1
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Attar AG, Paturej J, Banigan EJ, Erbaş A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. Nucleus 2024; 15:2351957. [PMID: 38753956 PMCID: PMC11407394 DOI: 10.1080/19491034.2024.2351957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/22/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Abnormal cell nuclear shapes are hallmarks of diseases, including progeria, muscular dystrophy, and many cancers. Experiments have shown that disruption of heterochromatin and increases in euchromatin lead to nuclear deformations, such as blebs and ruptures. However, the physical mechanisms through which chromatin governs nuclear shape are poorly understood. To investigate how heterochromatin and euchromatin might govern nuclear morphology, we studied chromatin microphase separation in a composite coarse-grained polymer and elastic shell simulation model. By varying chromatin density, heterochromatin composition, and heterochromatin-lamina interactions, we show how the chromatin phase organization may perturb nuclear shape. Increasing chromatin density stabilizes the lamina against large fluctuations. However, increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations by a "wetting"-like interaction. In contrast, fluctuations are insensitive to heterochromatin's internal structure. Our simulations suggest that peripheral heterochromatin accumulation could perturb nuclear morphology, while nuclear shape stabilization likely occurs through mechanisms other than chromatin microphase organization.
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Affiliation(s)
- Ali Goktug Attar
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
| | | | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
- Institute of Physics, University of Silesia, Chorzów, Poland
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2
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Perea Paizal J, Au SH, Bakal C. Nuclear rupture induced by capillary constriction forces promotes differential effects on metastatic and normal breast cells. Sci Rep 2024; 14:14793. [PMID: 38926422 PMCID: PMC11208511 DOI: 10.1038/s41598-024-64733-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
During metastatic dissemination, circulating tumour cells (CTCs) enter capillary beds, where they experience mechanical constriction forces. The transient and persistent effects of these forces on CTCs behaviour remain poorly understood. Here, we developed a high-throughput microfluidic platform mimicking human capillaries to investigate the impact of mechanical constriction forces on malignant and normal breast cell lines. We observed that capillary constrictions induced nuclear envelope rupture in both cancer and normal cells, leading to transient changes in nuclear and cytoplasmic area. Constriction forces transiently activated cGAS/STING and pathways involved in inflammation (NF-κB, STAT and IRF3), especially in the non-malignant cell line. Furthermore, the non-malignant cell line experienced transcriptional changes, particularly downregulation of epithelial markers, while the metastatic cell lines showed minimal alterations. These findings suggest that mechanical constriction forces within capillaries may promote differential effects in malignant and normal cell lines.
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Affiliation(s)
- Julia Perea Paizal
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
- Division of Cancer Biology, Chester Beatty Laboratories, Institute of Cancer Research, 237 Fulham Road, London, SW6 6JB, UK.
- Cancer Research UK Convergence Science Centre, Roderic Hill Building, Imperial College London, London, SW7 2BB, UK.
| | - Sam H Au
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
- Cancer Research UK Convergence Science Centre, Roderic Hill Building, Imperial College London, London, SW7 2BB, UK
| | - Chris Bakal
- Division of Cancer Biology, Chester Beatty Laboratories, Institute of Cancer Research, 237 Fulham Road, London, SW6 6JB, UK
- Cancer Research UK Convergence Science Centre, Roderic Hill Building, Imperial College London, London, SW7 2BB, UK
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3
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Gregory EF, Luxton GWG, Starr DA. Anchorage of H3K9-methylated heterochromatin to the nuclear periphery helps mediate P-cell nuclear migration though constricted spaces in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595380. [PMID: 38826247 PMCID: PMC11142143 DOI: 10.1101/2024.05.22.595380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Nuclei adjust their deformability while migrating through constrictions to enable structural changes and maintain nuclear integrity. The effect of heterochromatin anchored at the nucleoplasmic face of the inner nuclear membrane on nuclear morphology and deformability during in vivo nuclear migration through constricted spaces remains unclear. Here, we show that abolishing peripheral heterochromatin anchorage by eliminating CEC-4, a chromodomain protein that tethers H3K9-methylated chromatin to the nuclear periphery, disrupts constrained P-cell nuclear migration in Caenorhabditis elegans larvae in the absence of the established LINC complex-dependent pathway. CEC-4 acts in parallel to an actin and CDC-42-based pathway. We also demonstrate the necessity for the chromatin methyltransferases MET-2 and JMJD-1.2 during P-cell nuclear migration in the absence of functional LINC complexes. We conclude that H3K9-nethylated chromatin needs to be anchored to the nucleoplasmic face of the inner nuclear membrane to help facilitate nuclear migration through constricted spaces in vivo.
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Affiliation(s)
- Ellen F Gregory
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616 USA
| | - G W Gant Luxton
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616 USA
| | - Daniel A Starr
- Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616 USA
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4
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Mishra J, Chakraborty S, Niharika, Roy A, Manna S, Baral T, Nandi P, Patra SK. Mechanotransduction and epigenetic modulations of chromatin: Role of mechanical signals in gene regulation. J Cell Biochem 2024; 125:e30531. [PMID: 38345428 DOI: 10.1002/jcb.30531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/08/2024] [Accepted: 01/26/2024] [Indexed: 03/12/2024]
Abstract
Mechanical forces may be generated within a cell due to tissue stiffness, cytoskeletal reorganization, and the changes (even subtle) in the cell's physical surroundings. These changes of forces impose a mechanical tension within the intracellular protein network (both cytosolic and nuclear). Mechanical tension could be released by a series of protein-protein interactions often facilitated by membrane lipids, lectins and sugar molecules and thus generate a type of signal to drive cellular processes, including cell differentiation, polarity, growth, adhesion, movement, and survival. Recent experimental data have accentuated the molecular mechanism of this mechanical signal transduction pathway, dubbed mechanotransduction. Mechanosensitive proteins in the cell's plasma membrane discern the physical forces and channel the information to the cell interior. Cells respond to the message by altering their cytoskeletal arrangement and directly transmitting the signal to the nucleus through the connection of the cytoskeleton and nucleoskeleton before the information despatched to the nucleus by biochemical signaling pathways. Nuclear transmission of the force leads to the activation of chromatin modifiers and modulation of the epigenetic landscape, inducing chromatin reorganization and gene expression regulation; by the time chemical messengers (transcription factors) arrive into the nucleus. While significant research has been done on the role of mechanotransduction in tumor development and cancer progression/metastasis, the mechanistic basis of force-activated carcinogenesis is still enigmatic. Here, in this review, we have discussed the various cues and molecular connections to better comprehend the cellular mechanotransduction pathway, and we also explored the detailed role of some of the multiple players (proteins and macromolecular complexes) involved in mechanotransduction. Thus, we have described an avenue: how mechanical stress directs the epigenetic modifiers to modulate the epigenome of the cells and how aberrant stress leads to the cancer phenotype.
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Affiliation(s)
- Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
| | - Samir K Patra
- Epigenetics and Cancer Research Laboratory, Department of Life Science, Biochemistry and Molecular Biology Group, National Institute of Technology, Rourkela, Odisha, India
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5
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Ahmad M, Imran A, Movileanu L. Overlapping characteristics of weak interactions of two transcriptional regulators with WDR5. Int J Biol Macromol 2024; 258:128969. [PMID: 38158065 PMCID: PMC10922662 DOI: 10.1016/j.ijbiomac.2023.128969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
The WD40 repeat protein 5 (WDR5) is a nuclear hub that critically influences gene expression by interacting with transcriptional regulators. Utilizing the WDR5 binding motif (WBM) site, WDR5 interacts with the myelocytomatosis (MYC), an oncoprotein transcription factor, and the retinoblastoma-binding protein 5 (RbBP5), a scaffolding element of an epigenetic complex. Given the clinical significance of these protein-protein interactions (PPIs), there is a pressing necessity for a quantitative assessment of these processes. Here, we use biolayer interferometry (BLI) to examine interactions of WDR5 with consensus peptide ligands of MYC and RbBP5. We found that both interactions exhibit relatively weak affinities arising from a fast dissociation process. Remarkably, live-cell imaging identified distinctive WDR5 localizations in the absence and presence of full-length binding partners. Although WDR5 tends to accumulate within nucleoli, WBM-mediated interactions with MYC and RbBP5 require their localization outside nucleoli. We utilize fluorescence resonance energy transfer (FRET) microscopy to confirm these weak interactions through a low FRET efficiency of the MYC-WDR5 and RbBP5-WDR5 complexes in living cells. In addition, we evaluate the impact of peptide and small-molecule inhibitors on these interactions. These outcomes form a fundamental basis for further developments to clarify the multitasking role of the WBM binding site of WDR5.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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6
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Attar AG, Paturej J, Banigan EJ, Erbas A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.16.571697. [PMID: 38168411 PMCID: PMC10760070 DOI: 10.1101/2023.12.16.571697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Abnormalities in the shapes of mammalian cell nuclei are hallmarks of a variety of diseases, including progeria, muscular dystrophy, and various cancers. Experiments have shown that there is a causal relationship between chromatin organization and nuclear morphology. Decreases in heterochromatin levels, perturbations to heterochromatin organization, and increases in euchromatin levels all lead to misshapen nuclei, which exhibit deformations, such as nuclear blebs and nuclear ruptures. However, the polymer physical mechanisms of how chromatin governs nuclear shape and integrity are poorly understood. To investigate how heterochromatin and euchromatin, which are thought to microphase separate in vivo , govern nuclear morphology, we implemented a composite coarse-grained polymer and elastic shell model. By varying chromatin volume fraction (density), heterochromatin levels and structure, and heterochromatin-lamina interactions, we show how the spatial organization of chromatin polymer phases within the nucleus could perturb nuclear shape in some scenarios. Increasing the volume fraction of chromatin in the cell nucleus stabilizes the nuclear lamina against large fluctuations. However, surprisingly, we find that increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations in our simulations by a "wetting"-like interaction. In contrast, shape fluctuations are largely insensitive to the internal structure of the heterochromatin, such as the presence or absence of chromatin-chromatin crosslinks. Therefore, our simulations suggest that heterochromatin accumulation at the nuclear periphery could perturb nuclear morphology in a nucleus or nuclear region that is sufficiently soft, while stabilization of the nucleus via heterochromatin likely occurs through mechanisms other than chromatin microphase organization.
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7
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Sekhon H, Ha JH, Presti MF, Procopio SB, Jarvis AR, Mirsky PO, John AM, Loh SN. Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells. Nat Methods 2023; 20:1920-1929. [PMID: 37945909 PMCID: PMC11080272 DOI: 10.1038/s41592-023-02065-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023]
Abstract
A grand challenge in biosensor design is to develop a single-molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Here, we created a family of adaptable, turn-on maturation (ATOM) biosensors consisting of a monobody (circularly permuted at one of two positions) or a nanobody (circularly permuted at one of three positions) inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells coexpressing cyan, yellow and red ATOM sensors detected biosensor targets that were specifically localized to various subcellular compartments. Fluorescence activation involved ligand-dependent chromophore maturation with turn-on ratios of up to 62-fold in cells and 100-fold in vitro. Endoplasmic reticulum- and mitochondria-localized ATOM sensors detected ligands that were targeted to those organelles. The ATOM design was validated with three monobodies and one nanobody inserted into distinct fluorescent proteins, suggesting that customized ATOM sensors can be generated quickly.
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Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Spencer B Procopio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ava R Jarvis
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Paige O Mirsky
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Anna M John
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
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8
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Chinchole A, Gupta S, Tyagi S. To stay in shape and keep moving: MLL emerges as a new transcriptional regulator of Rho GTPases. Small GTPases 2023; 14:55-62. [PMID: 37671980 PMCID: PMC10484036 DOI: 10.1080/21541248.2023.2254437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
RhoA, Rac1 and CDC42 are small G proteins that play a crucial role in regulating various cellular processes, such as the formation of actin cytoskeleton, cell shape and cell migration. Our recent results suggest that MLL is responsible for maintaining the balance of these small Rho GTPases. MLL depletion affects the stability of Rho GTPases, leading to a decrease in their protein levels and loss of activity. These changes manifest in the form of abnormal cell shape and disrupted actin cytoskeleton, resulting in reduced cell spreading and migration. Interestingly, their chaperone protein RhoGDI1 but not the Rho GTPases, is under the direct transcriptional regulation of MLL. Here, we comment on the possible implications of these observations on the signalling by Rho GTPases protein network.
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Affiliation(s)
- Akash Chinchole
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD) Uppal, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Shreyta Gupta
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD) Uppal, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD) Uppal, Hyderabad, India
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9
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Berg IK, Currey ML, Gupta S, Berrada Y, Nguyen BV, Pho M, Patteson AE, Schwarz JM, Banigan EJ, Stephens AD. Transcription inhibition suppresses nuclear blebbing and rupture independently of nuclear rigidity. J Cell Sci 2023; 136:jcs261547. [PMID: 37756607 PMCID: PMC10660790 DOI: 10.1242/jcs.261547] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Chromatin plays an essential role in the nuclear mechanical response and determining nuclear shape, which maintain nuclear compartmentalization and function. However, major genomic functions, such as transcription activity, might also impact cell nuclear shape via blebbing and rupture through their effects on chromatin structure and dynamics. To test this idea, we inhibited transcription with several RNA polymerase II inhibitors in wild-type cells and perturbed cells that presented increased nuclear blebbing. Transcription inhibition suppressed nuclear blebbing for several cell types, nuclear perturbations and transcription inhibitors. Furthermore, transcription inhibition suppressed nuclear bleb formation, bleb stabilization and bleb-based nuclear ruptures. Interestingly, transcription inhibition did not alter the histone H3 lysine 9 (H3K9) modification state, nuclear rigidity, and actin compression and contraction, which typically control nuclear blebbing. Polymer simulations suggested that RNA polymerase II motor activity within chromatin could drive chromatin motions that deform the nuclear periphery. Our data provide evidence that transcription inhibition suppresses nuclear blebbing and rupture, in a manner separate and distinct from chromatin rigidity.
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Affiliation(s)
- Isabel K. Berg
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Marilena L. Currey
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sarthak Gupta
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - Yasmin Berrada
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Bao V. Nguyen
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Mai Pho
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Alison E. Patteson
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - J. M. Schwarz
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
- Indian Creek Farm, Ithaca, NY 14850, USA
| | - Edward J. Banigan
- Institute of Medical Engineering & Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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10
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de Lope-Planelles A, González-Novo R, Madrazo E, Peralta-Carrero G, Cruz Rodríguez MP, Zamora-Carreras H, Torrano V, López-Menéndez H, Roda-Navarro P, Monroy F, Redondo-Muñoz J. Mechanical stress confers nuclear and functional changes in derived leukemia cells from persistent confined migration. Cell Mol Life Sci 2023; 80:316. [PMID: 37801090 PMCID: PMC10558412 DOI: 10.1007/s00018-023-04968-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/07/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
Nuclear deformability plays a critical role in cell migration. During this process, the remodeling of internal components of the nucleus has a direct impact on DNA damage and cell behavior; however, how persistent migration promotes nuclear changes leading to phenotypical and functional consequences remains poorly understood. Here, we described that the persistent migration through physical barriers was sufficient to promote permanent modifications in migratory-altered cells. We found that derived cells from confined migration showed changes in lamin B1 localization, cell morphology and transcription. Further analysis confirmed that migratory-altered cells showed functional differences in DNA repair, cell response to chemotherapy and cell migration in vivo homing experiments. Experimental modulation of actin polymerization affected the redistribution of lamin B1, and the basal levels of DNA damage in migratory-altered cells. Finally, since major nuclear changes were present in migratory-altered cells, we applied a multidisciplinary biochemical and biophysical approach to identify that confined conditions promoted a different biomechanical response of the nucleus in migratory-altered cells. Our observations suggest that mechanical compression during persistent cell migration has a role in stable nuclear and genomic alterations that might handle the genetic instability and cellular heterogeneity in aging diseases and cancer.
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Affiliation(s)
- Ana de Lope-Planelles
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Raquel González-Novo
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Elena Madrazo
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Gracia Peralta-Carrero
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - María Pilar Cruz Rodríguez
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Héctor Zamora-Carreras
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Verónica Torrano
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Horacio López-Menéndez
- Department of Physical Chemistry, Complutense University, Madrid, Spain
- Translational Biophysics, Hospital Doce de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Pedro Roda-Navarro
- Department of Immunology, School of Medicine, University Complutense de Madrid and 12 de Octubre Health Research Institute (Imas12) Madrid, Madrid, Spain
| | - Francisco Monroy
- Department of Physical Chemistry, Complutense University, Madrid, Spain
- Translational Biophysics, Hospital Doce de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Javier Redondo-Muñoz
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain.
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11
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Bastianello G, Foiani M. Mechanisms controlling the mechanical properties of the nuclei. Curr Opin Cell Biol 2023; 84:102222. [PMID: 37619290 DOI: 10.1016/j.ceb.2023.102222] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/26/2023]
Abstract
The mechanical properties of the nucleus influence different cellular and nuclear functions and have relevant implications for several human diseases. The nucleus protects genetic information while acting as a mechano-sensory hub in response to internal and external forces. Cells have evolved mechano-transduction signaling to respond to physical cellular and nuclear perturbations and adopted a multitude of molecular pathways to maintain nuclear shape stability and prevent morphological abnormalities of the nucleus. Here we describe those key biological processes that control nuclear mechanics and discuss emerging perspectives on the mechanobiology of the nucleus as a diagnostic tool and clinical target.
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Affiliation(s)
- Giulia Bastianello
- IFOM, The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Oncology and Haemato-Oncology Department, University of Milan, Milan 20122, Italy.
| | - Marco Foiani
- IFOM, The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Oncology and Haemato-Oncology Department, University of Milan, Milan 20122, Italy.
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12
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Chen Y, Su H, Zhao J, Na Z, Jiang K, Bacchiocchi A, Loh KH, Halaban R, Wang Z, Cao X, Slavoff SA. Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5. Cell Rep 2023; 42:113145. [PMID: 37725512 PMCID: PMC10629662 DOI: 10.1016/j.celrep.2023.113145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
The conserved WD40-repeat protein WDR5 interacts with multiple proteins both inside and outside the nucleus. However, it is currently unclear whether and how the distribution of WDR5 between complexes is regulated. Here, we show that an unannotated microprotein EMBOW (endogenous microprotein binder of WDR5) dually encoded in the human SCRIB gene interacts with WDR5 and regulates its binding to multiple interaction partners, including KMT2A and KIF2A. EMBOW is cell cycle regulated, with two expression maxima at late G1 phase and G2/M phase. Loss of EMBOW decreases WDR5 interaction with KIF2A, aberrantly shortens mitotic spindle length, prolongs G2/M phase, and delays cell proliferation. In contrast, loss of EMBOW increases WDR5 interaction with KMT2A, leading to WDR5 binding to off-target genes, erroneously increasing H3K4me3 levels, and activating transcription of these genes. Together, these results implicate EMBOW as a regulator of WDR5 that regulates its interactions and prevents its off-target binding in multiple contexts.
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Affiliation(s)
- Yanran Chen
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Haomiao Su
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Jianing Zhao
- Frontier Innovation Center, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200433, China
| | - Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Kevin Jiang
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ken H Loh
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zhentian Wang
- Frontier Innovation Center, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200433, China
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China.
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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13
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González-Novo R, de Lope-Planelles A, Cruz Rodríguez MP, González-Murillo Á, Madrazo E, Acitores D, García de Lacoba M, Ramírez M, Redondo-Muñoz J. 3D environment controls H3K4 methylation and the mechanical response of the nucleus in acute lymphoblastic leukemia cells. Eur J Cell Biol 2023; 102:151343. [PMID: 37494871 DOI: 10.1016/j.ejcb.2023.151343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, and the infiltration of leukemic cells is critical for disease progression and relapse. Nuclear deformability plays a critical role in cancer cell invasion through confined spaces; however, the direct impact of epigenetic changes on the nuclear deformability of leukemic cells remains unclear. Here, we characterized how 3D collagen matrix conditions induced H3K4 methylation in ALL cell lines and clinical samples. We used specific shRNA and chemical inhibitors to target WDR5 (a core subunit involved in H3K4 methylation) and determined that targeting WDR5 reduced the H3K4 methylation induced by the 3D environment and the invasiveness of ALL cells in vitro and in vivo. Intriguingly, targeting WDR5 did not reduce the adhesion or the chemotactic response of leukemia cells, suggesting a different mechanism by which H3K4 methylation might govern ALL cell invasiveness. Finally, we conducted biochemical, and biophysical experiments to determine that 3D environments promoted the alteration of the chromatin, the morphology, and the mechanical behavior of the nucleus in ALL cells. Collectively, our data suggest that 3D environments control an upregulation of H3K4 methylation in ALL cells, and targeting WDR5 might serve as a promising therapeutic target against ALL invasiveness in vivo.
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Affiliation(s)
- Raquel González-Novo
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Ana de Lope-Planelles
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - María Pilar Cruz Rodríguez
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - África González-Murillo
- Oncolohematology Unit, Hospital Universitario Niño Jesús, Madrid, Spain; Health Research Institute La Princesa, Madrid, Spain
| | - Elena Madrazo
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - David Acitores
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Mario García de Lacoba
- Bioinformatics and Biostatistics Unit, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Manuel Ramírez
- Oncolohematology Unit, Hospital Universitario Niño Jesús, Madrid, Spain; Health Research Institute La Princesa, Madrid, Spain
| | - Javier Redondo-Muñoz
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain.
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14
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Hertzog M, Erdel F. The Material Properties of the Cell Nucleus: A Matter of Scale. Cells 2023; 12:1958. [PMID: 37566037 PMCID: PMC10416959 DOI: 10.3390/cells12151958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
Chromatin regulatory processes physically take place in the environment of the cell nucleus, which is filled with the chromosomes and a plethora of smaller biomolecules. The nucleus contains macromolecular assemblies of different sizes, from nanometer-sized protein complexes to micrometer-sized biomolecular condensates, chromosome territories, and nuclear bodies. This multiscale organization impacts the transport processes within the nuclear interior, the global mechanical properties of the nucleus, and the way the nucleus senses and reacts to mechanical stimuli. Here, we discuss recent work on these aspects, including microrheology and micromanipulation experiments assessing the material properties of the nucleus and its subcomponents. We summarize how the properties of multiscale media depend on the time and length scales probed in the experiment, and we reconcile seemingly contradictory observations made on different scales. We also revisit the concept of liquid-like and solid-like material properties for complex media such as the nucleus. We propose that the nucleus can be considered a multiscale viscoelastic medium composed of three major components with distinct properties: the lamina, the chromatin network, and the nucleoplasmic fluid. This multicomponent organization enables the nucleus to serve its different functions as a reaction medium on the nanoscale and as a mechanosensor and structural scaffold on the microscale.
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Affiliation(s)
| | - Fabian Erdel
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, 169 Avenue Marianne Grunberg-Manago, 31062 Toulouse, France
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15
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Hsia CR, Melters DP, Dalal Y. The Force is Strong with This Epigenome: Chromatin Structure and Mechanobiology. J Mol Biol 2023; 435:168019. [PMID: 37330288 PMCID: PMC10567996 DOI: 10.1016/j.jmb.2023.168019] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
All life forms sense and respond to mechanical stimuli. Throughout evolution, organisms develop diverse mechanosensing and mechanotransduction pathways, leading to fast and sustained mechanoresponses. Memory and plasticity characteristics of mechanoresponses are thought to be stored in the form of epigenetic modifications, including chromatin structure alterations. These mechanoresponses in the chromatin context share conserved principles across species, such as lateral inhibition during organogenesis and development. However, it remains unclear how mechanotransduction mechanisms alter chromatin structure for specific cellular functions, and if altered chromatin structure can mechanically affect the environment. In this review, we discuss how chromatin structure is altered by environmental forces via an outside-in pathway for cellular functions, and the emerging concept of how chromatin structure alterations can mechanically affect nuclear, cellular, and extracellular environments. This bidirectional mechanical feedback between chromatin of the cell and the environment can potentially have important physiological implications, such as in centromeric chromatin regulation of mechanobiology in mitosis, or in tumor-stroma interactions. Finally, we highlight the current challenges and open questions in the field and provide perspectives for future research.
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Affiliation(s)
- Chieh-Ren Hsia
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/JeremiahHsia
| | - Daniël P Melters
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/dpmelters
| | - Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/NCIYaminiDalal
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16
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Sekhon H, Ha JH, Presti MF, Procopio SB, Mirsky PO, John AM, Loh SN. Adaptable, Turn-On Monobody (ATOM) Fluorescent Biosensors for Multiplexed Detection in Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534597. [PMID: 37034669 PMCID: PMC10081266 DOI: 10.1101/2023.03.28.534597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A grand challenge in biosensor design is to develop a single molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Conceptually, this can be achieved by fusing a small, antibody-like binding domain to a fluorescent protein in such a way that target binding activates fluorescence. Although this design is simple to envision, its execution is not obvious. Here, we created a family of adaptable, turn-on monobody (ATOM) biosensors consisting of a monobody, circularly permuted at one of two positions, inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells co-expressing cyan, yellow, and red ATOM sensors detected the biosensor targets (WDR5, SH2, and hRAS proteins) that were localized to the nucleus, cytoplasm, and plasma membrane, respectively, with high specificity. ER- and mitochondria-localized ATOM sensors also detected ligands that were targeted to those organelles. Fluorescence activation involved ligand-dependent chromophore maturation with fluorescence turn-on ratios of >20-fold in cells and up to 100-fold in vitro . The sensing mechanism was validated with three arbitrarily chosen monobodies inserted into jellyfish as well as anemone lineages of fluorescent proteins, suggesting that ATOM sensors with different binding specificities and additional colors can be generated relatively quickly.
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17
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Tuning between Nuclear Organization and Functionality in Health and Disease. Cells 2023; 12:cells12050706. [PMID: 36899842 PMCID: PMC10000962 DOI: 10.3390/cells12050706] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The organization of eukaryotic genome in the nucleus, a double-membraned organelle separated from the cytoplasm, is highly complex and dynamic. The functional architecture of the nucleus is confined by the layers of internal and cytoplasmic elements, including chromatin organization, nuclear envelope associated proteome and transport, nuclear-cytoskeletal contacts, and the mechano-regulatory signaling cascades. The size and morphology of the nucleus could impose a significant impact on nuclear mechanics, chromatin organization, gene expression, cell functionality and disease development. The maintenance of nuclear organization during genetic or physical perturbation is crucial for the viability and lifespan of the cell. Abnormal nuclear envelope morphologies, such as invagination and blebbing, have functional implications in several human disorders, including cancer, accelerated aging, thyroid disorders, and different types of neuro-muscular diseases. Despite the evident interplay between nuclear structure and nuclear function, our knowledge about the underlying molecular mechanisms for regulation of nuclear morphology and cell functionality during health and illness is rather poor. This review highlights the essential nuclear, cellular, and extracellular components that govern the organization of nuclei and functional consequences associated with nuclear morphometric aberrations. Finally, we discuss the recent developments with diagnostic and therapeutic implications targeting nuclear morphology in health and disease.
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18
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Materials and extracellular matrix rigidity highlighted in tissue damages and diseases: Implication for biomaterials design and therapeutic targets. Bioact Mater 2023; 20:381-403. [PMID: 35784640 PMCID: PMC9234013 DOI: 10.1016/j.bioactmat.2022.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/05/2022] [Accepted: 06/10/2022] [Indexed: 11/21/2022] Open
Abstract
Rigidity (or stiffness) of materials and extracellular matrix has proven to be one of the most significant extracellular physicochemical cues that can control diverse cell behaviors, such as contractility, motility, and spreading, and the resultant pathophysiological phenomena. Many 2D materials engineered with tunable rigidity have enabled researchers to elucidate the roles of matrix biophysical cues in diverse cellular events, including migration, lineage specification, and mechanical memory. Moreover, the recent findings accumulated under 3D environments with viscoelastic and remodeling properties pointed to the importance of dynamically changing rigidity in cell fate control, tissue repair, and disease progression. Thus, here we aim to highlight the works related with material/matrix-rigidity-mediated cell and tissue behaviors, with a brief outlook into the studies on the effects of material/matrix rigidity on cell behaviors in 2D systems, further discussion of the events and considerations in tissue-mimicking 3D conditions, and then examination of the in vivo findings that concern material/matrix rigidity. The current discussion will help understand the material/matrix-rigidity-mediated biological phenomena and further leverage the concepts to find therapeutic targets and to design implantable materials for the treatment of damaged and diseased tissues. Discuss the cutting-edge findings on the role of matrix rigidity in dictating diverse cell behaviors. Underscore the dynamic matrix rigidity that interplays with cells, and the related pathophysiological phenomena. Illuminate the significance of matrix rigidity in clinically-relevant settings.
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19
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Jin Y, Kim H, Min S, Choi YS, Seo SJ, Jeong E, Kim SK, Lee HA, Jo SH, Park JH, Park BW, Sim WS, Kim JJ, Ban K, Kim YG, Park HJ, Cho SW. Three-dimensional heart extracellular matrix enhances chemically induced direct cardiac reprogramming. SCIENCE ADVANCES 2022; 8:eabn5768. [PMID: 36516259 PMCID: PMC9750148 DOI: 10.1126/sciadv.abn5768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 11/12/2022] [Indexed: 06/17/2023]
Abstract
Direct cardiac reprogramming has emerged as a promising therapeutic approach for cardiac regeneration. Full chemical reprogramming with small molecules to generate cardiomyocytes may be more amenable than genetic reprogramming for clinical applications as it avoids safety concerns associated with genetic manipulations. However, challenges remain regarding low conversion efficiency and incomplete cardiomyocyte maturation. Furthermore, the therapeutic potential of chemically induced cardiomyocytes (CiCMs) has not been investigated. Here, we report that a three-dimensional microenvironment reconstituted with decellularized heart extracellular matrix can enhance chemical reprogramming and cardiac maturation of fibroblasts to cardiomyocytes. The resultant CiCMs exhibit elevated cardiac marker expression, sarcomeric organization, and improved electrophysiological features and drug responses. We investigated the therapeutic potential of CiCMs reprogrammed in three-dimensional heart extracellular matrix in a rat model of myocardial infarction. Our platform can facilitate the use of CiCMs for regenerative medicine, disease modeling, and drug screening.
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Affiliation(s)
- Yoonhee Jin
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Department of Physiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyeok Kim
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sungjin Min
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yi Sun Choi
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Seung Ju Seo
- Department of Physiology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Eunseon Jeong
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Su Kyeom Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyang-Ae Lee
- Korea Institute of Toxicology, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Sung-Hyun Jo
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea
| | - Jae-Hyun Park
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Bong-Woo Park
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Woo-Sup Sim
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jin-Ju Kim
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Kiwon Ban
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon 999077, Hong Kong
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea
| | - Hun-Jun Park
- Department of Biomedicine and Health Sciences, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
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20
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González-Bermúdez B, Kobayashi H, Abarca-Ortega A, Córcoles-Lucas M, González-Sánchez M, De la Fuente M, Guinea GV, Elices M, Plaza GR. Aging is accompanied by T-cell stiffening and reduced interstitial migration through dysfunctional nuclear organization. Immunology 2022; 167:622-639. [PMID: 36054660 DOI: 10.1111/imm.13559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023] Open
Abstract
Age-associated changes in T-cell function play a central role in immunosenescence. The role of aging in the decreased T-cell repertoire, primarily because of thymic involution, has been extensively studied. However, increasing evidence indicates that aging also modulates the mechanical properties of cells and the internal ordering of diverse cell components. Cellular functions are generally dictated by the biophysical phenotype of cells, which itself is also tightly regulated at the molecular level. Based on previous evidence suggesting that the relative nuclear size contributes to variations of T-cell stiffness, here we examined whether age-associated changes in T-cell migration are dictated by biophysical parameters, in part through nuclear cytoskeleton organization and cell deformability. In this study, we first performed longitudinal analyses of a repertoire of 111 functional, biophysical and biomolecular features of the nucleus and cytoskeleton of mice CD4+ and CD8+ T cells, in both naive and memory state. Focusing on the pairwise correlations, we found that age-related changes in nuclear architecture and internal ordering were correlated with T-cell stiffening and declined interstitial migration. A similarity analysis confirmed that cell-to-cell variation was a direct result of the aging process and we applied regression models to identify biomarkers that can accurately estimate individuals' age. Finally, we propose a biophysical model for a comprehensive understanding of the results: aging involves an evolution of the relative nuclear size, in part through DNA-hypomethylation and nuclear lamin B1, which implies an increased cell stiffness, thus inducing a decline in cell migration.
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Affiliation(s)
- Blanca González-Bermúdez
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
- IdISSC, Madrid, Spain
| | - Hikaru Kobayashi
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Aldo Abarca-Ortega
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Ingeniería Mecánica, Universidad de Santiago de Chile, Santiago, Chile
| | - Miguel Córcoles-Lucas
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Mónica González-Sánchez
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Mónica De la Fuente
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Gustavo V Guinea
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
- IdISSC, Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Manuel Elices
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Gustavo R Plaza
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Madrid, Spain
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, Madrid, Spain
- IdISSC, Madrid, Spain
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21
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Calì B, Deygas M, Munari F, Marcuzzi E, Cassará A, Toffali L, Vetralla M, Bernard M, Piel M, Gagliano O, Mastrogiovanni M, Laudanna C, Elvassore N, Molon B, Vargas P, Viola A. Atypical CXCL12 signaling enhances neutrophil migration by modulating nuclear deformability. Sci Signal 2022; 15:eabk2552. [DOI: 10.1126/scisignal.abk2552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To reach inflamed tissues from the circulation, neutrophils must overcome physical constraints imposed by the tissue architecture, such as the endothelial barrier or the three-dimensional (3D) interstitial space. In these microenvironments, neutrophils are forced to migrate through spaces smaller than their own diameter. One of the main challenges for cell passage through narrow gaps is the deformation of the nucleus, the largest and stiffest organelle in cells. Here, we showed that chemokines, the extracellular signals that guide cell migration in vivo, modulated nuclear plasticity to support neutrophil migration in restricted microenvironments. Exploiting microfabricated devices, we found that the CXC chemokine CXCL12 enhanced the nuclear pliability of mouse bone marrow–derived neutrophils to sustain their migration in 3D landscapes. This previously uncharacterized function of CXCL12 was mediated by the atypical chemokine receptor ACKR3 (also known as CXCR7), required protein kinase A (PKA) activity, and induced chromatin compaction, which resulted in enhanced cell migration in 3D. Thus, we propose that chemical cues regulate the nuclear plasticity of migrating leukocytes to optimize their motility in restricted microenvironments.
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Affiliation(s)
- Bianca Calì
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Mathieu Deygas
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France
| | - Fabio Munari
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Elisabetta Marcuzzi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Antonino Cassará
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Lara Toffali
- University of Verona, Department of Medicine, Division of General Pathology, Verona, Italy
| | - Massimo Vetralla
- Venetian Institute of Molecular Medicine, Padova, Italy
- Department of Industrial Engineering, University of Padova, Padova, Italy
| | - Mathilde Bernard
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France
| | - Onelia Gagliano
- Venetian Institute of Molecular Medicine, Padova, Italy
- Department of Industrial Engineering, University of Padova, Padova, Italy
| | - Marta Mastrogiovanni
- Lymphocyte Cell Biology Unit, Department of Immunology, Institut Pasteur, INSERM-U1224, Ligue Nationale Contre le Cancer, Équipe Labellisée Ligue 2018, F-75015 Paris, France
- Sorbonne Université, Collège Doctoral, F-75005 Paris. France
| | - Carlo Laudanna
- University of Verona, Department of Medicine, Division of General Pathology, Verona, Italy
| | - Nicola Elvassore
- Venetian Institute of Molecular Medicine, Padova, Italy
- Department of Industrial Engineering, University of Padova, Padova, Italy
| | - Barbara Molon
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
- Venetian Institute of Molecular Medicine, Padova, Italy
| | - Pablo Vargas
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Antonella Viola
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
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22
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Kumar R, Chander Y, Khandelwal N, Verma A, Rawat KD, Shringi BN, Pal Y, Tripathi BN, Barua S, Kumar N. ROCK1/MLC2 inhibition induces decay of viral mRNA in BPXV infected cells. Sci Rep 2022; 12:17811. [PMID: 36280692 PMCID: PMC9592580 DOI: 10.1038/s41598-022-21610-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/29/2022] [Indexed: 01/19/2023] Open
Abstract
Rho-associated coiled-coil containing protein kinase 1 (ROCK1) intracellular cell signaling pathway regulates cell morphology, polarity, and cytoskeletal remodeling. We observed the activation of ROCK1/myosin light chain (MLC2) signaling pathway in buffalopox virus (BPXV) infected Vero cells. ROCK1 depletion by siRNA and specific small molecule chemical inhibitors (Thiazovivin and Y27632) resulted in a reduced BPXV replication, as evidenced by reductions in viral mRNA/protein synthesis, genome copy numbers and progeny virus particles. Further, we demonstrated that ROCK1 inhibition promotes deadenylation of viral mRNA (mRNA decay), mediated via inhibiting interaction with PABP [(poly(A)-binding protein] and enhancing the expression of CCR4-NOT (a multi-protein complex that plays an important role in deadenylation of mRNA). In addition, ROCK1/MLC2 mediated cell contraction, and perinuclear accumulation of p-MLC2 was shown to positively correlate with viral mRNA/protein synthesis. Finally, it was demonstrated that the long-term sequential passage (P = 50) of BPXV in the presence of Thiazovivin does not select for any drug-resistant virus variants. In conclusion, ROCK1/MLC2 cell signaling pathway facilitates BPXV replication by preventing viral mRNA decay and that the inhibitors targeting this pathway may have novel therapeutic effects against buffalopox.
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Affiliation(s)
- Ram Kumar
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India ,grid.464655.00000 0004 1768 5915Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India ,grid.418105.90000 0001 0643 7375Present Address: Animal Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, India
| | - Yogesh Chander
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India ,grid.418105.90000 0001 0643 7375Present Address: Animal Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, India ,grid.411892.70000 0004 0500 4297Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana India
| | - Nitin Khandelwal
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Assim Verma
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Krishan Dutt Rawat
- grid.411892.70000 0004 0500 4297Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana India
| | - Brij N. Shringi
- grid.464655.00000 0004 1768 5915Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India
| | - Yash Pal
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Bhupendra N. Tripathi
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India ,grid.418105.90000 0001 0643 7375Present Address: Animal Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, India
| | - Sanjay Barua
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Naveen Kumar
- grid.462601.70000 0004 1768 7902Present Address: National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
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23
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Chinchole A, Lone KA, Tyagi S. MLL regulates the actin cytoskeleton and cell migration by stabilising Rho GTPases via the expression of RhoGDI1. J Cell Sci 2022; 135:jcs260042. [PMID: 36111497 PMCID: PMC7615853 DOI: 10.1242/jcs.260042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/09/2022] [Indexed: 04/26/2024] Open
Abstract
Attainment of proper cell shape and the regulation of cell migration are essential processes in the development of an organism. The mixed lineage leukemia (MLL or KMT2A) protein, a histone 3 lysine 4 (H3K4) methyltransferase, plays a critical role in cell-fate decisions during skeletal development and haematopoiesis in higher vertebrates. Rho GTPases - RhoA, Rac1 and CDC42 - are small G proteins that regulate various key cellular processes, such as actin cytoskeleton formation, the maintenance of cell shape and cell migration. Here, we report that MLL regulates the homeostasis of these small Rho GTPases. Loss of MLL resulted in an abnormal cell shape and a disrupted actin cytoskeleton, which lead to diminished cell spreading and migration. MLL depletion affected the stability and activity of Rho GTPases in a SET domain-dependent manner, but these Rho GTPases were not direct transcriptional targets of MLL. Instead, MLL regulated the transcript levels of their chaperone protein RhoGDI1 (also known as ARHGDIA). Using MDA-MB-231, a triple-negative breast cancer cell line with high RhoGDI1 expression, we show that MLL depletion or inhibition by small molecules reduces tumour progression in nude mice. Our studies highlight the central regulatory role of MLL in Rho/Rac/CDC42 signalling pathways. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Akash Chinchole
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal 567104, India
| | - Kaisar Ahmad Lone
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad 500039, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad 121001, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad 500039, India
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24
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Nikolić M, Scarcelli G, Tanner K. Multimodal microscale mechanical mapping of cancer cells in complex microenvironments. Biophys J 2022; 121:3586-3599. [PMID: 36059196 PMCID: PMC9617162 DOI: 10.1016/j.bpj.2022.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/05/2022] [Accepted: 09/02/2022] [Indexed: 02/07/2023] Open
Abstract
The mechanical phenotype of the cell is critical for survival following deformations due to confinement and fluid flow. One idea is that cancer cells are plastic and adopt different mechanical phenotypes under different geometries that aid in their survival. Thus, an attractive goal is to disrupt cancer cells' ability to adopt multiple mechanical states. To begin to address this question, we aimed to quantify the diversity of these mechanical states using in vitro biomimetics to mimic in vivo two-dimensional (2D) and 3D extracellular matrix environments. Here, we used two modalities Brillouin microscopy (∼GHz) and broadband frequency (7-15 kHz) optical tweezer microrheology to measure microscale cell mechanics. We measured the response of intracellular mechanics of cancer cells cultured in 2D and 3D environments where we modified substrate stiffness, dimensionality (2D versus 3D), and presence of fibrillar topography. We determined that there was good agreement between two modalities despite the difference in timescale of the two measurements. These findings on cell mechanical phenotype in different environments confirm a correlation between modalities that employ different mechanisms at different temporal scales (Hz-kHz versus GHz). We also determined that observed heterogeneity in cell shape is more closely linked to the cells' mechanical state. Moreover, individual cells in multicellular spheroids exhibit a lower degree of mechanical heterogeneity when compared with single cells cultured in monodisperse 3D cultures. The observed decreased heterogeneity among cells in spheroids suggested that there is mechanical cooperativity between cells that make up a single spheroid.
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Affiliation(s)
- Miloš Nikolić
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland; Maryland Biophysics Program, IPST, University of Maryland, College Park, Maryland
| | - Giuliano Scarcelli
- Maryland Biophysics Program, IPST, University of Maryland, College Park, Maryland; Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Kandice Tanner
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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25
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Song Y, Soto J, Chen B, Hoffman T, Zhao W, Zhu N, Peng Q, Liu L, Ly C, Wong PK, Wang Y, Rowat AC, Kurdistani SK, Li S. Transient nuclear deformation primes epigenetic state and promotes cell reprogramming. NATURE MATERIALS 2022; 21:1191-1199. [PMID: 35927431 PMCID: PMC9529815 DOI: 10.1038/s41563-022-01312-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 06/14/2022] [Indexed: 05/22/2023]
Abstract
Cell reprogramming has wide applications in tissue regeneration, disease modelling and personalized medicine. In addition to biochemical cues, mechanical forces also contribute to the modulation of the epigenetic state and a variety of cell functions through distinct mechanisms that are not fully understood. Here we show that millisecond deformation of the cell nucleus caused by confinement into microfluidic channels results in wrinkling and transient disassembly of the nuclear lamina, local detachment of lamina-associated domains in chromatin and a decrease of histone methylation (histone H3 lysine 9 trimethylation) and DNA methylation. These global changes in chromatin at the early stage of cell reprogramming boost the conversion of fibroblasts into neurons and can be partially reproduced by inhibition of histone H3 lysine 9 and DNA methylation. This mechanopriming approach also triggers macrophage reprogramming into neurons and fibroblast conversion into induced pluripotent stem cells, being thus a promising mechanically based epigenetic state modulation method for cell engineering.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer Soto
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Binru Chen
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Tyler Hoffman
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Weikang Zhao
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Ninghao Zhu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Qin Peng
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Longwei Liu
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Chau Ly
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Pak Kin Wong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Yingxiao Wang
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Amy C Rowat
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
- Department of Integrative Biology & Physiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Song Li
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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26
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González-Bermúdez B, Abarca-Ortega A, González-Sánchez M, De la Fuente M, Plaza GR. Possibilities of using T-cell biophysical biomarkers of ageing. Expert Rev Mol Med 2022; 24:e35. [PMID: 36111609 PMCID: PMC9884748 DOI: 10.1017/erm.2022.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/02/2022] [Accepted: 09/10/2022] [Indexed: 11/07/2022]
Abstract
Ageing is interrelated with the development of immunosenescence. This article focuses on one of the cell sets of the adaptive immune system, T cells, and provides a review of the known changes in T cells associated with ageing. Such fundamental changes affect both cell molecular content and internal ordering. However, acquiring a complete description of the changes at these levels would require extensive measurements of parameters and, furthermore, important fine details of the internal ordering that may be difficult to detect. Therefore, an alternative approach for the characterisation of cells consists of the performance of physical measurements of the whole cell, such as deformability measurements or migration measurements: the physical parameters, complementing the commonly used chemical biomarkers, may contribute to a better understanding of the evolution of T-cell states during ageing. Mechanical measurements, among other biophysical measurements, have the advantage of their relative simplicity: one single parameter agglutinates the complex effects of the variety of changes that gradually appear in cells during ageing.
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Affiliation(s)
- Blanca González-Bermúdez
- Center for Biomedical Technology, Universidad Politécnica de Madrid, E-28223 Pozuelo de Alarcón, Spain
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, E-28040 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Aldo Abarca-Ortega
- Center for Biomedical Technology, Universidad Politécnica de Madrid, E-28223 Pozuelo de Alarcón, Spain
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, E-28040 Madrid, Spain
- Departamento de Ingeniería Mecánica, Universidad de Santiago de Chile, Santiago, Chile
| | - Mónica González-Sánchez
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Mónica De la Fuente
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Gustavo R. Plaza
- Center for Biomedical Technology, Universidad Politécnica de Madrid, E-28223 Pozuelo de Alarcón, Spain
- Department of Materials Science, E.T.S.I. de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, E-28040 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Clínico San Carlos, IdISSC, Madrid, Spain
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27
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Hsia CR, McAllister J, Hasan O, Judd J, Lee S, Agrawal R, Chang CY, Soloway P, Lammerding J. Confined migration induces heterochromatin formation and alters chromatin accessibility. iScience 2022; 25:104978. [PMID: 36117991 PMCID: PMC9474860 DOI: 10.1016/j.isci.2022.104978] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 01/17/2023] Open
Abstract
During migration, cells often squeeze through small constrictions, requiring extensive deformation. We hypothesized that nuclear deformation associated with such confined migration could alter chromatin organization and function. By studying cells migrating through microfluidic devices that mimic interstitial spaces in vivo, we found that confined migration results in increased H3K9me3 and H3K27me3 heterochromatin marks that persist for days. This "confined migration-induced heterochromatin" (CMiH) was distinct from heterochromatin formation during migration initiation. Confined migration decreased chromatin accessibility at intergenic regions near centromeres and telomeres, suggesting heterochromatin spreading from existing sites. Consistent with the overall decrease in accessibility, global transcription was decreased during confined migration. Intriguingly, we also identified increased accessibility at promoter regions of genes linked to chromatin silencing, tumor invasion, and DNA damage response. Inhibiting CMiH reduced migration speed, suggesting that CMiH promotes confined migration. Together, our findings indicate that confined migration induces chromatin changes that regulate cell migration and other functions.
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Affiliation(s)
- Chieh-Ren Hsia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jawuanna McAllister
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ovais Hasan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seoyeon Lee
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Richa Agrawal
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chao-Yuan Chang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Paul Soloway
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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28
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Zhao H, Xie J, Wu S, Sánchez OF, Zhang X, Freeman JL, Yuan C. Pre-differentiation exposure of PFOA induced persistent changes in DNA methylation and mitochondrial morphology in human dopaminergic-like neurons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119684. [PMID: 35764183 DOI: 10.1016/j.envpol.2022.119684] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/10/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Perfluorooctanoic acid (PFOA) is abundant in environment due to its historical uses in consumer products and industrial applications. Exposure to low doses of PFOA has been associated with various disease risks, including neurological disorders. The underlying mechanism, however, remains poorly understood. In this study, we examined the effects of low dose PFOA exposure at 0.4 and 4 μg/L on the morphology, epigenome, mitochondrion, and neuronal markers of dopaminergic (DA)-like SH-SY5Y cells. We observed persistent decreases in H3K4me3, H3K27me3 and 5 mC markers in nucleus along with alterations in nuclear size and chromatin compaction percentage in DA-like neurons differentiated from SH-SY5Y cells exposed to 0.4 and 4 μg/L PFOA. Among the selected epigenetic features, DNA methylation pattern can be used to distinguish between PFOA-exposed and naïve populations, suggesting the involvement of epigenetic regulation. Moreover, DA-like neurons with pre-differentiation PFOA exposure exhibit altered network connectivity, mitochondrial volume, and TH expression, implying impairment in DA neuron functionality. Collectively, our results revealed the prolonged effects of developmental PFOA exposure on the fitness of DA-like neurons and identified epigenome and mitochondrion as potential targets for bearing long-lasting changes contributing to increased risks of neurological diseases later in life.
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Affiliation(s)
- Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Shichen Wu
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Oscar F Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Xinle Zhang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA.
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29
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Kalukula Y, Stephens AD, Lammerding J, Gabriele S. Mechanics and functional consequences of nuclear deformations. Nat Rev Mol Cell Biol 2022; 23:583-602. [PMID: 35513718 PMCID: PMC9902167 DOI: 10.1038/s41580-022-00480-z] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 02/08/2023]
Abstract
As the home of cellular genetic information, the nucleus has a critical role in determining cell fate and function in response to various signals and stimuli. In addition to biochemical inputs, the nucleus is constantly exposed to intrinsic and extrinsic mechanical forces that trigger dynamic changes in nuclear structure and morphology. Emerging data suggest that the physical deformation of the nucleus modulates many cellular and nuclear functions. These functions have long been considered to be downstream of cytoplasmic signalling pathways and dictated by gene expression. In this Review, we discuss an emerging perspective on the mechanoregulation of the nucleus that considers the physical connections from chromatin to nuclear lamina and cytoskeletal filaments as a single mechanical unit. We describe key mechanisms of nuclear deformations in time and space and provide a critical review of the structural and functional adaptive responses of the nucleus to deformations. We then consider the contribution of nuclear deformations to the regulation of important cellular functions, including muscle contraction, cell migration and human disease pathogenesis. Collectively, these emerging insights shed new light on the dynamics of nuclear deformations and their roles in cellular mechanobiology.
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Affiliation(s)
- Yohalie Kalukula
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Sylvain Gabriele
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
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30
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Jain N, Lord JM, Vogel V. Mechanoimmunology: Are inflammatory epigenetic states of macrophages tuned by biophysical factors? APL Bioeng 2022; 6:031502. [PMID: 36051106 PMCID: PMC9427154 DOI: 10.1063/5.0087699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
Many inflammatory diseases that are responsible for a majority of deaths are still uncurable, in part as the underpinning pathomechanisms and how to combat them is still poorly understood. Tissue-resident macrophages play pivotal roles in the maintenance of tissue homeostasis, but if they gradually convert to proinflammatory phenotypes, or if blood-born proinflammatory macrophages persist long-term after activation, they contribute to chronic inflammation and fibrosis. While biochemical factors and how they regulate the inflammatory transcriptional response of macrophages have been at the forefront of research to identify targets for therapeutic interventions, evidence is increasing that physical factors also tune the macrophage phenotype. Recently, several mechanisms have emerged as to how physical factors impact the mechanobiology of macrophages, from the nuclear translocation of transcription factors to epigenetic modifications, perhaps even DNA methylation. Insight into the mechanobiology of macrophages and associated epigenetic modifications will deliver novel therapeutic options going forward, particularly in the context of increased inflammation with advancing age and age-related diseases. We review here how biophysical factors can co-regulate pro-inflammatory gene expression and epigenetic modifications and identify knowledge gaps that require urgent attention if this therapeutic potential is to be realized.
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Affiliation(s)
- Nikhil Jain
- Authors to whom correspondence should be addressed: and
| | | | - Viola Vogel
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zurich, Zurich, Switzerland
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31
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Valančiūtė A, Mathieson L, O’Connor RA, Scott JI, Vendrell M, Dorward DA, Akram AR, Dhaliwal K. Phototherapeutic Induction of Immunogenic Cell Death and CD8+ T Cell-Granzyme B Mediated Cytolysis in Human Lung Cancer Cells and Organoids. Cancers (Basel) 2022; 14:4119. [PMID: 36077656 PMCID: PMC9454585 DOI: 10.3390/cancers14174119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/12/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Augmenting T cell mediated tumor killing via immunogenic cancer cell death (ICD) is the cornerstone of emerging immunotherapeutic approaches. We investigated the potential of methylene blue photodynamic therapy (MB-PDT) to induce ICD in human lung cancer. Non-Small Cell Lung Cancer (NSCLC) cell lines and primary human lung cancer organoids were evaluated in co-culture killing assays with MB-PDT and light emitting diodes (LEDs). ICD was characterised using immunoblotting, immunofluorescence, flow cytometry and confocal microscopy. Phototherapy with MB treatment and low energy LEDs decreased the proliferation of NSCLC cell lines inducing early necrosis associated with reduced expression of the anti-apoptotic protein, Bcl2 and increased expression of ICD markers, calreticulin (CRT), intercellular cell-adhesion molecule-1 (ICAM-1) and major histocompatibility complex I (MHC-I) in NSCLC cells. MB-PDT also potentiated CD8+ T cell-mediated cytolysis of lung cancer via granzyme B in lung cancer cells and primary human lung cancer organoids.
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Affiliation(s)
- Asta Valančiūtė
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Layla Mathieson
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Richard A. O’Connor
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Jamie I. Scott
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Marc Vendrell
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - David A. Dorward
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Ahsan R. Akram
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Kevin Dhaliwal
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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Merino-Casallo F, Gomez-Benito MJ, Martinez-Cantin R, Garcia-Aznar JM. A mechanistic protrusive-based model for 3D cell migration. Eur J Cell Biol 2022; 101:151255. [PMID: 35843121 DOI: 10.1016/j.ejcb.2022.151255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Cell migration is essential for a variety of biological processes, such as embryogenesis, wound healing, and the immune response. After more than a century of research-mainly on flat surfaces-, there are still many unknowns about cell motility. In particular, regarding how cells migrate within 3D matrices, which more accurately replicate in vivo conditions. We present a novel in silico model of 3D mesenchymal cell migration regulated by the chemical and mechanical profile of the surrounding environment. This in silico model considers cell's adhesive and nuclear phenotypes, the effects of the steric hindrance of the matrix, and cells ability to degradate the ECM. These factors are crucial when investigating the increasing difficulty that migrating cells find to squeeze their nuclei through dense matrices, which may act as physical barriers. Our results agree with previous in vitro observations where fibroblasts cultured in collagen-based hydrogels did not durotax toward regions with higher collagen concentrations. Instead, they exhibited an adurotactic behavior, following a more random trajectory. Overall, cell's migratory response in 3D domains depends on its phenotype, and the properties of the surrounding environment, that is, 3D cell motion is strongly dependent on the context.
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Affiliation(s)
- Francisco Merino-Casallo
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Zaragoza 50018, Spain; Department of Mechanical Engineering, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Maria Jose Gomez-Benito
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Zaragoza 50018, Spain; Department of Mechanical Engineering, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Ruben Martinez-Cantin
- Robotics, Perception and Real Time Group (RoPeRT), Aragon Institute of Engineering Research (I3A), Zaragoza 50018, Spain; Department of Computer Science and System Engineering, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Jose Manuel Garcia-Aznar
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Zaragoza 50018, Spain; Department of Mechanical Engineering, Universidad de Zaragoza, Zaragoza 50009, Spain.
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Cortesi M, Giordano E. Non-destructive monitoring of 3D cell cultures: new technologies and applications. PeerJ 2022; 10:e13338. [PMID: 35582620 PMCID: PMC9107788 DOI: 10.7717/peerj.13338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/05/2022] [Indexed: 01/13/2023] Open
Abstract
3D cell cultures are becoming the new standard for cell-based in vitro research, due to their higher transferrability toward in vivo biology. The lack of established techniques for the non-destructive quantification of relevant variables, however, constitutes a major barrier to the adoption of these technologies, as it increases the resources needed for the experimentation and reduces its accuracy. In this review, we aim at addressing this limitation by providing an overview of different non-destructive approaches for the evaluation of biological features commonly quantified in a number of studies and applications. In this regard, we will cover cell viability, gene expression, population distribution, cell morphology and interactions between the cells and the environment. This analysis is expected to promote the use of the showcased technologies, together with the further development of these and other monitoring methods for 3D cell cultures. Overall, an extensive technology shift is required, in order for monolayer cultures to be superseded, but the potential benefit derived from an increased accuracy of in vitro studies, justifies the effort and the investment.
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Affiliation(s)
- Marilisa Cortesi
- Department of Electrical, Electronic and Information Engineering ”G.Marconi”, University of Bologna, Bologna, Italy
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Kensington, Australia
| | - Emanuele Giordano
- Department of Electrical, Electronic and Information Engineering ”G.Marconi”, University of Bologna, Bologna, Italy
- BioEngLab, Health Science and Technology, Interdepartmental Center for Industrial Research (HST-CIRI), University of Bologna, Ozzano Emilia, Italy
- Advanced Research Center on Electronic Systems (ARCES), University of Bologna, Bologna, Italy
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Focused Ultrasound Treatment of a Spheroid In Vitro Tumour Model. Cells 2022; 11:cells11091518. [PMID: 35563823 PMCID: PMC9099905 DOI: 10.3390/cells11091518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Ultrasound waves can be applied for diagnostic and therapeutic purposes. Focused ultrasound is approved for tissue ablation, e.g., in the treatment of uterine fibroids or essential tremors. Besides the non-invasive image-guided surgical intervention at temperatures above 55 °C, FUS is investigated in other fields like blood-brain barrier opening, hyperthermia, and neuromodulation. FUS offers potential as an adjuvant therapy in cancer treatment. Therefore, analysis of FUS effects on cancer cells is necessary. We performed studies on two human cancer cell line spheroids using a newly developed high-throughput in vitro FUS applicator with 32 individual transducers. This study aimed to perform basic experiments with a new in vitro FUS device on a 3D tumour model to acquire insight into the effects of FUS at the cellular level. These experiments may contribute to a better understanding and predictions of cancer treatment efficacy. Abstract Focused ultrasound (FUS) is a non-invasive technique producing a variety of biological effects by either thermal or mechanical mechanisms of ultrasound interaction with the targeted tissue. FUS could bring benefits, e.g., tumour sensitisation, immune stimulation, and targeted drug delivery, but investigation of FUS effects at the cellular level is still missing. New techniques are commonly tested in vitro on two-dimensional (2D) monolayer cancer cell culture models. The 3D tumour model—spheroid—is mainly utilised to mimic solid tumours from an architectural standpoint. It is a promising method to simulate the characteristics of tumours in vitro and their various responses to therapeutic alternatives. This study aimed to evaluate the effects of FUS on human prostate and glioblastoma cancer tumour spheroids in vitro. The experimental follow-up enclosed the measurements of spheroid integrity and growth kinetics, DNA damage, and cellular metabolic activity by measuring intracellular ATP content in the spheroids. Our results showed that pulsed FUS treatment induced molecular effects in 3D tumour models. With the disruption of the spheroid integrity, we observed an increase in DNA double-strand breaks, leading to damage in the cancer cells depending on the cancer cell type.
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Guenther C. β2-Integrins - Regulatory and Executive Bridges in the Signaling Network Controlling Leukocyte Trafficking and Migration. Front Immunol 2022; 13:809590. [PMID: 35529883 PMCID: PMC9072638 DOI: 10.3389/fimmu.2022.809590] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Leukocyte trafficking is an essential process of immunity, occurring as leukocytes travel within the bloodstream and as leukocyte migration within tissues. While it is now established that leukocytes can utilize the mesenchymal migration mode or amoeboid migration mode, differences in the migratory behavior of leukocyte subclasses and how these are realized on a molecular level in each subclass is not fully understood. To outline these differences, first migration modes and their dependence on parameters of the extracellular environments will be explained, as well as the intracellular molecular machinery that powers migration in general. Extracellular parameters are detected by adhesion receptors such as integrins. β2-integrins are surface receptors exclusively expressed on leukocytes and are essential for leukocytes exiting the bloodstream, as well as in mesenchymal migration modes, however, integrins are dispensable for the amoeboid migration mode. Additionally, the balance of different RhoGTPases - which are downstream of surface receptor signaling, including integrins - mediate formation of membrane structures as well as actin dynamics. Individual leukocyte subpopulations have been shown to express distinct RhoGTPase profiles along with their differences in migration behavior, which will be outlined. Emerging aspects of leukocyte migration include signal transduction from integrins via actin to the nucleus that regulates DNA status, gene expression profiles and ultimately leukocyte migratory phenotypes, as well as altered leukocyte migration in tumors, which will be touched upon.
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Affiliation(s)
- Carla Guenther
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
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36
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Han P, Gomez GA, Duda GN, Ivanovski S, Poh PS. Scaffold geometry modulation of mechanotransduction and its influence on epigenetics. Acta Biomater 2022; 163:259-274. [PMID: 35038587 DOI: 10.1016/j.actbio.2022.01.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 02/03/2023]
Abstract
The dynamics of cell mechanics and epigenetic signatures direct cell behaviour and fate, thus influencing regenerative outcomes. In recent years, the utilisation of 2D geometric (i.e. square, circle, hexagon, triangle or round-shaped) substrates for investigating cell mechanics in response to the extracellular microenvironment have gained increasing interest in regenerative medicine due to their tunable physicochemical properties. In contrast, there is relatively limited knowledge of cell mechanobiology and epigenetics in the context of 3D biomaterial matrices, i.e., hydrogels and scaffolds. Scaffold geometry provides biophysical signals that trigger a nucleus response (regulation of gene expression) and modulates cell behaviour and function. In this review, we explore the potential of additive manufacturing to incorporate multi length-scale geometry features on a scaffold. Then, we discuss how scaffold geometry direct cell and nuclear mechanosensing. We further discuss how cell epigenetics, particularly DNA/histone methylation and histone acetylation, are modulated by scaffold features that lead to specific gene expression and ultimately influence the outcome of tissue regeneration. Overall, we highlight that geometry of different magnitude scales can facilitate the assembly of cells and multicellular tissues into desired functional architectures through the mechanotransduction pathway. Moving forward, the challenge confronting biomedical engineers is the distillation of the vast knowledge to incorporate multiscaled geometrical features that would collectively elicit a favourable tissue regeneration response by harnessing the design flexibility of additive manufacturing. STATEMENT OF SIGNIFICANCE: It is well-established that cells sense and respond to their 2D geometric microenvironment by transmitting extracellular physiochemical forces through the cytoskeleton and biochemical signalling to the nucleus, facilitating epigenetic changes such as DNA methylation, histone acetylation, and microRNA expression. In this context, the current review presents a unique perspective and highlights the importance of 3D architectures (dimensionality and geometries) on cell and nuclear mechanics and epigenetics. Insight into current challenges around the study of mechanobiology and epigenetics utilising additively manufactured 3D scaffold geometries will progress biomaterials research in this space.
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Sanchez V, Britt W. Human Cytomegalovirus Egress: Overcoming Barriers and Co-Opting Cellular Functions. Viruses 2021; 14:v14010015. [PMID: 35062219 PMCID: PMC8778548 DOI: 10.3390/v14010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
The assembly of human cytomegalovirus (HCMV) and other herpesviruses includes both nuclear and cytoplasmic phases. During the prolonged replication cycle of HCMV, the cell undergoes remarkable changes in cellular architecture that include marked increases in nuclear size and structure as well as the reorganization of membranes in cytoplasm. Similarly, significant changes occur in cellular metabolism, protein trafficking, and cellular homeostatic functions. These cellular modifications are considered integral in the efficient assembly of infectious progeny in productively infected cells. Nuclear egress of HCMV nucleocapsids is thought to follow a pathway similar to that proposed for other members of the herpesvirus family. During this process, viral nucleocapsids must overcome structural barriers in the nucleus that limit transit and, ultimately, their delivery to the cytoplasm for final assembly of progeny virions. HCMV, similar to other herpesviruses, encodes viral functions that co-opt cellular functions to overcome these barriers and to bridge the bilaminar nuclear membrane. In this brief review, we will highlight some of the mechanisms that define our current understanding of HCMV egress, relying heavily on the current understanding of egress of the more well-studied α-herpesviruses, HSV-1 and PRV.
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Affiliation(s)
- Veronica Sanchez
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL 35294, USA;
- Correspondence:
| | - William Britt
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL 35294, USA;
- Department of Microbiology, University of Alabama School of Medicine, Birmingham, AL 35294, USA
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38
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Hobson CM, Falvo MR, Superfine R. A survey of physical methods for studying nuclear mechanics and mechanobiology. APL Bioeng 2021; 5:041508. [PMID: 34849443 PMCID: PMC8604565 DOI: 10.1063/5.0068126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/20/2021] [Indexed: 12/23/2022] Open
Abstract
It is increasingly appreciated that the cell nucleus is not only a home for DNA but also a complex material that resists physical deformations and dynamically responds to external mechanical cues. The molecules that confer mechanical properties to nuclei certainly contribute to laminopathies and possibly contribute to cellular mechanotransduction and physical processes in cancer such as metastasis. Studying nuclear mechanics and the downstream biochemical consequences or their modulation requires a suite of complex assays for applying, measuring, and visualizing mechanical forces across diverse length, time, and force scales. Here, we review the current methods in nuclear mechanics and mechanobiology, placing specific emphasis on each of their unique advantages and limitations. Furthermore, we explore important considerations in selecting a new methodology as are demonstrated by recent examples from the literature. We conclude by providing an outlook on the development of new methods and the judicious use of the current techniques for continued exploration into the role of nuclear mechanobiology.
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Affiliation(s)
| | - Michael R. Falvo
- Department of Physics and Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Richard Superfine
- Department of Applied Physical Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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39
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Veerasubramanian PK, Shao H, Meli VS, Phan TAQ, Luu TU, Liu WF, Downing TL. A Src-H3 acetylation signaling axis integrates macrophage mechanosensation with inflammatory response. Biomaterials 2021; 279:121236. [PMID: 34753038 PMCID: PMC8939266 DOI: 10.1016/j.biomaterials.2021.121236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/24/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022]
Abstract
Macrophages are mechanosensitive cells that can exquisitely fine-tune their function in response to their microenvironment. While macrophage polarization results in concomitant changes in cell morphology and epigenetic reprogramming, how biophysically-induced signaling cascades contribute to gene regulatory programs that drive polarization remains unknown. We reveal a cytoskeleton-dependent Src-H3 acetylation (H3Ac) axis responsible for inflammation-associated histone hyperacetylation. Inflammatory stimuli caused increases in traction forces, Src activity and H3Ac marks in macrophages, accompanied by reduced cell elongation and motility. These effects were curtailed following disruption of H3Ac-signaling through either micropattern-induced cell elongation or inhibition of H3Ac readers (BRD proteins) directly. Src activation relieves the suppression of p300 histone acetyltransferase (HAT) activity by PKCδ. Furthermore, while inhibition of Src reduced p300 HAT activity and H3Ac marks globally, local H3Ac levels within the Src promoter were increased, suggesting H3Ac regulates Src levels through feedback. Together, our study reveals an adhesome-to-epigenome regulatory nexus underlying macrophage mechanosensation, where Src modulates H3Ac-associated epigenetic signaling as a means of tuning inflammatory gene activity and macrophage fate decisions in response to microenvironmental cues.
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Affiliation(s)
- Praveen Krishna Veerasubramanian
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA; UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California Irvine, Irvine, CA, USA
| | - Hanjuan Shao
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA; UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California Irvine, Irvine, CA, USA
| | - Vijaykumar S Meli
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA; UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California Irvine, Irvine, CA, USA
| | - Tri Andrew Q Phan
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA; UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California Irvine, Irvine, CA, USA
| | - Thuy U Luu
- UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California Irvine, Irvine, CA, USA; Department of Pharmacological Sciences, University of California Irvine, Irvine, CA, USA
| | - Wendy F Liu
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA; UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California Irvine, Irvine, CA, USA; Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, USA; Institute for Immunology, University of California Irvine, Irvine, CA, USA; Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Timothy L Downing
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA; UCI Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center (CIRC), University of California Irvine, Irvine, CA, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, CA, USA; Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, USA.
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40
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Abstract
The cell nucleus is best known as the container of the genome. Its envelope provides a barrier for passive macromolecule diffusion, which enhances the control of gene expression. As its largest and stiffest organelle, the nucleus also defines the minimal space requirements of a cell. Internal or external pressures that deform a cell to its physical limits cause a corresponding nuclear deformation. Evidence is consolidating that the nucleus, in addition to its genetic functions, serves as a physical sensing device for critical cell body deformation. Nuclear mechanotransduction allows cells to adapt their acute behaviors, mechanical stability, paracrine signaling, and fate to their physical surroundings. This review summarizes the basic chemical and mechanical properties of nuclear components, and how these properties are thought to be utilized for mechanosensing.
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Affiliation(s)
- Philipp Niethammer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
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41
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Paradiso F, Serpelloni S, Francis LW, Taraballi F. Mechanical Studies of the Third Dimension in Cancer: From 2D to 3D Model. Int J Mol Sci 2021; 22:10098. [PMID: 34576261 PMCID: PMC8472581 DOI: 10.3390/ijms221810098] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
From the development of self-aggregating, scaffold-free multicellular spheroids to the inclusion of scaffold systems, 3D models have progressively increased in complexity to better mimic native tissues. The inclusion of a third dimension in cancer models allows researchers to zoom out from a significant but limited cancer cell research approach to a wider investigation of the tumor microenvironment. This model can include multiple cell types and many elements from the extracellular matrix (ECM), which provides mechanical support for the tissue, mediates cell-microenvironment interactions, and plays a key role in cancer cell invasion. Both biochemical and biophysical signals from the extracellular space strongly influence cell fate, the epigenetic landscape, and gene expression. Specifically, a detailed mechanistic understanding of tumor cell-ECM interactions, especially during cancer invasion, is lacking. In this review, we focus on the latest achievements in the study of ECM biomechanics and mechanosensing in cancer on 3D scaffold-based and scaffold-free models, focusing on each platform's level of complexity, up-to-date mechanical tests performed, limitations, and potential for further improvements.
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Affiliation(s)
- Francesca Paradiso
- Center for Musculoskeletal Regeneration, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA; (F.P.); (S.S.)
- Orthopedics and Sports Medicine, Houston Methodist Hospital, 6445 Main St., Houston, TX 77030, USA
- Reproductive Biology and Gynaecological Oncology Group, Swansea University Medical School, Singleton Park, Swansea, Wales SA2 8PP, UK;
| | - Stefano Serpelloni
- Center for Musculoskeletal Regeneration, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA; (F.P.); (S.S.)
- Orthopedics and Sports Medicine, Houston Methodist Hospital, 6445 Main St., Houston, TX 77030, USA
| | - Lewis W. Francis
- Reproductive Biology and Gynaecological Oncology Group, Swansea University Medical School, Singleton Park, Swansea, Wales SA2 8PP, UK;
| | - Francesca Taraballi
- Center for Musculoskeletal Regeneration, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA; (F.P.); (S.S.)
- Orthopedics and Sports Medicine, Houston Methodist Hospital, 6445 Main St., Houston, TX 77030, USA
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42
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Abstract
The cell nucleus is best known as the container of the genome. Its envelope provides a barrier for passive macromolecule diffusion, which enhances the control of gene expression. As its largest and stiffest organelle, the nucleus also defines the minimal space requirements of a cell. Internal or external pressures that deform a cell to its physical limits cause a corresponding nuclear deformation. Evidence is consolidating that the nucleus, in addition to its genetic functions, serves as a physical sensing device for critical cell body deformation. Nuclear mechanotransduction allows cells to adapt their acute behaviors, mechanical stability, paracrine signaling, and fate to their physical surroundings. This review summarizes the basic chemical and mechanical properties of nuclear components, and how these properties are thought to be utilized for mechanosensing. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Philipp Niethammer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
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43
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Imran A, Moyer BS, Canning AJ, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions. Biochem J 2021; 478:2145-2161. [PMID: 34032265 PMCID: PMC8214142 DOI: 10.1042/bcj20210253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023]
Abstract
Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Brandon S. Moyer
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
| | - Ashley J. Canning
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Dan Kalina
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- The BioInspired Institute, Syracuse University, Syracuse, New York, 13244, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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44
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Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Ritland Politz JC, Tait LJ, Scalzo D, Telling A, Groudine M, Brangwynne CP, Marko JF, Stephens AD. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. eLife 2021; 10:e63972. [PMID: 34106828 PMCID: PMC8233041 DOI: 10.7554/elife.63972] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation controls nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1α (CBX5) is unknown. We used a novel HP1α auxin-inducible degron human cell line to rapidly degrade HP1α. Degradation did not alter transcription, local chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1α is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1αI165E indicate that chromatin crosslinking via HP1α dimerization is critical, while polymer simulations demonstrate the importance of chromatin-chromatin crosslinkers in mechanics. In mitotic chromosomes, HP1α similarly bolsters stiffness while aiding in mitotic alignment and faithful segregation. HP1α is therefore a critical chromatin-crosslinking protein that provides mechanical strength to chromosomes and the nucleus throughout the cell cycle and supports cellular functions.
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Affiliation(s)
- Amy R Strom
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Ronald J Biggs
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Katherine Chiu
- Biology Department, University of Massachusetts AmherstAmherstUnited States
| | - Cameron Herman
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Jimena Collado
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | | | - Leah J Tait
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - David Scalzo
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Agnes Telling
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Mark Groudine
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Clifford P Brangwynne
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Department of Physics and Astronomy, Northwestern UniversityEvanstonUnited States
| | - Andrew D Stephens
- Biology Department, University of Massachusetts AmherstAmherstUnited States
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45
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Song Y, Soto J, Li S. Mechanical regulation of histone modifications and cell plasticity. CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 2020; 24:100872. [PMID: 33214755 PMCID: PMC7671577 DOI: 10.1016/j.cossms.2020.100872] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Cell plasticity is important in development and tissue remodeling. Cells can sense physical and chemical cues from their local microenvironment and transduce the signals into the nucleus to regulate the epigenetic state and gene expression, resulting in a change in cell phenotype. In this review, we highlight the role of mechanical cues in regulating stem cell differentiation and cell reprogramming through the modulation of histone modifications. The effects of various mechanical cues, including matrix stiffness, mechanical stretch, and shear stress, on cell fate during tissue regeneration and remodeling will be discussed. Taken together, recent work demonstrates that the alterations in histone modifications by mechanical stimuli can facilitate epigenetic changes during cell phenotypic switching, which has potential applications in the development of biomaterials and bioreactors for cell engineering.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer Soto
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Song Li
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
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46
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Veerasubramanian PK, Trinh A, Akhtar N, Liu WF, Downing TL. Biophysical and epigenetic regulation of cancer stemness, invasiveness and immune action. CURRENT TISSUE MICROENVIRONMENT REPORTS 2020; 1:277-300. [PMID: 33817661 PMCID: PMC8015331 DOI: 10.1007/s43152-020-00021-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW The tumor microenvironment (TME) is an amalgam of multiple dysregulated biophysical cues that can alter cellular behavior through mechanotransductive signaling and epigenetic modifications. Through this review, we seek to characterize the extent of biophysical and epigenetic regulation of cancer stemness and tumor-associated immune cells in order to identify ideal targets for cancer therapy. RECENT FINDINGS Recent studies have identified cancer stemness and immune action as significant contributors to neoplastic disease, due to their susceptibility to microenvironmental influences. Matrix stiffening, altered vasculature, and resultant hypoxia within the TME can influence cancer stem cell (CSC) and immune cell behavior, as well as alter the epigenetic landscapes involved in cancer development. SUMMARY This review highlights the importance of aberrant biophysical cues in driving cancer progression through altered behavior of CSCs and immune cells, which in turn sustains further biophysical dysregulation. We examine current and potential therapeutic approaches that break this self-sustaining cycle of disease progression by targeting the presented biophysical and epigenetic signatures of cancer. We also summarize strategies including the normalization of the TME, targeted drug delivery, and inhibition of cancer-enabling epigenetic players.
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Affiliation(s)
- Praveen Krishna Veerasubramanian
- Department of Biomedical Engineering, University of California-Irvine, Irvine, CA, USA
- The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California-Irvine, Irvine, CA, USA
| | - Annie Trinh
- The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California-Irvine, Irvine, CA, USA
- Department of Microbiology and Molecular Genetics, University of California-Irvine, Irvine, CA, USA
| | - Navied Akhtar
- Department of Biomedical Engineering, University of California-Irvine, Irvine, CA, USA
- The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California-Irvine, Irvine, CA, USA
| | - Wendy F. Liu
- Department of Biomedical Engineering, University of California-Irvine, Irvine, CA, USA
- The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California-Irvine, Irvine, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California-Irvine, Irvine, CA, USA
| | - Timothy L. Downing
- Department of Biomedical Engineering, University of California-Irvine, Irvine, CA, USA
- The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California-Irvine, Irvine, CA, USA
- Department of Microbiology and Molecular Genetics, University of California-Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California-Irvine, Irvine, CA, USA
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ASH2L drives proliferation and sensitivity to bleomycin and other genotoxins in Hodgkin's lymphoma and testicular cancer cells. Cell Death Dis 2020; 11:1019. [PMID: 33257682 PMCID: PMC7705021 DOI: 10.1038/s41419-020-03231-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 12/24/2022]
Abstract
It is of clinical importance to identify biomarkers predicting the efficacy of DNA damaging drugs (genotoxins) so that nonresponders are not unduly exposed to the deleterious effects of otherwise inefficient drugs. Here, we initially focused on the bleomycin genotoxin because of the limited information about the genes implicated in the sensitivity or resistance to this compound. Using a whole-genome CRISPR/Cas9 gene knockout approach, we identified ASH2L, a core component of the H3K4 methyl transferase complex, as a protein required for bleomycin sensitivity in L1236 Hodgkin lymphoma. Knocking down ASH2L in these cells and in the NT2D1 testicular cancer cell line rendered them resistant to bleomycin, etoposide, and cisplatin but did not affect their sensitivity toward ATM or ATR inhibitors. ASH2L knockdown decreased cell proliferation and facilitated DNA repair via homologous recombination and nonhomologous end-joining mechanisms. Data from the Tumor Cancer Genome Atlas indicate that patients with testicular cancer carrying alterations in the ASH2L gene are more likely to relapse than patients with unaltered ASH2L genes. The cell models we have used are derived from cancers currently treated either partially (Hodgkin’s lymphoma), or entirely (testicular cancer) with genotoxins. For such cancers, ASH2L levels could be used as a biomarker to predict the response to genotoxins. In situations where tumors are expressing low levels of ASH2L, which may allow them to resist genotoxic treatment, the use of ATR or ATM inhibitors may be more efficacious as our data indicate that ASH2L knockdown does not affect sensitivity to these inhibitors.
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48
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Steering cell behavior through mechanobiology in 3D: A regenerative medicine perspective. Biomaterials 2020; 268:120572. [PMID: 33285439 DOI: 10.1016/j.biomaterials.2020.120572] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 09/04/2020] [Accepted: 11/21/2020] [Indexed: 12/14/2022]
Abstract
Mechanobiology, translating mechanical signals into biological ones, greatly affects cellular behavior. Steering cellular behavior for cell-based regenerative medicine approaches requires a thorough understanding of the orchestrating molecular mechanisms, among which mechanotransducive ones are being more and more elucidated. Because of their wide use and highly mechanotransduction dependent differentiation, this review focuses on mesenchymal stromal cells (MSCs), while also briefly relating the discussed results to other cell types. While the mechanotransduction pathways are relatively well-studied in 2D, much remains unknown of the role and regulation of these pathways in 3D. Ultimately, cells need to be cultured in a 3D environment to create functional de novo tissue. In this review, we explore the literature on the roles of different material properties on cellular behavior and mechanobiology in 2D and 3D. For example, while stiffness plays a dominant role in 2D MSCs differentiation, it seems to be of subordinate importance in 3D MSCs differentiation, where matrix remodeling seems to be key. Also, the role and regulation of some of the main mechanotransduction players are discussed, focusing on MSCs. We have only just begun to fundamentally understand MSCs and other stem cells behavior in 3D and more fundamental research is required to advance biomaterials able to replicate the stem cell niche and control cell activity. This better understanding will contribute to smarter tissue engineering scaffold design and the advancement of regenerative medicine.
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MLL4-associated condensates counterbalance Polycomb-mediated nuclear mechanical stress in Kabuki syndrome. Nat Genet 2020; 52:1397-1411. [PMID: 33169020 PMCID: PMC7610431 DOI: 10.1038/s41588-020-00724-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/22/2020] [Indexed: 12/21/2022]
Abstract
The genetic elements required to tune gene expression are partitioned in active and repressive nuclear condensates. Chromatin compartments include transcriptional clusters whose dynamic establishment and functioning depend on multivalent interactions occurring among transcription factors, cofactors and basal transcriptional machinery. However, how chromatin players contribute to the assembly of transcriptional condensates is poorly understood. By interrogating the effect of KMT2D (also known as MLL4) haploinsufficiency in Kabuki syndrome, we found that mixed lineage leukemia 4 (MLL4) contributes to the assembly of transcriptional condensates through liquid-liquid phase separation. MLL4 loss of function impaired Polycomb-dependent chromatin compartmentalization, altering the nuclear architecture. By releasing the nuclear mechanical stress through inhibition of the mechanosensor ATR, we re-established the mechanosignaling of mesenchymal stem cells and their commitment towards chondrocytes both in vitro and in vivo. This study supports the notion that, in Kabuki syndrome, the haploinsufficiency of MLL4 causes an altered functional partitioning of chromatin, which determines the architecture and mechanical properties of the nucleus.
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Gerlitz G. The Emerging Roles of Heterochromatin in Cell Migration. Front Cell Dev Biol 2020; 8:394. [PMID: 32528959 PMCID: PMC7266953 DOI: 10.3389/fcell.2020.00394] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022] Open
Abstract
Cell migration is a key process in health and disease. In the last decade an increasing attention is given to chromatin organization in migrating cells. In various types of cells induction of migration leads to a global increase in heterochromatin levels. Heterochromatin is required for optimal cell migration capabilities, since various interventions with heterochromatin formation impeded the migration rate of numerous cell types. Heterochromatin supports the migration process by affecting both the mechanical properties of the nucleus as well as the genetic processes taking place within it. Increased heterochromatin levels elevate nuclear rigidity in a manner that allows faster cell migration in 3D environments. Condensed chromatin and a more rigid nucleus may increase nuclear durability to shear stress and prevent DNA damage during the migration process. In addition, heterochromatin reorganization in migrating cells is important for induction of migration-specific transcriptional plan together with inhibition of many other unnecessary transcriptional changes. Thus, chromatin organization appears to have a key role in the cellular migration process.
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Affiliation(s)
- Gabi Gerlitz
- Department of Molecular Biology and Ariel Center for Applied Cancer Research, Faculty of Life Sciences, Ariel University, Ariel, Israel
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