1
|
Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [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: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
Collapse
Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
| |
Collapse
|
2
|
Petelinšek N, Mommer S. Tough Hydrogels for Load-Bearing Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307404. [PMID: 38225751 DOI: 10.1002/advs.202307404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/08/2023] [Indexed: 01/17/2024]
Abstract
Tough hydrogels have emerged as a promising class of materials to target load-bearing applications, where the material has to resist multiple cycles of extreme mechanical impact. A variety of chemical interactions and network architectures are used to enhance the mechanical properties and fracture mechanics of hydrogels making them stiffer and tougher. In recent years, the mechanical properties of tough, high-performance hydrogels have been benchmarked, however, this is often incomplete as important variables like water content are largely ignored. In this review, the aim is to clarify the reported mechanical properties of state-of-the-art tough hydrogels by providing a comprehensive library of fracture and mechanical property data. First, common methods for mechanical characterization of such high-performance hydrogels are introduced. Then, various modes of energy dissipation to obtain tough hydrogels are discussed and used to categorize the individual datasets helping to asses the material's (fracture) mechanical properties. Finally, current applications are considered, tough high-performance hydrogels are compared with existing materials, and promising future opportunities are discussed.
Collapse
Affiliation(s)
- Nika Petelinšek
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
| | - Stefan Mommer
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, Zurich, 8092, Switzerland
| |
Collapse
|
3
|
Wirtz D, Du W, Zhu J, Wu Y, Kiemen A, Wan Z, Hanna E, Sun S. Mechano-induced homotypic patterned domain formation by monocytes. RESEARCH SQUARE 2023:rs.3.rs-3372987. [PMID: 37790337 PMCID: PMC10543314 DOI: 10.21203/rs.3.rs-3372987/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Matrix stiffness and corresponding mechano-signaling play indispensable roles in cellular phenotypes and functions. How tissue stiffness influences the behavior of monocytes, a major circulating leukocyte of the innate system, and how it may promote the emergence of collective cell behavior is less understood. Here, using tunable collagen-coated hydrogels of physiological stiffness, we show that human primary monocytes undergo a dynamic local phase separation to form highly regular, reversible, multicellular, multi-layered domains on soft matrix. Local activation of the β2 integrin initiates inter-cellular adhesion, while global soluble inhibitory factors maintain the steady state domain pattern over days. Patterned domain formation generated by monocytes is unique among other key immune cells, including macrophages, B cells, T cells, and NK cells. While inhibiting their phagocytic capability, domain formation promotes monocytes' survival. We develop a computational model based on the Cahn-Hilliard equation of phase separation, combined with a Turing mechanism of local activation and global inhibition suggested by our experiments, and provides experimentally validated predictions of the role of seeding density and both chemotactic and random cell migration on domain pattern formation. This work reveals that, unlike active matters, cells can generate complex cell phases by exploiting their mechanosensing abilities and combined short-range interactions and long-range signals to enhance their survival.
Collapse
|
4
|
Hirose S, Hesnard J, Ghazi N, Roussel D, Voituron Y, Cochet-Escartin O, Rieu JP, Anjard C, Funamoto K. The aerotaxis of Dictyostelium discoideum is independent of mitochondria, nitric oxide and oxidative stress. Front Cell Dev Biol 2023; 11:1134011. [PMID: 37397260 PMCID: PMC10307954 DOI: 10.3389/fcell.2023.1134011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Spatial and temporal variations of oxygen environments affect the behaviors of various cells and are involved in physiological and pathological events. Our previous studies with Dictyostelium discoideum as a model of cell motility have demonstrated that aerotaxis toward an oxygen-rich region occurs below 2% O2. However, while the aerotaxis of Dictyostelium seems to be an effective strategy to search for what is essential for survival, the mechanism underlying this phenomenon is still largely unclear. One hypothesis is that an oxygen concentration gradient generates a secondary oxidative stress gradient that would direct cell migration towards higher oxygen concentration. Such mechanism was inferred but not fully demonstrated to explain the aerotaxis of human tumor cells. Here, we investigated the role on aerotaxis of flavohemoglobins, proteins that can both act as potential oxygen sensors and modulators of nitric oxide and oxidative stress. The migratory behaviors of Dictyostelium cells were observed under both self-generated and imposed oxygen gradients. Furthermore, their changes by chemicals generating or preventing oxidative stress were tested. The trajectories of the cells were then analyzed through time-lapse phase-contrast microscopic images. The results indicate that both oxidative and nitrosative stresses are not involved in the aerotaxis of Dictyostelium but cause cytotoxic effects that are enhanced upon hypoxia.
Collapse
Affiliation(s)
- Satomi Hirose
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Institute of Fluid Science, Tohoku University, Sendai, Japan
| | - Julie Hesnard
- Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, France
| | - Nasser Ghazi
- Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, France
| | - Damien Roussel
- LEHNA, UMR CNRS 5023, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Yann Voituron
- LEHNA, UMR CNRS 5023, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Oliver Cochet-Escartin
- Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, France
| | - Jean-Paul Rieu
- Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, France
| | - Christophe Anjard
- Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, France
| | - Kenichi Funamoto
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Institute of Fluid Science, Tohoku University, Sendai, Japan
| |
Collapse
|