchymal stem cells (MSCs). The stoichiometry of total A-type lamins (including progerin) versus B-type lamins measured for Progeria iPS-MSCs prove similar to that of normal MSCs, with total A-type lamins more abundant than B-type lamins. However, progerin behaves more like farnesylated B-type lamins in mechanically-induced segregation from nuclear blebs. Phosphorylation of progerin at multiple sites in iPS-MSCs cultured on rigid plastic is also lower than that of normal lamin-A and C. Reduction of nuclear tension upon i) cell rounding/detachment from plastic, ii) culture on soft gels, and iii) inhibition of actomyosin stress increases phosphorylation and degradation of lamin-C > lamin-A > progerin. Such mechano-sensitivity diminishes, however, with passage as progerin and DNA damage accumulate. Lastly, transcription-regulating retinoids exert equal effects on both diseased and normal A-type lamins, suggesting a differential mechano-responsiveness might best explain the stiff tissue defects in Progeria.
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Affiliation(s)
- Sangkyun Cho
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Amal Abbas
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Jerome Irianto
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Irena L. Ivanovska
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuntao Xia
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Manu Tewari
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Dennis E. Discher
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA,CONTACT Dennis E. Discher , University of Pennsylvania, 129 Towne Bldg, Philadelphia, PA 19104
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25
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Nair PR, Alvey C, Jin X, Irianto J, Ivanovska I, Discher DE. Filomicelles Deliver a Chemo-Differentiation Combination of Paclitaxel and Retinoic Acid That Durably Represses Carcinomas in Liver to Prolong Survival. Bioconjug Chem 2018; 29:914-927. [PMID: 29451777 DOI: 10.1021/acs.bioconjchem.7b00816] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Drug resistance and relapse is common in cancer treatments with chemotherapeutics, and while drug combinations with naturally occurring, differentiation-inducing retinoic acid (RA) provide remission-free cures for one type of liquid tumor, solid tumors present major problems for delivery. Here, inspired by filoviruses that can be microns in length, flexible filomicelles that self-assemble from an amphiphilic block copolymer (PEG-PCL) are shown to effectively deliver RA and paclitaxel (TAX) to several solid tumor models, particularly in the liver. These hydrophobic compounds synergistically load into the cores of the elongated micelles, and the coloaded micelles prove most effective at causing cell death, ploidy, and durable regression of tumors compared to free drugs or to separately loaded drugs. RA-TAX filomicelles also reduce mortality of human lung or liver derived cancers engrafted at liver, intraperitoneal, and subcutaneous sites in immunodeficient mice. In vitro studies show that the dual drug micelles effectively suppress proliferation while upregulating a generic differentiation marker. The results highlight the potency of dual-loaded filomicelles in killing cancer cells or else driving their differentiation away from growth.
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Affiliation(s)
- Praful R Nair
- NanoBioPolymers Lab, and Physical Sciences Oncology Center @ Penn , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Cory Alvey
- NanoBioPolymers Lab, and Physical Sciences Oncology Center @ Penn , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Xiaoling Jin
- NanoBioPolymers Lab, and Physical Sciences Oncology Center @ Penn , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Jerome Irianto
- NanoBioPolymers Lab, and Physical Sciences Oncology Center @ Penn , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Irena Ivanovska
- NanoBioPolymers Lab, and Physical Sciences Oncology Center @ Penn , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Dennis E Discher
- NanoBioPolymers Lab, and Physical Sciences Oncology Center @ Penn , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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Ivanovska IL, Xia Y, Irianto J, Discher DE. Curvature Dependence of Nuclear Rupture Frequency Revealed by AFM Force Spectroscopy. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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27
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Alvey C, Pfeifer C, Irianto J, Xia Y, Smith L, Dooling L, Discher DE. Mechanosensing of Solid Tumors by Cancer-Attacking Macrophages. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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28
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29
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Buxboim A, Irianto J, Swift J, Athirasala A, Shin JW, Rehfeldt F, Discher DE. Coordinated increase of nuclear tension and lamin-A with matrix stiffness outcompetes lamin-B receptor that favors soft tissue phenotypes. Mol Biol Cell 2017; 28:3333-3348. [PMID: 28931598 PMCID: PMC5687034 DOI: 10.1091/mbc.e17-06-0393] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/06/2017] [Accepted: 09/13/2017] [Indexed: 12/31/2022] Open
Abstract
Matrix stiffness that is sensed by a cell or measured by a purely physical probe reflects the intrinsic elasticity of the matrix and also how thick or thin the matrix is. Here, mesenchymal stem cells (MSCs) and their nuclei spread in response to thickness-corrected matrix microelasticity, with increases in nuclear tension and nuclear stiffness resulting from increases in myosin-II and lamin-A,C. Linearity between the widely varying projected area of a cell and its nucleus across many matrices, timescales, and myosin-II activity levels indicates a constant ratio of nucleus-to-cell volume, despite MSCs' lineage plasticity. Nuclear envelope fluctuations are suppressed on the stiffest matrices, and fluctuation spectra reveal a high nuclear tension that matches trends from traction force microscopy and from increased lamin-A,C. Transcriptomes of many diverse tissues and MSCs further show that lamin-A,C's increase with tissue or matrix stiffness anti-correlates with lamin-B receptor (LBR), which contributes to lipid/sterol biosynthesis. Adipogenesis (a soft lineage) indeed increases LBR:lamin-A,C protein stoichiometry in MSCs versus osteogenesis (stiff). The two factors compete for lamin-B in response to matrix elasticity, knockdown, myosin-II inhibition, and even constricted migration that disrupts and segregates lamins in situ. Matrix stiffness-driven contractility thus tenses the nucleus to favor lamin-A,C accumulation and suppress soft tissue phenotypes.
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Affiliation(s)
- Amnon Buxboim
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
- Department/Graduate Group of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Jerome Irianto
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Joe Swift
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Avathamsa Athirasala
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Jae-Won Shin
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Florian Rehfeldt
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E Discher
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, Philadelphia, PA 19104
- Department/Graduate Group of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
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30
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Bennett RR, Pfeifer CR, Irianto J, Xia Y, Discher DE, Liu AJ. Elastic-Fluid Model for DNA Damage and Mutation from Nuclear Fluid Segregation Due to Cell Migration. Biophys J 2017; 112:2271-2279. [PMID: 28591600 DOI: 10.1016/j.bpj.2017.04.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/10/2023] Open
Abstract
When cells migrate through constricting pores, they incur DNA damage and develop genomic variation. Experiments show that this damage is not due to DNA breakage from mechanical stress on chromatin in the deformed nucleus. Here we propose a model for a mechanism by which nuclear deformation can lead to DNA damage. We treat the nucleus as an elastic-fluid system with an elastic component (chromatin) and fluid component that can be squeezed out when the nucleus is deformed. We couple the elastic-fluid model to the kinetics of DNA breakage and repair by assuming that the local volume fraction of the elastic component controls the rate of damage per unit volume due to naturally occurring DNA breaks, whereas the volume fraction of the fluid component controls the rate of repair of DNA breaks per unit volume by repair factors, which are soluble in the fluid. By comparing our results to a number of experiments on controlled migration through pores, we show that squeeze-out of the fluid, and hence of the mobile repair factors, is sufficient to account for the extent of DNA damage and genomic variation observed experimentally. We also use our model for migration through a cylindrical pore to estimate the variation with tissue stiffness of the mutation rate in tumors.
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Affiliation(s)
- Rachel R Bennett
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charlotte R Pfeifer
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania; Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jerome Irianto
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yuntao Xia
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dennis E Discher
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania; Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrea J Liu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania.
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31
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Alvey CM, Spinler KR, Irianto J, Pfeifer CR, Hayes B, Xia Y, Cho S, Dingal PCPD, Hsu J, Smith L, Tewari M, Discher DE. SIRPA-Inhibited, Marrow-Derived Macrophages Engorge, Accumulate, and Differentiate in Antibody-Targeted Regression of Solid Tumors. Curr Biol 2017; 27:2065-2077.e6. [PMID: 28669759 DOI: 10.1016/j.cub.2017.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/24/2017] [Accepted: 06/01/2017] [Indexed: 12/22/2022]
Abstract
Marrow-derived macrophages are highly phagocytic, but whether they can also traffic into solid tumors and engulf cancer cells is questionable, given the well-known limitations of tumor-associated macrophages (TAMs). Here, SIRPα on macrophages from mouse and human marrow was inhibited to block recognition of its ligand, the "marker of self" CD47 on all other cells. These macrophages were then systemically injected into mice with fluorescent human tumors that had been antibody targeted. Within days, the tumors regressed, and single-cell fluorescence analyses showed that the more the macrophages engulfed, the more they accumulated within regressing tumors. Human-marrow-derived macrophages engorged on the human tumors, while TAMs were minimally phagocytic, even toward CD47-knockdown tumors. Past studies had opsonized tumors in situ with antibody and/or relied on mouse TAMs but had not injected SIRPα-inhibited cells; also, unlike past injections of anti-CD47, blood parameters remained normal and safe. Consistent with tumor-selective engorge-and-accumulate processes in vivo, phagocytosis in vitro inhibited macrophage migration through micropores that mimic features of dense 3D tissue. Accumulation of SIRPα-inhibited macrophages in tumors favored tumor regression for 1-2 weeks, but donor macrophages quickly differentiated toward non-phagocytic, high-SIRPα TAMs. Analyses of macrophages on soft (like marrow) or stiff (like solid tumors) collagenous gels demonstrated a stiffness-driven, retinoic-acid-modulated upregulation of SIRPα and the mechanosensitive nuclear marker lamin-A. Mechanosensitive differentiation was similarly evident in vivo and likely limited the anti-tumor effects, as confirmed by re-initiation of tumor regression by fresh injections of SIRPα-inhibited macrophages. Macrophage motility, phagocytosis, and differentiation in vivo are thus coupled.
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Affiliation(s)
- Cory M Alvey
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Pharmacological Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyle R Spinler
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerome Irianto
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte R Pfeifer
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brandon Hayes
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuntao Xia
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sangkyun Cho
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - P C P Dave Dingal
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jake Hsu
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucas Smith
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manu Tewari
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dennis E Discher
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Pharmacological Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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32
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Pfeifer CR, Alvey CM, Irianto J, Discher DE. Genome variation across cancers scales with tissue stiffness - an invasion-mutation mechanism and implications for immune cell infiltration. ACTA ACUST UNITED AC 2017; 2:103-114. [PMID: 29082336 DOI: 10.1016/j.coisb.2017.04.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many different types of soft and solid tumors have now been sequenced, and meta-analyses suggest that genomic variation across tumors scales with the stiffness of the tumors' tissues of origin. The opinion expressed here is based on a review of current genomics data, and it considers multiple 'mechanogenomics' mechanisms to potentially explain this scaling of mutation rate with tissue stiffness. Since stiff solid tissues have higher density of fibrous collagen matrix, which should decrease tissue porosity, cancer cell proliferation could be affected and so could invasion into stiff tissues as the nucleus is squeezed sufficiently to enhance DNA damage. Diversification of a cancer genome after constricted migration is now clear. Understanding genome changes that give rise to neo-antigens is important to selection as well as to the development of immunotherapies, and we discuss engineered monocytes/macrophages as particularly relevant to understanding infiltration into solid tumors.
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Affiliation(s)
- Charlotte R Pfeifer
- Physical Sciences Oncology Center at Penn (PSOC@Penn), University of Pennsylvania, Philadelphia, PA 19104.,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104.,Graduate Group / Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Cory M Alvey
- Physical Sciences Oncology Center at Penn (PSOC@Penn), University of Pennsylvania, Philadelphia, PA 19104.,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104.,Graduate Group / Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104
| | - Jerome Irianto
- Physical Sciences Oncology Center at Penn (PSOC@Penn), University of Pennsylvania, Philadelphia, PA 19104.,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E Discher
- Physical Sciences Oncology Center at Penn (PSOC@Penn), University of Pennsylvania, Philadelphia, PA 19104.,Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104.,Graduate Group / Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA 19104.,Graduate Group / Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104
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33
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Xia Y, Irianto J, Pfeifer C, Greenberg R, Discher D. Inhibition of a DNA Repair Kinase ATM Leads to Cell Death in 3D Migration Independent of DNA Damage. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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34
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Pfeifer CR, Irianto J, Bennett RR, Xia Y, Ivanovska IL, Liu AJ, Greenberg RA, Discher DE. Nuclear Constriction Segregates Mobile Nuclear Proteins Away from Chromatin. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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35
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Cho S, Majkut S, Abbas A, Vogel K, Irianto J, Chen CY, Tewari M, Liu A, Prosser B, Discher DE. As the Beating Heart Stiffens in Development, So Does the Nuclear Lamina. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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36
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Abstract
Cells sense and respond to properties of their microenvironment that can affect cell morphology, protein levels and localization, gene expression, and even nuclear integrity. Tissue micro-stiffness, largely influenced by extracellular matrix, varies dramatically within an organism and can be a useful parameter to both clarify and organize a wide range of cell and molecular processes, such as genomic changes in cancer.
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Affiliation(s)
- Jerome Irianto
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte R Pfeifer
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuntao Xia
- 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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37
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Cho S, Irianto J, Discher DE. Mechanosensing by the nucleus: From pathways to scaling relationships. J Cell Biol 2017; 216:305-315. [PMID: 28043971 PMCID: PMC5294790 DOI: 10.1083/jcb.201610042] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/05/2016] [Accepted: 12/14/2016] [Indexed: 01/01/2023] Open
Abstract
Cho, Irianto, and Discher review emerging mechanisms of nuclear mechanosensing and propose through meta-analyses of published data the universality of mechanosensing pathways. The nucleus is linked mechanically to the extracellular matrix via multiple polymers that transmit forces to the nuclear envelope and into the nuclear interior. Here, we review some of the emerging mechanisms of nuclear mechanosensing, which range from changes in protein conformation and transcription factor localization to chromosome reorganization and membrane dilation up to rupture. Nuclear mechanosensing encompasses biophysically complex pathways that often converge on the main structural proteins of the nucleus, the lamins. We also perform meta-analyses of public transcriptomics and proteomics data, which indicate that some of the mechanosensing pathways relaying signals from the collagen matrix to the nucleus apply to a broad range of species, tissues, and diseases.
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Affiliation(s)
- Sangkyun Cho
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Jerome Irianto
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E Discher
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
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38
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Irianto J, Xia Y, Pfeifer CR, Athirasala A, Ji J, Alvey C, Tewari M, Bennett RR, Harding SM, Liu AJ, Greenberg RA, Discher DE. DNA Damage Follows Repair Factor Depletion and Portends Genome Variation in Cancer Cells after Pore Migration. Curr Biol 2016; 27:210-223. [PMID: 27989676 DOI: 10.1016/j.cub.2016.11.049] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/11/2016] [Accepted: 11/23/2016] [Indexed: 11/25/2022]
Abstract
Migration through micron-size constrictions has been seen to rupture the nucleus, release nuclear-localized GFP, and cause localized accumulations of ectopic 53BP1-a DNA repair protein. Here, constricted migration of two human cancer cell types and primary mesenchymal stem cells (MSCs) increases DNA breaks throughout the nucleoplasm as assessed by endogenous damage markers and by electrophoretic "comet" measurements. Migration also causes multiple DNA repair proteins to segregate away from DNA, with cytoplasmic mis-localization sustained for many hours as is relevant to delayed repair. Partial knockdown of repair factors that also regulate chromosome copy numbers is seen to increase DNA breaks in U2OS osteosarcoma cells without affecting migration and with nucleoplasmic patterns of damage similar to constricted migration. Such depletion also causes aberrant levels of DNA. Migration-induced nuclear damage is nonetheless reversible for wild-type and sub-cloned U2OS cells, except for lasting genomic differences between stable clones as revealed by DNA arrays and sequencing. Gains and losses of hundreds of megabases in many chromosomes are typical of the changes and heterogeneity in bone cancer. Phenotypic differences that arise from constricted migration of U2OS clones are further illustrated by a clone with a highly elongated and stable MSC-like shape that depends on microtubule assembly downstream of the transcription factor GATA4. Such changes are consistent with reversion to a more stem-like state upstream of cancerous osteoblastic cells. Migration-induced genomic instability can thus associate with heritable changes.
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Affiliation(s)
- Jerome Irianto
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuntao Xia
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte R Pfeifer
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group, Department of Physics and Astronomy, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Avathamsa Athirasala
- Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiazheng Ji
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cory Alvey
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manu Tewari
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel R Bennett
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group, Department of Physics and Astronomy, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shane M Harding
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrea J Liu
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group, Department of Physics and Astronomy, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roger A Greenberg
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dennis E Discher
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group, Department of Physics and Astronomy, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA.
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39
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Irianto J, Xia Y, Pfeifer CR, Greenberg RA, Discher DE. As a Nucleus Enters a Small Pore, Chromatin Stretches and Maintains Integrity, Even with DNA Breaks. Biophys J 2016; 112:446-449. [PMID: 28341535 DOI: 10.1016/j.bpj.2016.09.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/17/2016] [Accepted: 09/30/2016] [Indexed: 10/20/2022] Open
Abstract
As a cell pushes or pulls its nucleus through a small constriction, the chromatin must distort and somehow maintain genomic stability despite ever-present double-strand breaks in the DNA. Here we visualize within a living cell the pore-size dependent deformation of a specific locus engineered into chromosome-1 and cleaved. An mCherry-tagged nuclease targets the submicron locus, causing DNA cleavage and recruiting repair factors such as GFP-53BP1 to a large region around the locus. Aspiration of a cell and its nucleus into a micropipette shows that chromatin aligns and stretches parallel to the pore. Extension is largest in small pores, increasing >10-fold but remaining 30-fold shorter than the DNA contour length in the locus. Brochard and de Gennes' blob model for tube geometry fits the data, with a simple modification for chromatin crowding. Continuity of the highly extended, cleaved chromatin is also maintained, consistent with folding and cross bridging of the DNA. Surprisingly, extensional integrity is unaffected by an inhibitor of the DNA repair scaffold.
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Affiliation(s)
- Jerome Irianto
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yuntao Xia
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charlotte R Pfeifer
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, Pennsylvania; Graduate Group/Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Roger A Greenberg
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dennis E Discher
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, Pennsylvania; Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, Pennsylvania; Graduate Group/Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania.
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40
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Irianto J, Pfeifer CR, Bennett RR, Xia Y, Ivanovska IL, Liu AJ, Greenberg RA, Discher DE. Nuclear constriction segregates mobile nuclear proteins away from chromatin. Mol Biol Cell 2016; 27:4011-4020. [PMID: 27798234 PMCID: PMC5156542 DOI: 10.1091/mbc.e16-06-0428] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/13/2016] [Accepted: 10/18/2016] [Indexed: 11/11/2022] Open
Abstract
Nuclear distortion such as in 3D migration concentrates chromatin locally and causes complementary segregation of mobile factors within the nucleus. This is unavoidable because chromatin is compressible. As a cell squeezes its nucleus through adjacent tissue, penetrates a basement membrane, or enters a small blood capillary, chromatin density and nuclear factors could in principle be physically perturbed. Here, in cancer cell migration through rigid micropores and in passive pulling into micropipettes, local compaction of chromatin is observed coincident with depletion of mobile factors. Heterochromatin/euchromatin was previously estimated from molecular mobility measurements to occupy a volume fraction f of roughly two-thirds of the nuclear volume, but based on the relative intensity of DNA and histones in several cancer cell lines drawn into narrow constrictions, f can easily increase locally to nearly 100%. By contrast, mobile proteins in the nucleus, including a dozen that function as DNA repair proteins (e.g., BRCA1, 53BP1) or nucleases (e.g., Cas9, FokI), are depleted within the constriction, approaching 0%. Such losses—compounded by the occasional rupture of the nuclear envelope—can have important functional consequences. Studies of a nuclease that targets a locus in chromosome-1 indeed show that constricted migration delays DNA damage.
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Affiliation(s)
- Jerome Irianto
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104.,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Charlotte R Pfeifer
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104.,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104.,Graduate Group/Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Rachel R Bennett
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104.,Graduate Group/Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Yuntao Xia
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104.,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Irena L Ivanovska
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104.,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrea J Liu
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104.,Graduate Group/Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Roger A Greenberg
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104.,Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E Discher
- Physical Sciences Oncology Center at Penn, University of Pennsylvania, Philadelphia, PA 19104 .,Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104.,Graduate Group/Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
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41
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Abstract
Dysmorphic nuclei are commonly seen in cancers and provide strong motivation for studying the main structural proteins of nuclei, the lamins, in cancer. Past studies have also demonstrated the significance of microenvironment mechanics to cancer progression, which is extremely interesting because the lamina was recently shown to be mechanosensitive. Here, we review current knowledge relating cancer progression to lamina biophysics. Lamin levels can constrain cancer cell migration in 3D and thereby impede tumor growth, and lamins can also protect a cancer cell's genome. In addition, lamins can influence transcriptional regulators (RAR, SRF, YAP/TAZ) and chromosome conformation in lamina associated domains. Further investigation of the roles for lamins in cancer and even DNA damage may lead to new therapies or at least to a clearer understanding of lamins as bio-markers in cancer progression.
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Affiliation(s)
- Jerome Irianto
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte R. Pfeifer
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Irena L. Ivanovska
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - 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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Cho S, Majkut S, Tewari M, Irianto J, Discher DE. As the Beating Heart Stiffens in Development, So does the Nuclear Lamina. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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43
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Pfeifer CR, Irianto J, Discher DE. Segregation of Mobile Nuclear Proteins Away from Chromatin when the Nucleus is Constricted. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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44
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Irianto J, Pfeifer CR, Athirasala A, Ivanovska IL, Greenberg RE, Discher DE. Cell Invasion through Stiff Constrictions causes Mutations While Damaging the Nucleus. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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45
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Buxboim A, Swift J, Irianto J, Spinler KR, Dingal PCDP, Athirasala A, Kao YRC, Cho S, Harada T, Shin JW, Discher DE. Matrix elasticity regulates lamin-A,C phosphorylation and turnover with feedback to actomyosin. Curr Biol 2014; 24:1909-17. [PMID: 25127216 DOI: 10.1016/j.cub.2014.07.001] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/28/2014] [Accepted: 07/01/2014] [Indexed: 01/01/2023]
Abstract
Tissue microenvironments are characterized not only in terms of chemical composition but also by collective properties such as stiffness, which influences the contractility of a cell, its adherent morphology, and even differentiation. The nucleoskeletal protein lamin-A,C increases with matrix stiffness, confers nuclear mechanical properties, and influences differentiation of mesenchymal stem cells (MSCs), whereas B-type lamins remain relatively constant. Here we show in single-cell analyses that matrix stiffness couples to myosin-II activity to promote lamin-A,C dephosphorylation at Ser22, which regulates turnover, lamina physical properties, and actomyosin expression. Lamin-A,C phosphorylation is low in interphase versus dividing cells, and its levels rise with states of nuclear rounding in which myosin-II generates little to no tension. Phosphorylated lamin-A,C localizes to nucleoplasm, and phosphorylation is enriched on lamin-A,C fragments and is suppressed by a cyclin-dependent kinase (CDK) inhibitor. Lamin-A,C knockdown in primary MSCs suppresses transcripts predominantly among actomyosin genes, especially in the serum response factor (SRF) pathway. Levels of myosin-IIA thus parallel levels of lamin-A,C, with phosphosite mutants revealing a key role for phosphoregulation. In modeling the system as a parsimonious gene circuit, we show that tension-dependent stabilization of lamin-A,C and myosin-IIA can suitably couple nuclear and cell morphology downstream of matrix mechanics.
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Affiliation(s)
- Amnon Buxboim
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA; Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joe Swift
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerome Irianto
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyle R Spinler
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - P C Dave P Dingal
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Avathamsa Athirasala
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yun-Ruei C Kao
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sangkyun Cho
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Takamasa Harada
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jae-Won Shin
- 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; Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Harada T, Swift J, Irianto J, Shin JW, Spinler KR, Athirasala A, Diegmiller R, Dingal PCDP, Ivanovska IL, Discher DE. Nuclear lamin stiffness is a barrier to 3D migration, but softness can limit survival. ACTA ACUST UNITED AC 2014; 204:669-82. [PMID: 24567359 PMCID: PMC3941057 DOI: 10.1083/jcb.201308029] [Citation(s) in RCA: 399] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Lamins impede 3D migration but also promote survival against migration-induced stresses. Cell migration through solid tissue often involves large contortions of the nucleus, but biological significance is largely unclear. The nucleoskeletal protein lamin-A varies both within and between cell types and was shown here to contribute to cell sorting and survival in migration through constraining micropores. Lamin-A proved rate-limiting in 3D migration of diverse human cells that ranged from glioma and adenocarcinoma lines to primary mesenchymal stem cells (MSCs). Stoichiometry of A- to B-type lamins established an activation barrier, with high lamin-A:B producing extruded nuclear shapes after migration. Because the juxtaposed A and B polymer assemblies respectively conferred viscous and elastic stiffness to the nucleus, subpopulations with different A:B levels sorted in 3D migration. However, net migration was also biphasic in lamin-A, as wild-type lamin-A levels protected against stress-induced death, whereas deep knockdown caused broad defects in stress resistance. In vivo xenografts proved consistent with A:B-based cell sorting, and intermediate A:B-enhanced tumor growth. Lamins thus impede 3D migration but also promote survival against migration-induced stresses.
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Affiliation(s)
- Takamasa Harada
- Molecular and Cell Biophysics Lab and 2 Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
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Irianto J, Ramaswamy G, Serra R, Knight MM. Depletion of chondrocyte primary cilia reduces the compressive modulus of articular cartilage. J Biomech 2013; 47:579-82. [PMID: 24345381 PMCID: PMC3899052 DOI: 10.1016/j.jbiomech.2013.11.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/20/2013] [Accepted: 11/24/2013] [Indexed: 02/05/2023]
Abstract
Primary cilia are slender, microtubule based structures found in the majority of cell types with one cilium per cell. In articular cartilage, primary cilia are required for chondrocyte mechanotransduction and the development of healthy tissue. Loss of primary cilia in Col2aCre;ift88(fl/fl) transgenic mice results in up-regulation of osteoarthritic (OA) markers and development of OA like cartilage with greater thickness and reduced mechanical stiffness. However no previous studies have examined whether loss of primary cilia influences the intrinsic mechanical properties of articular cartilage matrix in the form of the modulus or just the structural properties of the tissue. The present study describes a modified analytical model to derive the viscoelastic moduli based on previous experimental indentation data. Results show that the increased thickness of the articular cartilage in the Col2aCre;ift88(fl/fl) transgenic mice is associated with a reduction in both the instantaneous and equilibrium moduli at indentation strains of greater than 20%. This reveals that the loss of primary cilia causes a significant reduction in the mechanical properties of cartilage particularly in the deeper zones and possibly the underlying bone. This is consistent with histological analysis and confirms the importance of primary cilia in the development of a mechanically functional articular cartilage.
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Affiliation(s)
- Jerome Irianto
- Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary University of London, Mile End Rd, London E1 4NS, United Kingdom
| | - Girish Ramaswamy
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Rosa Serra
- Arthritis & Musculoskeletal Diseases Center, UAB School of Medicine and Dentistry, Birmingham, AL, USA
| | - Martin M Knight
- Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary University of London, Mile End Rd, London E1 4NS, United Kingdom.
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Irianto J, Lee DA, Knight MM. Quantification of chromatin condensation level by image processing. Med Eng Phys 2013; 36:412-7. [PMID: 24099693 DOI: 10.1016/j.medengphy.2013.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/03/2013] [Accepted: 09/09/2013] [Indexed: 10/26/2022]
Abstract
The level of chromatin condensation is related to the silencing/activation of chromosomal territories and therefore impacts on gene expression. Chromatin condensation changes during cell cycle, progression and differentiation, and is influenced by various physicochemical and epigenetic factors. This study describes a validated experimental technique to quantify chromatin condensation. A novel image processing procedure is developed using Sobel edge detection to quantify the level of chromatin condensation from nuclei images taken by confocal microscopy. The algorithm was developed in MATLAB and used to quantify different levels of chromatin condensation in chondrocyte nuclei achieved through alteration in osmotic pressure. The resulting chromatin condensation parameter (CCP) is in good agreement with independent multi-observer qualitative visual assessment. This image processing technique thereby provides a validated unbiased parameter for rapid and highly reproducible quantification of the level of chromatin condensation.
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Affiliation(s)
- Jerome Irianto
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary, University of London, London, United Kingdom.
| | - David A Lee
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary, University of London, London, United Kingdom
| | - Martin M Knight
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary, University of London, London, United Kingdom
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49
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Irianto J, Swift J, Martins RP, McPhail GD, Knight MM, Discher DE, Lee DA. Osmotic challenge drives rapid and reversible chromatin condensation in chondrocytes. Biophys J 2013; 104:759-69. [PMID: 23442954 DOI: 10.1016/j.bpj.2013.01.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/20/2012] [Accepted: 01/07/2013] [Indexed: 02/02/2023] Open
Abstract
Changes in extracellular osmolality have been shown to alter gene expression patterns and metabolic activity of various cell types, including chondrocytes. However, mechanisms by which physiological or pathological changes in osmolality impact chondrocyte function remain unclear. Here we use quantitative image analysis, electron microscopy, and a DNase I assay to show that hyperosmotic conditions (>400 mOsm/kg) induce chromatin condensation, while hypoosmotic conditions (100 mOsm/kg) cause decondensation. Large density changes (p < 0.001) occur over a very narrow range of physiological osmolalities, which suggests that chondrocytes likely experience chromatin condensation and decondensation during a daily loading cycle. The effect of changes in osmolality on nuclear morphology (p < 0.01) and chromatin condensation (p < 0.001) also differed between chondrocytes in monolayer culture and three-dimensional agarose, suggesting a role for cell adhesion. The relationship between condensation and osmolality was accurately modeled by a polymer gel model which, along with the rapid nature of the chromatin condensation (<20 s), reveals the basic physicochemical nature of the process. Alterations in chromatin structure are expected to influence gene expression and thereby regulate chondrocyte activity in response to osmotic changes.
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Affiliation(s)
- Jerome Irianto
- Institute of Bioengineering, School of Engineering and Material Science, Queen Mary, University of London, London, United Kingdom.
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50
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Chen J, Irianto J, Inamdar S, Pravincumar P, Lee DA, Bader DL, Knight MM. Cell mechanics, structure, and function are regulated by the stiffness of the three-dimensional microenvironment. Biophys J 2013; 103:1188-97. [PMID: 22995491 DOI: 10.1016/j.bpj.2012.07.054] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 07/06/2012] [Accepted: 07/27/2012] [Indexed: 11/17/2022] Open
Abstract
This study adopts a combined computational and experimental approach to determine the mechanical, structural, and metabolic properties of isolated chondrocytes cultured within three-dimensional hydrogels. A series of linear elastic and hyperelastic finite-element models demonstrated that chondrocytes cultured for 24 h in gels for which the relaxation modulus is <5 kPa exhibit a cellular Young's modulus of ∼5 kPa. This is notably greater than that reported for isolated chondrocytes in suspension. The increase in cell modulus occurs over a 24-h period and is associated with an increase in the organization of the cortical actin cytoskeleton, which is known to regulate cell mechanics. However, there was a reduction in chromatin condensation, suggesting that changes in the nucleus mechanics may not be involved. Comparison of cells in 1% and 3% agarose showed that cells in the stiffer gels rapidly develop a higher Young's modulus of ∼20 kPa, sixfold greater than that observed in the softer gels. This was associated with higher levels of actin organization and chromatin condensation, but only after 24 h in culture. Further studies revealed that cells in stiffer gels synthesize less extracellular matrix over a 28-day culture period. Hence, this study demonstrates that the properties of the three-dimensional microenvironment regulate the mechanical, structural, and metabolic properties of living cells.
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Affiliation(s)
- J Chen
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London, United Kingdom
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