1
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Maremonti MI, Causa F. A computational model for single cell Lamin-A structural organization after microfluidic compression. Biotechnol Bioeng 2024. [PMID: 39020522 DOI: 10.1002/bit.28810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 05/06/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024]
Abstract
In recent years, nuclear mechanobiology gained a lot of attention for the study of cell responses to external cues like adhesive forces, applied compression, and/or shear-stresses. In details, the Lamin-A protein-as major constituent of the cell nucleus structure-plays a crucial role in the overall nucleus mechanobiological response. However, modeling and analysis of Lamin-A protein organization upon rapid compression conditions in microfluidics are still difficult to be performed. Here, we introduce the possibility to control an applied microfluidic compression on single cells, deforming them up to the nucleus level. In a wide range of stresses (~1-102 kPa) applied on healthy and cancer cells, we report increasing Lamin-A intensities which scale as a power law with the applied compression. Then, an increase up to two times of the nuclear viscosity is measured in healthy cells, due to the modified Lamin-A organization. This is ascribable to the increasing assembly of Lamin-A filament-like branches which increment both in number and elongation (up to branches four-time longer). Moreover, the solution of a computational model of differential equations is presented as a powerful tool for a single cell prediction of the Lamin-A assembly as a function of the applied compression.
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Affiliation(s)
- Maria Isabella Maremonti
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples "Federico II", Naples, Italy
| | - Filippo Causa
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples "Federico II", Naples, Italy
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2
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Li B, Xiong W, Zuo W, Shi Y, Wang T, Chang L, Wu Y, Ma H, Bian Q, Chang ACY. Proximal telomeric decompaction due to telomere shortening drives FOXC1-dependent myocardial senescence. Nucleic Acids Res 2024; 52:6269-6284. [PMID: 38634789 PMCID: PMC11194093 DOI: 10.1093/nar/gkae274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 02/29/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Telomeres, TTAGGGn DNA repeat sequences located at the ends of eukaryotic chromosomes, play a pivotal role in aging and are targets of DNA damage response. Although we and others have demonstrated presence of short telomeres in genetic cardiomyopathic and heart failure cardiomyocytes, little is known about the role of telomere lengths in cardiomyocyte. Here, we demonstrate that in heart failure patient cardiomyocytes, telomeres are shortened compared to healthy controls. We generated isogenic human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) with short telomeres (sTL-CMs) and normal telomeres (nTL-CMs) as model. Compared to nTL-CMs, short telomeres result in cardiac dysfunction and expression of senescent markers. Using Hi-C and RNASeq, we observe that short telomeres induced TAD insulation decrease near telomeric ends and this correlated with a transcription upregulation in sTL-CMs. FOXC1, a key transcription factor involved in early cardiogenesis, was upregulated in sTL-CMs and its protein levels were negatively correlated with telomere lengths in heart failure patients. Overexpression of FOXC1 induced hiPSC-CM aging, mitochondrial and contractile dysfunction; knockdown of FOXC1 rescued these phenotypes. Overall, the work presented demonstrate that increased chromatin accessibility due to telomere shortening resulted in the induction of FOXC1-dependent expression network responsible for contractile dysfunction and myocardial senescence.
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Affiliation(s)
- Bin Li
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Weiyao Xiong
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Wu Zuo
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Yuanyuan Shi
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Teng Wang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Lingling Chang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Yueheng Wu
- Department of Cardiovascular Medicine, Guangdong General Hospital, Guangzhou, Guangdong, China
| | - Heng Ma
- Department of Physiology and Pathophysiology, Fourth Military Medical University, No. 169 Changle West Rd, Xi'an 710032, China
| | - Qian Bian
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Alex C Y Chang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
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3
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Bermudez A, Latham ZD, Ma AJ, Bi D, Hu JK, Lin NYC. Regulation of Chromatin Modifications through Coordination of Nucleus Size and Epithelial Cell Morphology Heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590164. [PMID: 38712099 PMCID: PMC11071433 DOI: 10.1101/2024.04.18.590164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cell morphology heterogeneity within epithelial collectives is a pervasive phenomenon intertwined with tissue mechanical properties. Despite its widespread occurrence, the underlying mechanisms driving cell morphology heterogeneity and its consequential biological ramifications remain elusive. Here, we investigate the dynamic evolution of epithelial cell morphology and nucleus morphology during crowding, unveiling a consistent correlation between the two. Our investigation reveals a persistent log-normal probability distribution characterizing both cell and nucleus areas across diverse crowding stages and epithelial model systems. We showed that this morphological diversity arises from asymmetric partitioning during cell division and is perpetuated through actomyosin-mediated regulation of cell-nucleus size coordination. Moreover, we provide insights into the impact of nucleus morphology on chromatin dynamics, demonstrating that constraining nucleus area leads to downregulation of the euchromatic mark H3K9ac and upregulation of the heterochromatic mark H3K27me3 through modulation of histone demethylase UTX expression. These findings under-score the significance of cell morphology heterogeneity as a driver of chromatin state diversity, shaping functional variability within epithelial tissues.
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Subramanian D, Tjahjono N, Hernandez PA, Varner VD, Petroll WM, Schmidtke DW. Fabrication of Micropatterns of Aligned Collagen Fibrils. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:2551-2561. [PMID: 38277615 PMCID: PMC11001481 DOI: 10.1021/acs.langmuir.3c02676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Many tissues in vivo contain aligned structures such as filaments, fibrils, and fibers, which expose cells to anisotropic structural and topographical cues that range from the nanometer to micrometer scales. Understanding how cell behavior is regulated by these cues during physiological and pathological processes (e.g., wound healing, cancer invasion) requires substrates that can expose cells to anisotropic cues over several length scales. In this study, we developed a novel method of fabricating micropatterns of aligned collagen fibrils of different geometry onto PDMS-coated glass coverslips that allowed us to investigate the roles of topography and confinement on corneal cell behavior. When corneal cells were cultured on micropatterns of aligned collagen fibrils in the absence of confinement, the degree of cell alignment increased from 40 ± 14 to 82 ± 5% as the size of the micropattern width decreased from 750 to 50 μm. Although the cell area (∼2500 μm2), cell length (∼160 μm), and projected nuclear area (∼175 μm2) were relatively constant on the different micropattern widths, cells displayed an increased aspect ratio as the width of the aligned collagen fibril micropatterns decreased. We also observed that the morphology of cells adhering to the surrounding uncoated PDMS was dependent upon both the size of the aligned collagen fibril micropattern and the distance from the micropatterns. When corneal cells were confined to the micropatterns of aligned collagen fibrils by a Pluronic coating to passivate the surrounding area, a similar trend in increasing cell alignment was observed (35 ± 10 to 89 ± 2%). However, the projected nuclear area decreased significantly (∼210 to 130 μm2) as the micropattern width decreased from 750 to 50 μm. The development of this method allows for the deposition of aligned collagen fibril micropatterns of different geometries on a transparent and elastic substrate and provides an excellent model system to investigate the role of anisotropic cues in cell behavior.
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Affiliation(s)
- Divya Subramanian
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX
| | - Nathaniel Tjahjono
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX
| | - Paula A. Hernandez
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, TX, 75390
- Department of Biomedical Engineering, University of Texas Southwestern Medical Center at Dallas, TX, 75390
| | - Victor D. Varner
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX
- Department of Surgery, University of Texas Southwestern Medical Center at Dallas, TX, 75390
| | - W. Matthew Petroll
- Department of Ophthalmology, University of Texas Southwestern Medical Center at Dallas, TX, 75390
| | - David W. Schmidtke
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX
- Department of Surgery, University of Texas Southwestern Medical Center at Dallas, TX, 75390
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5
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Kim HS, Taghizadeh A, Taghizadeh M, Kim HW. Advanced materials technologies to unravel mechanobiological phenomena. Trends Biotechnol 2024; 42:179-196. [PMID: 37666712 DOI: 10.1016/j.tibtech.2023.08.002] [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: 05/29/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 09/06/2023]
Abstract
Advancements in materials-driven mechanobiology have yielded significant progress. Mechanobiology explores how cellular and tissue mechanics impact development, physiology, and disease, where extracellular matrix (ECM) dynamically interacts with cells. Biomaterial-based platforms emulate synthetic ECMs, offering precise control over cellular behaviors by adjusting mechanical properties. Recent technological advances enable in vitro models replicating active mechanical stimuli in vivo. These models manipulate cellular mechanics even at a subcellular level. In this review we discuss recent material-based mechanomodulatory studies in mechanobiology. We highlight the endeavors to mimic the dynamic properties of native ECM during pathophysiological processes like cellular homeostasis, lineage specification, development, aging, and disease progression. These insights may inform the design of accurate in vitro mechanomodulatory platforms that replicate ECM mechanics.
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Affiliation(s)
- Hye Sung Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Mechanobiology Dental Medicine Research Center, Dankook University, Cheonan 31116, Republic of Korea; Department of Nanobiomedical Science and BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Republic of Korea
| | - Ali Taghizadeh
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Mechanobiology Dental Medicine Research Center, Dankook University, Cheonan 31116, Republic of Korea; Department of Nanobiomedical Science and BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Republic of Korea
| | - Mohsen Taghizadeh
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Mechanobiology Dental Medicine Research Center, Dankook University, Cheonan 31116, Republic of Korea; Department of Nanobiomedical Science and BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Republic of Korea
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Mechanobiology Dental Medicine Research Center, Dankook University, Cheonan 31116, Republic of Korea; Department of Nanobiomedical Science and BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Republic of Korea.
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6
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Rai R, Sodeinde T, Boston A, Chang S. Telomeres cooperate with the nuclear envelope to maintain genome stability. Bioessays 2024; 46:e2300184. [PMID: 38047499 DOI: 10.1002/bies.202300184] [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: 09/25/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023]
Abstract
Mammalian telomeres have evolved safeguards to prevent their recognition as DNA double-stranded breaks by suppressing the activation of various DNA sensing and repair proteins. We have shown that the telomere-binding proteins TRF2 and RAP1 cooperate to prevent telomeres from undergoing aberrant homology-directed recombination by mediating t-loop protection. Our recent findings also suggest that mammalian telomere-binding proteins interact with the nuclear envelope to maintain chromosome stability. RAP1 interacts with nuclear lamins through KU70/KU80, and disruption of RAP1 and TRF2 function result in nuclear envelope rupture, promoting telomere-telomere recombination to form structures termed ultrabright telomeres. In this review, we discuss the importance of the interactions between shelterin components and the nuclear envelope to maintain telomere homeostasis and genome stability.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ava Boston
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
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7
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Baumann C, Zhang X, Kandasamy MK, Mei X, Chen S, Tehrani KF, Mortensen LJ, Watford W, Lall A, De La Fuente R. Acute irradiation induces a senescence-like chromatin structure in mammalian oocytes. Commun Biol 2023; 6:1258. [PMID: 38086992 PMCID: PMC10716162 DOI: 10.1038/s42003-023-05641-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The mechanisms leading to changes in mesoscale chromatin organization during cellular aging are unknown. Here, we used transcriptional activator-like effectors, RNA-seq and superresolution analysis to determine the effects of genotoxic stress on oocyte chromatin structure. Major satellites are organized into tightly packed globular structures that coalesce into chromocenters and dynamically associate with the nucleolus. Acute irradiation significantly enhanced chromocenter mobility in transcriptionally inactive oocytes. In transcriptionally active oocytes, irradiation induced a striking unfolding of satellite chromatin fibers and enhanced the expression of transcripts required for protection from oxidative stress (Fermt1, Smg1), recovery from DNA damage (Tlk2, Rad54l) and regulation of heterochromatin assembly (Zfp296, Ski-oncogene). Non-irradiated, senescent oocytes exhibit not only high chromocenter mobility and satellite distension but also a high frequency of extra chromosomal satellite DNA. Notably, analysis of biological aging using an oocyte-specific RNA clock revealed cellular communication, posttranslational protein modifications, chromatin and histone dynamics as the top cellular processes that are dysregulated in both senescent and irradiated oocytes. Our results indicate that unfolding of heterochromatin fibers following acute genotoxic stress or cellular aging induced the formation of distended satellites and that abnormal chromatin structure together with increased chromocenter mobility leads to chromosome instability in senescent oocytes.
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Affiliation(s)
- Claudia Baumann
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, USA
| | - Xiangyu Zhang
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, USA
| | | | - Xiaohan Mei
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Division of Surgical Research, University of Missouri, School of Medicine, Columbia, MO, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Shiyou Chen
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Division of Surgical Research, University of Missouri, School of Medicine, Columbia, MO, USA
| | - Kayvan F Tehrani
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, USA
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, USA
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Luke J Mortensen
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, USA
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, USA
| | - Wendy Watford
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Ashley Lall
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, USA
| | - Rabindranath De La Fuente
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, USA.
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8
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Wang X, Agrawal V, Dunton CL, Liu Y, Virk RKA, Patel PA, Carter L, Pujadas EM, Li Y, Jain S, Wang H, Ni N, Tsai HM, Rivera-Bolanos N, Frederick J, Roth E, Bleher R, Duan C, Ntziachristos P, He TC, Reid RR, Jiang B, Subramanian H, Backman V, Ameer GA. Chromatin reprogramming and bone regeneration in vitro and in vivo via the microtopography-induced constriction of cell nuclei. Nat Biomed Eng 2023; 7:1514-1529. [PMID: 37308586 PMCID: PMC10804399 DOI: 10.1038/s41551-023-01053-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/10/2023] [Indexed: 06/14/2023]
Abstract
Topographical cues on cells can, through contact guidance, alter cellular plasticity and accelerate the regeneration of cultured tissue. Here we show how changes in the nuclear and cellular morphologies of human mesenchymal stromal cells induced by micropillar patterns via contact guidance influence the conformation of the cells' chromatin and their osteogenic differentiation in vitro and in vivo. The micropillars impacted nuclear architecture, lamin A/C multimerization and 3D chromatin conformation, and the ensuing transcriptional reprogramming enhanced the cells' responsiveness to osteogenic differentiation factors and decreased their plasticity and off-target differentiation. In mice with critical-size cranial defects, implants with micropillar patterns inducing nuclear constriction altered the cells' chromatin conformation and enhanced bone regeneration without the need for exogenous signalling molecules. Our findings suggest that medical device topographies could be designed to facilitate bone regeneration via chromatin reprogramming.
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Affiliation(s)
- Xinlong Wang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Cody L Dunton
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Yugang Liu
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA
| | - Ranya K A Virk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Priyam A Patel
- Quantitative Data Science Core, Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lucas Carter
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Emily M Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Yue Li
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Na Ni
- Molecular Oncology Laboratory, Department of Orthopedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Hsiu-Ming Tsai
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - Nancy Rivera-Bolanos
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Eric Roth
- Department of Materials Sciences and Engineering, Northwestern University, Evanston, IL, USA
| | - Reiner Bleher
- Department of Materials Sciences and Engineering, Northwestern University, Evanston, IL, USA
| | - Chongwen Duan
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA
| | - Panagiotis Ntziachristos
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tong Chuan He
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA
- Molecular Oncology Laboratory, Department of Orthopedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, USA
| | - Russell R Reid
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA
- Laboratory of Craniofacial Biology and Development, Section of Plastic and Reconstructive Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL, USA
| | - Bin Jiang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hariharan Subramanian
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA.
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
| | - Guillermo A Ameer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
- Center for Advanced Regenerative Engineering, Northwestern University, Evanston, IL, USA.
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, USA.
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Chemistry of Life Process Institute, Northwestern University, Chicago, IL, USA.
- International Institute for Nanotechnology, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Institute for Bionanotechnology, Northwestern University, Chicago, IL, USA.
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9
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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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10
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Jain I, Rao M, Tran PT. Reliable and robust control of nucleus centering is contingent on nonequilibrium force patterns. iScience 2023; 26:106665. [PMID: 37182105 PMCID: PMC10173738 DOI: 10.1016/j.isci.2023.106665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/23/2023] [Accepted: 04/09/2023] [Indexed: 05/16/2023] Open
Abstract
Cell centers their division apparatus to ensure symmetric cell division, a challenging task when the governing dynamics is stochastic. Using fission yeast, we show that the patterning of nonequilibrium polymerization forces of microtubule (MT) bundles controls the precise localization of spindle pole body (SPB), and hence the division septum, at the onset of mitosis. We define two cellular objectives, reliability, the mean SPB position relative to the geometric center, and robustness, the variance of the SPB position, which are sensitive to genetic perturbations that change cell length, MT bundle number/orientation, and MT dynamics. We show that simultaneous control of reliability and robustness is required to minimize septum positioning error achieved by the wild type (WT). A stochastic model for the MT-based nucleus centering, with parameters measured directly or estimated using Bayesian inference, recapitulates the maximum fidelity of WT. Using this, we perform a sensitivity analysis of the parameters that control nuclear centering.
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Affiliation(s)
- Ishutesh Jain
- Institut Curie, PSL Universite, Sorbonne Universite, CNRS UMR 144, 75005 Paris, France
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences - TIFR, Bangalore 560065, India
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences - TIFR, Bangalore 560065, India
- Corresponding author
| | - Phong T. Tran
- Institut Curie, PSL Universite, Sorbonne Universite, CNRS UMR 144, 75005 Paris, France
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
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11
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Martino S, Carollo PS, Barra V. A Glimpse into Chromatin Organization and Nuclear Lamina Contribution in Neuronal Differentiation. Genes (Basel) 2023; 14:genes14051046. [PMID: 37239406 DOI: 10.3390/genes14051046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
During embryonic development, stem cells undergo the differentiation process so that they can specialize for different functions within the organism. Complex programs of gene transcription are crucial for this process to happen. Epigenetic modifications and the architecture of chromatin in the nucleus, through the formation of specific regions of active as well as inactive chromatin, allow the coordinated regulation of the genes for each cell fate. In this mini-review, we discuss the current knowledge regarding the regulation of three-dimensional chromatin structure during neuronal differentiation. We also focus on the role the nuclear lamina plays in neurogenesis to ensure the tethering of the chromatin to the nuclear envelope.
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Affiliation(s)
- Salvatore Martino
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Pietro Salvatore Carollo
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), 90015 Cefalù, Italy
| | - Viviana Barra
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
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12
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Rai R, Biju K, Sun W, Sodeinde T, Al-Hiyasat A, Morgan J, Ye X, Li X, Chen Y, Chang S. Homology directed telomere clustering, ultrabright telomere formation and nuclear envelope rupture in cells lacking TRF2 B and RAP1. Nat Commun 2023; 14:2144. [PMID: 37059728 PMCID: PMC10104862 DOI: 10.1038/s41467-023-37761-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
Double-strand breaks (DSBs) due to genotoxic stress represent potential threats to genome stability. Dysfunctional telomeres are recognized as DSBs and are repaired by distinct DNA repair mechanisms. RAP1 and TRF2 are telomere binding proteins essential to protect telomeres from engaging in homology directed repair (HDR), but how this occurs remains unclear. In this study, we examined how the basic domain of TRF2 (TRF2B) and RAP1 cooperate to repress HDR at telomeres. Telomeres lacking TRF2B and RAP1 cluster into structures termed ultrabright telomeres (UTs). HDR factors localize to UTs, and UT formation is abolished by RNaseH1, DDX21 and ADAR1p110, suggesting that they contain DNA-RNA hybrids. Interaction between the BRCT domain of RAP1 and KU70/KU80 is also required to repress UT formation. Expressing TRF2∆B in Rap1-/- cells resulted in aberrant lamin A localization in the nuclear envelope and dramatically increased UT formation. Expressing lamin A phosphomimetic mutants induced nuclear envelope rupturing and aberrant HDR-mediated UT formation. Our results highlight the importance of shelterin and proteins in the nuclear envelope in repressing aberrant telomere-telomere recombination to maintain telomere homeostasis.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
| | - Kevin Biju
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wenqi Sun
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Amer Al-Hiyasat
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Jaida Morgan
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Xianwen Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Xueqing Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
- Department of Pathology, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
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13
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Campellone KG, Lebek NM, King VL. Branching out in different directions: Emerging cellular functions for the Arp2/3 complex and WASP-family actin nucleation factors. Eur J Cell Biol 2023; 102:151301. [PMID: 36907023 DOI: 10.1016/j.ejcb.2023.151301] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 02/07/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
The actin cytoskeleton impacts practically every function of a eukaryotic cell. Historically, the best-characterized cytoskeletal activities are in cell morphogenesis, motility, and division. The structural and dynamic properties of the actin cytoskeleton are also crucial for establishing, maintaining, and changing the organization of membrane-bound organelles and other intracellular structures. Such activities are important in nearly all animal cells and tissues, although distinct anatomical regions and physiological systems rely on different regulatory factors. Recent work indicates that the Arp2/3 complex, a broadly expressed actin nucleator, drives actin assembly during several intracellular stress response pathways. These newly described Arp2/3-mediated cytoskeletal rearrangements are coordinated by members of the Wiskott-Aldrich Syndrome Protein (WASP) family of actin nucleation-promoting factors. Thus, the Arp2/3 complex and WASP-family proteins are emerging as crucial players in cytoplasmic and nuclear activities including autophagy, apoptosis, chromatin dynamics, and DNA repair. Characterizations of the functions of the actin assembly machinery in such stress response mechanisms are advancing our understanding of both normal and pathogenic processes, and hold great promise for providing insights into organismal development and interventions for disease.
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Affiliation(s)
- Kenneth G Campellone
- Department of Molecular and Cell Biology, Institute for Systems Genomics; University of Connecticut; Storrs, CT, USA.
| | - Nadine M Lebek
- Department of Molecular and Cell Biology, Institute for Systems Genomics; University of Connecticut; Storrs, CT, USA
| | - Virginia L King
- Department of Molecular and Cell Biology, Institute for Systems Genomics; University of Connecticut; Storrs, CT, USA
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14
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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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15
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Di Cristo C, Vivo M. Analysis of Polycomb Epigenetic Marks in HeLa Spheroids. Methods Mol Biol 2023; 2655:221-229. [PMID: 37213000 DOI: 10.1007/978-1-0716-3143-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Biochemical composition of the nucleus affects both its physical properties and its morphology. In recent years, several studies demonstrated the formation of f-actin in the nuclei. These filaments intermingle with the chromatin fibers underlying the crucial role of the mechanical force in chromatin remodeling, being thus involved in transcription, differentiation, replication, and DNA repair. Given the suggested role of Ezh2 in the cross-talk between f-actin and chromatin, we describe here how to obtain HeLa cell spheroids and a method to perform immunofluorescence analysis of nuclear epigenetic marks in a 3D cell culture system.
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Affiliation(s)
- Carlo Di Cristo
- Dipartimento di Scienze e Tecnologie (DST), Università del Sannio, Benevento, Italy
| | - Maria Vivo
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Fisciano, Italy.
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16
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Rapid Downregulation of H3K4me3 Binding to Immunoregulatory Genes in Altered Gravity in Primary Human M1 Macrophages. Int J Mol Sci 2022; 24:ijms24010603. [PMID: 36614046 PMCID: PMC9820304 DOI: 10.3390/ijms24010603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
The sensitivity of human immune system cells to gravity changes has been investigated in numerous studies. Human macrophages mediate innate and thus rapid immune defense on the one hand and activate T- and B-cell-based adaptive immune response on the other hand. In this process they finally act as immunoeffector cells, and are essential for tissue regeneration and remodeling. Recently, we demonstrated in the human Jurkat T cell line that genes are differentially regulated in cluster structures under altered gravity. In order to study an in vivo near system of immunologically relevant human cells under physically real microgravity, we performed parabolic flight experiments with primary human M1 macrophages under highly standardized conditions and performed chromatin immunoprecipitation DNA sequencing (ChIP-Seq) for whole-genome epigenetic detection of the DNA-binding loci of the main transcription complex RNA polymerase II and the transcription-associated epigenetic chromatin modification H3K4me3. We identified an overall downregulation of H3K4me3 binding loci in altered gravity, which were unequally distributed inter- and intrachromosomally throughout the genome. Three-quarters of all affected loci were located on the p arm of the chromosomes chr5, chr6, chr9, and chr19. The genomic distribution of the downregulated H3K4me3 loci corresponds to a substantial extent to immunoregulatory genes. In microgravity, analysis of RNA polymerase II binding showed increased binding to multiple loci at coding sequences but decreased binding to central noncoding regions. Detection of altered DNA binding of RNA polymerase II provided direct evidence that gravity changes can lead to altered transcription. Based on this study, we hypothesize that the rapid transcriptional response to changing gravitational forces is specifically encoded in the epigenetic organization of chromatin.
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17
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Palma K, Signore IA, Meynard MM, Ibarra J, Armijo-Weingart L, Cayuleo M, Härtel S, Concha ML. Ontogenesis of the asymmetric parapineal organ in the zebrafish epithalamus. Front Cell Dev Biol 2022; 10:999265. [PMID: 36568973 PMCID: PMC9780773 DOI: 10.3389/fcell.2022.999265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
The parapineal organ is a midline-derived epithalamic structure that in zebrafish adopts a left-sided position at embryonic stages to promote the development of left-right asymmetries in the habenular nuclei. Despite extensive knowledge about its embryonic and larval development, it is still unknown whether the parapineal organ and its profuse larval connectivity with the left habenula are present in the adult brain or whether, as assumed from historical conceptions, this organ degenerates during ontogeny. This paper addresses this question by performing an ontogenetic analysis using an integrative morphological, ultrastructural and neurochemical approach. We find that the parapineal organ is lost as a morphological entity during ontogeny, while parapineal cells are incorporated into the posterior wall of the adult left dorsal habenular nucleus as small clusters or as single cells. Despite this integration, parapineal cells retain their structural, neurochemical and connective features, establishing a reciprocal synaptic connection with the more dorsal habenular neuropil. Furthermore, we describe the ultrastructure of parapineal cells using transmission electron microscopy and report immunoreactivity in parapineal cells with antibodies against substance P, tachykinin, serotonin and the photoreceptor markers arrestin3a and rod opsin. Our findings suggest that parapineal cells form an integral part of a neural circuit associated with the left habenula, possibly acting as local modulators of the circuit. We argue that the incorporation of parapineal cells into the habenula may be part of an evolutionarily relevant developmental mechanism underlying the presence/absence of the parapineal organ in teleosts, and perhaps in a broader sense in vertebrates.
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Affiliation(s)
- Karina Palma
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile,Biomedical Neuroscience Institute, Santiago, Chile
| | - Iskra A. Signore
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile,Biomedical Neuroscience Institute, Santiago, Chile
| | - Margarita M. Meynard
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile,Biomedical Neuroscience Institute, Santiago, Chile,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Jazmin Ibarra
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile,Biomedical Neuroscience Institute, Santiago, Chile
| | | | - Marcos Cayuleo
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile,Biomedical Neuroscience Institute, Santiago, Chile
| | - Steffen Härtel
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile,Biomedical Neuroscience Institute, Santiago, Chile,National Center for Health Information Systems (CENS), Santiago, Chile
| | - Miguel L. Concha
- Integrative Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile,Biomedical Neuroscience Institute, Santiago, Chile,Center for Geroscience, Brain Health and Metabolism, Santiago, Chile,*Correspondence: Miguel L. Concha,
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18
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Pillai S, Munguia-Lopez JG, Tran SD. Hydrogels for Salivary Gland Tissue Engineering. Gels 2022; 8:730. [PMID: 36354638 PMCID: PMC9690182 DOI: 10.3390/gels8110730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 09/19/2023] Open
Abstract
Mimicking the complex architecture of salivary glands (SGs) outside their native niche is challenging due their multicellular and highly branched organization. However, significant progress has been made to recapitulate the gland structure and function using several in vitro and ex vivo models. Hydrogels are polymers with the potential to retain a large volume of water inside their three-dimensional structure, thus simulating extracellular matrix properties that are essential for the cell and tissue integrity. Hydrogel-based culture of SG cells has seen a tremendous success in terms of developing platforms for cell expansion, building an artificial gland, and for use in transplantation to rescue loss of SG function. Both natural and synthetic hydrogels have been used widely in SG tissue engineering applications owing to their properties that support the proliferation, reorganization, and polarization of SG epithelial cells. While recent improvements in hydrogel properties are essential to establish more sophisticated models, the emphasis should still be made towards supporting factors such as mechanotransduction and associated signaling cues. In this concise review, we discuss considerations of an ideal hydrogel-based biomaterial for SG engineering and their associated signaling pathways. We also discuss the current advances made in natural and synthetic hydrogels for SG tissue engineering applications.
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Affiliation(s)
| | | | - Simon D. Tran
- McGill Craniofacial Tissue Engineering and Stem Cells Laboratory, Faculty of Dental Medicine and Oral Health Sciences, McGill University, 3640 Rue University, Montreal, QC H3A 0C7, Canada
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19
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Kim JK, Han SB, Park SI, Kim IS, Kim DH. Nuclear transport of STAT6 determines the matrix rigidity dependent M2 activation of macrophages. Biomaterials 2022; 290:121859. [DOI: 10.1016/j.biomaterials.2022.121859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/04/2022] [Accepted: 10/09/2022] [Indexed: 11/28/2022]
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20
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Efremov AK, Hovan L, Yan J. Nucleus size and its effect on nucleosome stability in living cells. Biophys J 2022; 121:4189-4204. [PMID: 36146936 PMCID: PMC9675033 DOI: 10.1016/j.bpj.2022.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/15/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
DNA architectural proteins play a major role in organization of chromosomal DNA in living cells by packaging it into chromatin, whose spatial conformation is determined by an intricate interplay between the DNA-binding properties of architectural proteins and physical constraints applied to the DNA by a tight nuclear space. Yet, the exact effects of the nucleus size on DNA-protein interactions and chromatin structure currently remain obscure. Furthermore, there is even no clear understanding of molecular mechanisms responsible for the nucleus size regulation in living cells. To find answers to these questions, we developed a general theoretical framework based on a combination of polymer field theory and transfer-matrix calculations, which showed that the nucleus size is mainly determined by the difference between the surface tensions of the nuclear envelope and the endoplasmic reticulum membrane as well as the osmotic pressure exerted by cytosolic macromolecules on the nucleus. In addition, the model demonstrated that the cell nucleus functions as a piezoelectric element, changing its electrostatic potential in a size-dependent manner. This effect has been found to have a profound impact on stability of nucleosomes, revealing a previously unknown link between the nucleus size and chromatin structure. Overall, our study provides new insights into the molecular mechanisms responsible for regulation of the nucleus size, as well as the potential role of nuclear organization in shaping the cell response to environmental cues.
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Affiliation(s)
- Artem K Efremov
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China; Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
| | - Ladislav Hovan
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
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21
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Thiel CS, Vahlensieck C, Ullrich O. Assoziation schneller Reaktionen der Genexpression mit Änderungen der 3D-Chromatinkonformation in veränderter Schwerkraft. FLUGMEDIZIN · TROPENMEDIZIN · REISEMEDIZIN - FTR 2022. [DOI: 10.1055/a-1928-0420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
ZUSAMMENFASSUNGDie molekularen Prinzipien bei der Transduktion von Schwerkraftänderungen in zelluläre Antwort- und Anpassungsprozesse sind bisher weitgehend unbekannt. Wir konnten in humanen Jurkat-T-Zellen zeigen, dass Gene bei veränderter Schwerkraft in Clusterstrukturen („gravity-responsive chromosomal regions“, GRCRs) differenziell reguliert werden. Durch Kombination mit Hochdurchsatz-Chromatin-Konformationsanalysen (Hi-C) konnte eine hochsignifikante Assoziation von GRCRs mit strukturellen 3D-Chromatinveränderungen identifiziert werden, die vor allem auf den kleinen Chromosomen (chr16–chr22) kolokalisieren. Wir fanden weiterhin Hinweise auf einen mechanistischen Zusammenhang zwischen Spleißprozessen und differenzieller Genexpression bei veränderter Schwerkraft. Somit haben wir erste Belege dafür gefunden, dass Änderungen der Schwerkraft in den Zellkern übertragen werden und dort 3D-Chromosomen-Konformationsänderungen hervorrufen, die mit einer schnellen Transkriptionsantwort verbunden sind. Wir vermuten, dass die schnelle genomische Antwort auf veränderte Gravitationskräfte in der Organisation des Chromatins spezifisch codiert ist.
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Affiliation(s)
- Cora S. Thiel
- Innovation Cluster Space and Aviation (UZH Space Hub), Universität Zürich, Schweiz
- Anatomisches Institut, Universität Zürich, Schweiz
- Raumfahrtmedizin, Fachbereich Wirtschaftsingenieurwesen, Ernst-Abbe-Hochschule Jena
- Weltraumbiotechnologie, Fakultät für Maschinenbau, Otto-von-Guericke-Universität Magdeburg
| | - Christian Vahlensieck
- Innovation Cluster Space and Aviation (UZH Space Hub), Universität Zürich, Schweiz
- Anatomisches Institut, Universität Zürich, Schweiz
| | - Oliver Ullrich
- Innovation Cluster Space and Aviation (UZH Space Hub), Universität Zürich, Schweiz
- Anatomisches Institut, Universität Zürich, Schweiz
- Raumfahrtmedizin, Fachbereich Wirtschaftsingenieurwesen, Ernst-Abbe-Hochschule Jena
- Weltraumbiotechnologie, Fakultät für Maschinenbau, Otto-von-Guericke-Universität Magdeburg
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22
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3D microenvironment attenuates simulated microgravity-mediated changes in T cell transcriptome. Cell Mol Life Sci 2022; 79:508. [PMID: 36063234 DOI: 10.1007/s00018-022-04531-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022]
Abstract
Human space travel and exploration are of interest to both the industrial and scientific community. However, there are many adverse effects of spaceflight on human physiology. In particular, there is a lack of understanding of the extent to which microgravity affects the immune system. T cells, key players of the adaptive immune system and long-term immunity, are present not only in blood circulation but also reside within the tissue. As of yet, studies investigating the effects of microgravity on T cells are limited to peripheral blood or traditional 2D cell culture that recapitulates circulating blood. To better mimic interstitial tissue, 3D cell culture has been well established for physiologically and pathologically relevant models. In this work, we utilize 2D cell culture and 3D collagen matrices to gain an understanding of how simulated microgravity, using a random positioning machine, affects both circulating and tissue-resident T cells. T cells were studied in both resting and activated stages. We found that 3D cell culture attenuates the effects of simulated microgravity on the T cells transcriptome and nuclear irregularities compared to 2D cell culture. Interestingly, simulated microgravity appears to have less effect on activated T cells compared to those in the resting stage. Overall, our work provides novel insights into the effects of simulated microgravity on circulating and tissue-resident T cells which could provide benefits for the health of space travellers.
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23
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Ye H, Jiang C, Li L, Li H, Rong Z, Lin Y. Live-cell imaging of genomic loci with Cas9 variants. Biotechnol J 2022; 17:e2100381. [PMID: 36058644 DOI: 10.1002/biot.202100381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/14/2022] [Accepted: 08/22/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Endonuclease-deactivated clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease (dCas9) has been repurposed for live-cell imaging of genomic loci. Engineered or evolved dCas9 variants have been developed to increase the applicability of the CRISPR/dCas9 system. However, there have been no systematic comparisons of these dCas9 variants in terms of their performance in the visualization of genomic loci. MAIN METHODS AND MAJOR RESULTS Here we demonstrate that dSpCas9 and its variants deSpCas9(1.1), dSpCas9-HF1, devoCas9, and dxCas9(3.7) can be used for CRISPR-based live-cell genomic imaging. dSpCas9 had the greatest utility, with a high labeling efficiency of repetitive sequences-including those with a low number of repeats-and good compatibility with target RNA sequences at the MUC4 locus that varied in length from 13 to 23 nucleotides. We combined CRISPR-Tag with the dSpCas9 imaging system to observe the dynamics of the Tet promoter and found that its movement was restricted when it was active. CONCLUSIONS AND IMPLICATIONS These novel Cas9 variants provide a new set of tools for investigating the spatiotemporal regulation of gene expression through live imaging of genomic sites.
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Affiliation(s)
- Huiying Ye
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Chao Jiang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lian Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Hui Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,School of Systems Science, Beijing Normal University, Beijing, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.,Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China.,Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, China
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24
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Xu Z, Li Y, Li P, Sun Y, Lv S, Wang Y, He X, Xu J, Xu Z, Li L, Li Y. Soft substrates promote direct chemical reprogramming of fibroblasts into neurons. Acta Biomater 2022; 152:255-272. [PMID: 36041647 DOI: 10.1016/j.actbio.2022.08.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/13/2022] [Accepted: 08/23/2022] [Indexed: 11/01/2022]
Abstract
Fibroblasts can be directly reprogrammed via a combination of small molecules to generate induced neurons (iNs), bypassing intermediate stages. This method holds great promise for regenerative medicine; however, it remains inefficient. Recently, studies have suggested that physical cues may improve the direct reprogramming of fibroblasts into neurons, but the underlying mechanisms remain to be further explored, and the physical factors reported to date do not exhibit the full properties of the extracellular matrix (ECM). Previous in vitro studies mainly used rigid polystyrene dishes, while one of the characteristics of the native in-vivo environment of neurons is the soft nature of brain ECM. The reported stiffness of brain tissue is very soft ranging between 100 Pa and 3 kPa, and the effect of substrate stiffness on direct neuronal reprogramming has not been explored. Here, we show for the first time that soft substrates substantially improved the production efficiency and quality of iNs, without needing to co-culture with glial cells during reprogramming, producing more glutamatergic neurons with electrophysiological functions in a shorter time. Transcriptome sequencing indicated that soft substrates might promote glutamatergic neuron reprogramming through integrins, actin cytoskeleton, Hippo signalling pathway, and regulation of mesenchymal-to-epithelial transition, and competing endogenous RNA network analysis provided new targets for neuronal reprogramming. We demonstrated that soft substrates may promote neuronal reprogramming by inhibiting microRNA-615-3p-targeting integrin subunit beta 4. Our findings can aid the development of regenerative therapies and help improve our understanding of neuronal reprogramming. STATEMENT OF SIGNIFICANCE: : First, we have shown that low stiffness promotes direct reprogramming on the basis of small molecule combinations. To the best of our knowledge, this is the first report on this type of method, which may greatly promote the progress of neural reprogramming. Second, we found that miR-615-3p may interact with ITGB4, and the soft substrates may promote neural reprogramming by inhibiting microRNA (miR)-615-3p targeting integrin subunit beta 4 (ITGB4). We are the first to report on this mechanism. Our findings will provide more functional neurons for subsequent basic and clinical research in neurological regenerative medicine, and will help to improve the overall understanding of neural reprogramming. This work also provides new ideas for the design of medical biomaterials for nerve regeneration.
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Affiliation(s)
- Ziran Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Yan Li
- Division of Orthopedics and Biotechnology, Department for Clinical Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden.
| | - Pengdong Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China.
| | - Yingying Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; Department of Stomatology, The First Hospital of Jilin University, Changchun 130021, China.
| | - Shuang Lv
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Yin Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Xia He
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; Department of Pathology, Shanxi Bethune Hospital, Taiyuan 030032, China.
| | - Jinying Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; Department of Burns Surgery, The First Hospital of Jilin University, Changchun 130000, China.
| | - Zhixiang Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Yulin Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
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25
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Zhang R, Zhang D, Sun X, Song X, Yan KC, Liang H. Polyvinyl alcohol/gelatin hydrogels regulate cell adhesion and chromatin accessibility. Int J Biol Macromol 2022; 219:672-684. [PMID: 35952815 DOI: 10.1016/j.ijbiomac.2022.08.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022]
Abstract
Cell adhesion has a critical influence on various processes such as cancer metastasis and wound healing. Many substrates have been used for studying cell adhesion and its related biological processes, it is still highly desirable to have a simply prepared and low-cost substrate suitable for regulating cell adhesion. In this study, we produced a series of polyvinyl alcohol/gelatin hydrogels with different gelatin concentrations via dry-annealing method. Our data showed that the protein adsorbing capability was enhanced and cell adhesion area and the ratio of non-spherical cells were increased with the increment of gelatin concentration. We also observed that varying cell adhesion conditions induced by polyvinyl alcohol /gelatin hydrogels resulted in expression level changes of genes involved in mechanotransduction from extracellular matrices (ECM) to the nucleus. In particular, we detected a widespread increase in chromatin accessibility under poor cell adhesion condition. This work provides a useful hydrogel system for regulating cell adhesion and opens up new possibilities for the design of biomaterials for cell adhesion study.
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Affiliation(s)
- Ran Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Duo Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Xingyue Sun
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Xiaoyuan Song
- MOE Key Laboratory for Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Karen Chang Yan
- Mechanical Engineering and Biomedical Engineering, The College of New Jersey, Ewing, NJ, USA.
| | - Haiyi Liang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China; School of Civil Engineering, Anhui Jianzhu University, Hefei, China; IAT-Chungu Joint Laboratory for Additive Manufacturing, Anhui Chungu 3D printing Institute of Intelligent Equipment and Industrial Technology, Wuhu, China.
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26
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Khalil K, Eon A, Janody F. Cell Architecture-Dependent Constraints: Critical Safeguards to Carcinogenesis. Int J Mol Sci 2022; 23:ijms23158622. [PMID: 35955754 PMCID: PMC9369145 DOI: 10.3390/ijms23158622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Animal cells display great diversity in their shape. These morphological characteristics result from crosstalk between the plasma membrane and the force-generating capacities of the cytoskeleton macromolecules. Changes in cell shape are not merely byproducts of cell fate determinants, they also actively drive cell fate decisions, including proliferation and differentiation. Global and local changes in cell shape alter the transcriptional program by a multitude of mechanisms, including the regulation of physical links between the plasma membrane and the nuclear envelope and the mechanical modulation of cation channels and signalling molecules. It is therefore not surprising that anomalies in cell shape contribute to several diseases, including cancer. In this review, we discuss the possibility that the constraints imposed by cell shape determine the behaviour of normal and pro-tumour cells by organizing the whole interconnected regulatory network. In turn, cell behaviour might stabilize cells into discrete shapes. However, to progress towards a fully transformed phenotype and to acquire plasticity properties, pro-tumour cells might need to escape these cell shape restrictions. Thus, robust controls of the cell shape machinery may represent a critical safeguard against carcinogenesis.
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Affiliation(s)
- Komal Khalil
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Master Programme in Oncology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Alice Eon
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Magistère Européen de Génétique, Université Paris Cité, 5 Rue Thomas Mann, 75013 Paris, France
| | - Florence Janody
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Correspondence:
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27
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Liu W, Padhi A, Zhang X, Narendran J, Anastasio MA, Nain AS, Irudayaraj J. Dynamic Heterochromatin States in Anisotropic Nuclei of Cells on Aligned Nanofibers. ACS NANO 2022; 16:10754-10767. [PMID: 35803582 PMCID: PMC9332347 DOI: 10.1021/acsnano.2c02660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cancer cell nucleus deforms as it invades the interstitial spaces in tissues and the tumor microenvironment. While alteration of the chromatin structure in a deformed nucleus is expected and documented, the chromatin structure in the nuclei of cells on aligned matrices has not been elucidated. In this work we elucidate the spatiotemporal organization of heterochromatin in the elongated nuclei of cells on aligned nanofibers with stimulated emission depletion nanoscopy and fluorescence correlation spectroscopy. We show that the anisotropy of nuclei is sufficient to drive H3K9me3-heterochromatin alterations, with enhanced H3K9me3 nanocluster compaction and aggregation states that otherwise are indistinguishable from diffraction-limited microscopy. We interrogated the higher-order heterochromatin structures within major chromatin compartments in anisotropic nuclei and discovered a wider spatial dispersion of nanodomain clusters in the nucleoplasm and condensed larger nanoclusters near the periphery and pericentromeric heterochromatin. Upon examining the spatiotemporal dynamics of heterochromatin in anisotropic nuclei, we observed reduced mobility of the constitutive heterochromatin mark H3K9me3 and the associated heterochromatin protein 1 (HP1α) at the nucleoplasm and periphery regions, correlating with increased viscosity and changes in gene expression. Since heterochromatin remodeling is crucial to genome integrity, our results reveal an unconventional H3K9me3 heterochromatin distribution, providing cues to an altered chromatin state due to perturbations of the nuclei in aligned fiber configurations.
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Affiliation(s)
- Wenjie Liu
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Cancer Center at Illinois,
Micro and Nanotechnology Laboratory, Beckman
Institute, Carl Woese Institute for Genomic Biology, Urbana, Illinois 61801, United States
| | - Abinash Padhi
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Xiaohui Zhang
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Jairaj Narendran
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Mark A. Anastasio
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Amrinder S. Nain
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Joseph Irudayaraj
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Cancer Center at Illinois,
Micro and Nanotechnology Laboratory, Beckman
Institute, Carl Woese Institute for Genomic Biology, Urbana, Illinois 61801, United States
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28
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Pundel OJ, Blowes LM, Connelly JT. Extracellular Adhesive Cues Physically Define Nucleolar Structure and Function. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105545. [PMID: 35122409 PMCID: PMC8981897 DOI: 10.1002/advs.202105545] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/19/2022] [Indexed: 05/14/2023]
Abstract
Adhesive cues from the extracellular matrix (ECM) specify the size and shape of the nucleus via mechanical forces transmitted through the cytoskeleton. However, the effects of these biophysical stimuli on internal nuclear architecture and cellular responses remain poorly understood. This study investigates the direct impact of ECM adhesion on nucleolar remodeling in human keratinocytes using micropatterned substrates. Limited adhesion on small micropatterns promotes fusion of nucleoli, alongside a reduction in nuclear volume and condensation of heterochromatin. These changes in nucleolar architecture are mediated by altered chromatin biomechanics and depend on integration of the nucleus with the actin cytoskeleton. Functionally, nucleolar remodeling regulates ribogenesis and protein synthesis in keratinocytes and is associated with specific transcriptional changes in ribogenesis genes. Together, these findings demonstrate that cell shape and nuclear morphology control nucleolar structure and function and implicate the nucleolus as a key mechano-sensing element within the cell.
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Affiliation(s)
- Oscar J. Pundel
- Centre for Cell Biology and Cutaneous Research4 Newark StreetLondonE1 2ATUK
| | - Liisa M. Blowes
- Centre for Cell Biology and Cutaneous Research4 Newark StreetLondonE1 2ATUK
| | - John T. Connelly
- Centre for Cell Biology and Cutaneous Research4 Newark StreetLondonE1 2ATUK
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29
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Luciano M, Versaevel M, Vercruysse E, Procès A, Kalukula Y, Remson A, Deridoux A, Gabriele S. Appreciating the role of cell shape changes in the mechanobiology of epithelial tissues. BIOPHYSICS REVIEWS 2022; 3:011305. [PMID: 38505223 PMCID: PMC10903419 DOI: 10.1063/5.0074317] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/23/2022] [Indexed: 03/21/2024]
Abstract
The wide range of epithelial cell shapes reveals the complexity and diversity of the intracellular mechanisms that serve to construct their morphology and regulate their functions. Using mechanosensitive steps, epithelial cells can sense a variety of different mechanochemical stimuli and adapt their behavior by reshaping their morphology. These changes of cell shape rely on a structural reorganization in space and time that generates modifications of the tensional state and activates biochemical cascades. Recent studies have started to unveil how the cell shape maintenance is involved in mechanical homeostatic tasks to sustain epithelial tissue folding, identity, and self-renewal. Here, we review relevant works that integrated mechanobiology to elucidate some of the core principles of how cell shape may be conveyed into spatial information to guide collective processes such as epithelial morphogenesis. Among many other parameters, we show that the regulation of the cell shape can be understood as the result of the interplay between two counteracting mechanisms: actomyosin contractility and intercellular adhesions, and that both do not act independently but are functionally integrated to operate on molecular, cellular, and tissue scales. We highlight the role of cadherin-based adhesions in force-sensing and mechanotransduction, and we report recent developments that exploit physics of liquid crystals to connect cell shape changes to orientational order in cell aggregates. Finally, we emphasize that the further intermingling of different disciplines to develop new mechanobiology assays will lead the way toward a unified picture of the contribution of cell shape to the pathophysiological behavior of epithelial tissues.
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Affiliation(s)
- Marine Luciano
- University of Mons, Interfaces and Complex Fluids Laboratory, Mechanobiology and Biomaterials Group, Research Institute for Biosciences, CIRMAP, 20 Place du Parc, B-7000 Mons, Belgium
| | - Marie Versaevel
- University of Mons, Interfaces and Complex Fluids Laboratory, Mechanobiology and Biomaterials Group, Research Institute for Biosciences, CIRMAP, 20 Place du Parc, B-7000 Mons, Belgium
| | - Eléonore Vercruysse
- University of Mons, Interfaces and Complex Fluids Laboratory, Mechanobiology and Biomaterials Group, Research Institute for Biosciences, CIRMAP, 20 Place du Parc, B-7000 Mons, Belgium
| | - Anthony Procès
- University of Mons, Interfaces and Complex Fluids Laboratory, Mechanobiology and Biomaterials Group, Research Institute for Biosciences, CIRMAP, 20 Place du Parc, B-7000 Mons, Belgium
| | - Yohalie Kalukula
- University of Mons, Interfaces and Complex Fluids Laboratory, Mechanobiology and Biomaterials Group, Research Institute for Biosciences, CIRMAP, 20 Place du Parc, B-7000 Mons, Belgium
| | - Alexandre Remson
- University of Mons, Interfaces and Complex Fluids Laboratory, Mechanobiology and Biomaterials Group, Research Institute for Biosciences, CIRMAP, 20 Place du Parc, B-7000 Mons, Belgium
| | - Amandine Deridoux
- University of Mons, Interfaces and Complex Fluids Laboratory, Mechanobiology and Biomaterials Group, Research Institute for Biosciences, CIRMAP, 20 Place du Parc, B-7000 Mons, Belgium
| | - Sylvain Gabriele
- University of Mons, Interfaces and Complex Fluids Laboratory, Mechanobiology and Biomaterials Group, Research Institute for Biosciences, CIRMAP, 20 Place du Parc, B-7000 Mons, Belgium
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30
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Rubin J, van Wijnen AJ, Uzer G. Architectural control of mesenchymal stem cell phenotype through nuclear actin. Nucleus 2022; 13:35-48. [PMID: 35133922 PMCID: PMC8837231 DOI: 10.1080/19491034.2022.2029297] [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] [Indexed: 11/18/2022] Open
Abstract
There is growing appreciation that architectural components of the nucleus regulate gene accessibility by altering chromatin organization. While nuclear membrane connector proteins link the mechanosensitive actin cytoskeleton to the nucleoskeleton, actin’s contribution to the inner architecture of the nucleus remains enigmatic. Control of actin transport into the nucleus, plus the presence of proteins that control actin structure (the actin tool-box) within the nucleus, suggests that nuclear actin may support biomechanical regulation of gene expression. Cellular actin structure is mechanoresponsive: actin cables generated through forces experienced at the plasma membrane transmit force into the nucleus. We posit that dynamic actin remodeling in response to such biomechanical cues provides a novel level of structural control over the epigenetic landscape. We here propose to bring awareness to the fact that mechanical forces can promote actin transfer into the nucleus and control structural arrangements as illustrated in mesenchymal stem cells, thereby modulating lineage commitment.
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Affiliation(s)
- Janet Rubin
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Andre J van Wijnen
- Department of Biochemistry, University of Vermont Medical School, Burlington, Vt, USA
| | - Gunes Uzer
- Department of Mechanical & Biomedical Engineering, Boise State University, Boise, ID, USA
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31
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Madrazo E, González-Novo R, Ortiz-Placín C, García de Lacoba M, González-Murillo Á, Ramírez M, Redondo-Muñoz J. Fast H3K9 methylation promoted by CXCL12 contributes to nuclear changes and invasiveness of T-acute lymphoblastic leukemia cells. Oncogene 2022; 41:1324-1336. [PMID: 34999734 DOI: 10.1038/s41388-021-02168-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 12/09/2021] [Accepted: 12/22/2021] [Indexed: 02/06/2023]
Abstract
T-acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy that comprises the accumulation of malignant T-cells. Despite current therapies, failure to conventional treatments and relapse are frequent in children with T-ALL. It is known that the chemokine CXCL12 modulates leukemia survival and dissemination; however, our understanding of molecular mechanisms used by T-ALL cells to infiltrate and respond to leukemia cells-microenvironment interactions is still vague. In the present study, we showed that CXCL12 promoted H3K9 methylation in cell lines and primary T-ALL cells within minutes. We thus identified that CXCL12-mediated H3K9 methylation affected the global chromatin configuration and the nuclear mechanics of T-ALL cells. Importantly, we characterized changes in the genomic profile of T-ALL cells associated with rapid CXCL12 stimulation. We showed that blocking CXCR4 and protein kinase C (PKC) impaired the H3K9 methylation induced by CXCL12 in T-ALL cells. Finally, blocking H3K9 methyltransferases reduced the efficiency of T-ALL cells to deform their nuclei, migrate across confined spaces, and home to spleen and bone marrow in vivo models. Together, our data show novel functions for CXL12 as a master regulator of nuclear deformability and epigenetic changes in T-ALL cells, and its potential as a promising pharmacological target against T-ALL dissemination.
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Affiliation(s)
- Elena Madrazo
- 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
| | - Cándido Ortiz-Placín
- Department of Molecular Medicine, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - Mario García de Lacoba
- Bioinformatics and Biostatistics Unit, Centro de Investigaciones Biológicas Margarita Salas (CIB Margarita Salas-CSIC), Madrid, Spain
| | - África González-Murillo
- Department of Paediatric Haematology & Oncology, Hospital Universitario Niño Jesús, Madrid, Spain
- Health Research Institute La Princesa, Madrid, Spain
| | - Manuel Ramírez
- Department of Paediatric Haematology & Oncology, 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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32
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Agsu G, Gaillard J, Cadot B, Blanchoin L, Fabre E, Théry M. Reconstituting the Interaction Between Purified Nuclei and Microtubule Network. Methods Mol Biol 2022; 2430:385-399. [PMID: 35476346 DOI: 10.1007/978-1-0716-1983-4_25] [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] [Indexed: 06/14/2023]
Abstract
The nucleus is the stiffest organelle in the cell. Several morphogenetic processes depend on its deformation such as cell migration, cell differentiation, or senescence. Recent studies have revealed various mechanisms involved in the regulation of nucleus stiffness and deformation. The implication of chromatin swelling, lamin density, actin filament, and microtubule network revealed that nucleus shape is the outcome of a fine balance between various sources of external forces and numerous means of internal resistance. In adherent cells, the actin network is the dominant player in external force production, whereas in nonadherent cells microtubules seem to take over. It is therefore important to set up reconstitution assays in order to decipher the exact contribution of each player in this mechanical balance. In this method, we describe a nucleus purification protocol that is suitable for nonadherent cells. We also show that purified nuclei can interact with microtubules and that nuclei purified from distinct cell types get differentially wrapped into the array of microtubules. A combination with a microtubule gliding assay offers the possibility to counterbalance the binding to the nucleus membrane by active motor-based forces pulling on microtubules. So this protocol allows an in-depth study of microtubule-nucleus interactions in vitro.
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Affiliation(s)
- Gökçe Agsu
- INSERM, CEA, U976 - HIPI, Institut de Recherche Saint Louis, Université de Paris, Paris, France
- CEA, INRA, CNRS, UMR5168 - LPCV, Interdisciplinary Research Institute of Grenoble, Université Grenoble-Alpes, Grenoble, France
| | - Jérémie Gaillard
- INSERM, CEA, U976 - HIPI, Institut de Recherche Saint Louis, Université de Paris, Paris, France
- CEA, INRA, CNRS, UMR5168 - LPCV, Interdisciplinary Research Institute of Grenoble, Université Grenoble-Alpes, Grenoble, France
| | - Bruno Cadot
- INSERM - Sorbonne Université UMR974 - Center for Research in Myology, Paris, France
| | - Laurent Blanchoin
- INSERM, CEA, U976 - HIPI, Institut de Recherche Saint Louis, Université de Paris, Paris, France
- CEA, INRA, CNRS, UMR5168 - LPCV, Interdisciplinary Research Institute of Grenoble, Université Grenoble-Alpes, Grenoble, France
| | - Emmanuelle Fabre
- IRSL, INSERM, U944, CNRS, UMR7212, Université de Paris, Paris, France.
| | - Manuel Théry
- INSERM, CEA, U976 - HIPI, Institut de Recherche Saint Louis, Université de Paris, Paris, France.
- CEA, INRA, CNRS, UMR5168 - LPCV, Interdisciplinary Research Institute of Grenoble, Université Grenoble-Alpes, Grenoble, France.
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33
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Natesan R, Gowrishankar K, Kuttippurathu L, Kumar PBS, Rao M. Active Remodeling of Chromatin and Implications for In Vivo Folding. J Phys Chem B 2021; 126:100-109. [DOI: 10.1021/acs.jpcb.1c08655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ramakrishnan Natesan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Lakshmi Kuttippurathu
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - P. B. Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 668557, Kerala, India
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
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34
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Cao H, Duan L, Zhang Y, Cao J, Zhang K. Current hydrogel advances in physicochemical and biological response-driven biomedical application diversity. Signal Transduct Target Ther 2021; 6:426. [PMID: 34916490 PMCID: PMC8674418 DOI: 10.1038/s41392-021-00830-x] [Citation(s) in RCA: 258] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 02/05/2023] Open
Abstract
Hydrogel is a type of versatile platform with various biomedical applications after rational structure and functional design that leverages on material engineering to modulate its physicochemical properties (e.g., stiffness, pore size, viscoelasticity, microarchitecture, degradability, ligand presentation, stimulus-responsive properties, etc.) and influence cell signaling cascades and fate. In the past few decades, a plethora of pioneering studies have been implemented to explore the cell-hydrogel matrix interactions and figure out the underlying mechanisms, paving the way to the lab-to-clinic translation of hydrogel-based therapies. In this review, we first introduced the physicochemical properties of hydrogels and their fabrication approaches concisely. Subsequently, the comprehensive description and deep discussion were elucidated, wherein the influences of different hydrogels properties on cell behaviors and cellular signaling events were highlighted. These behaviors or events included integrin clustering, focal adhesion (FA) complex accumulation and activation, cytoskeleton rearrangement, protein cyto-nuclei shuttling and activation (e.g., Yes-associated protein (YAP), catenin, etc.), cellular compartment reorganization, gene expression, and further cell biology modulation (e.g., spreading, migration, proliferation, lineage commitment, etc.). Based on them, current in vitro and in vivo hydrogel applications that mainly covered diseases models, various cell delivery protocols for tissue regeneration and disease therapy, smart drug carrier, bioimaging, biosensor, and conductive wearable/implantable biodevices, etc. were further summarized and discussed. More significantly, the clinical translation potential and trials of hydrogels were presented, accompanied with which the remaining challenges and future perspectives in this field were emphasized. Collectively, the comprehensive and deep insights in this review will shed light on the design principles of new biomedical hydrogels to understand and modulate cellular processes, which are available for providing significant indications for future hydrogel design and serving for a broad range of biomedical applications.
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Affiliation(s)
- Huan Cao
- Department of Nuclear Medicine, West China Hospital, and National Engineering Research Center for Biomaterials, Sichuan University, 610064, Chengdu, P. R. China
- Department of Medical Ultrasound and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301 Yan-chang-zhong Road, 200072, Shanghai, People's Republic of China
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Lixia Duan
- Department of Medical Ultrasound and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301 Yan-chang-zhong Road, 200072, Shanghai, People's Republic of China
| | - Yan Zhang
- Department of Medical Ultrasound and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301 Yan-chang-zhong Road, 200072, Shanghai, People's Republic of China
| | - Jun Cao
- Department of Nuclear Medicine, West China Hospital, and National Engineering Research Center for Biomaterials, Sichuan University, 610064, Chengdu, P. R. China.
| | - Kun Zhang
- Department of Medical Ultrasound and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301 Yan-chang-zhong Road, 200072, Shanghai, People's Republic of China.
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35
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Goelzer M, Goelzer J, Ferguson ML, Neu CP, Uzer G. Nuclear envelope mechanobiology: linking the nuclear structure and function. Nucleus 2021; 12:90-114. [PMID: 34455929 PMCID: PMC8432354 DOI: 10.1080/19491034.2021.1962610] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
The nucleus, central to cellular activity, relies on both direct mechanical input as well as its molecular transducers to sense external stimuli and respond by regulating intra-nuclear chromatin organization that determines cell function and fate. In mesenchymal stem cells of musculoskeletal tissues, changes in nuclear structures are emerging as a key modulator of their differentiation and proliferation programs. In this review we will first introduce the structural elements of the nucleoskeleton and discuss the current literature on how nuclear structure and signaling are altered in relation to environmental and tissue level mechanical cues. We will focus on state-of-the-art techniques to apply mechanical force and methods to measure nuclear mechanics in conjunction with DNA, RNA, and protein visualization in living cells. Ultimately, combining real-time nuclear deformations and chromatin dynamics can be a powerful tool to study mechanisms of how forces affect the dynamics of genome function.
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Affiliation(s)
- Matthew Goelzer
- Materials Science and Engineering, Boise State University, Boise, ID, US
| | | | - Matthew L. Ferguson
- Biomolecular Science, Boise State University, Boise, ID, US
- Physics, Boise State University, Boise, ID, US
| | - Corey P. Neu
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, US
| | - Gunes Uzer
- Mechanical and Biomedical Engineering, Boise State University, Boise, ID, US
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36
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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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37
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Kennedy Z, Newberg J, Goelzer M, Judex S, Fitzpatrick CK, Uzer G. Modeling stem cell nucleus mechanics using confocal microscopy. Biomech Model Mechanobiol 2021; 20:2361-2372. [PMID: 34424419 PMCID: PMC8599651 DOI: 10.1007/s10237-021-01513-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 08/14/2021] [Indexed: 11/24/2022]
Abstract
Nuclear mechanics is emerging as a key component of stem cell function and differentiation. While changes in nuclear structure can be visually imaged with confocal microscopy, mechanical characterization of the nucleus and its sub-cellular components require specialized testing equipment. A computational model permitting cell-specific mechanical information directly from confocal and atomic force microscopy of cell nuclei would be of great value. Here, we developed a computational framework for generating finite element models of isolated cell nuclei from multiple confocal microscopy scans and simple atomic force microscopy (AFM) tests. Confocal imaging stacks of isolated mesenchymal stem cells were converted into finite element models and siRNA-mediated Lamin A/C depletion isolated chromatin and Lamin A/C structures. Using AFM-measured experimental stiffness values, a set of conversion factors were determined for both chromatin and Lamin A/C to map the voxel intensity of the original images to the element stiffness, allowing the prediction of nuclear stiffness in an additional set of other nuclei. The developed computational framework will identify the contribution of a multitude of sub-nuclear structures and predict global nuclear stiffness of multiple nuclei based on simple nuclear isolation protocols, confocal images and AFM tests.
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Affiliation(s)
- Zeke Kennedy
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA
| | - Joshua Newberg
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA
| | - Matthew Goelzer
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA
| | - Stefan Judex
- Biomedical Engineering, Stony Brook University, Stony Brook, USA
| | - Clare K Fitzpatrick
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA
| | - Gunes Uzer
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA.
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38
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Price CC, Mathur J, Boerckel JD, Pathak A, Shenoy VB. Dynamic self-reinforcement of gene expression determines acquisition of cellular mechanical memory. Biophys J 2021; 120:5074-5089. [PMID: 34627766 PMCID: PMC8633715 DOI: 10.1016/j.bpj.2021.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/17/2021] [Accepted: 10/05/2021] [Indexed: 01/26/2023] Open
Abstract
Mechanotransduction describes activation of gene expression by changes in the cell's physical microenvironment. Recent experiments show that mechanotransduction can lead to long-term "mechanical memory," in which cells cultured on stiff substrates for sufficient time (priming phase) maintain altered phenotype after switching to soft substrates (dissipation phase) as compared to unprimed controls. The timescale of memory acquisition and retention is orders of magnitude larger than the timescale of mechanosensitive cellular signaling, and memory retention time changes continuously with priming time. We develop a model that captures these features by accounting for positive reinforcement in mechanical signaling. The sensitivity of reinforcement represents the dynamic transcriptional state of the cell composed of protein lifetimes and three-dimensional chromatin organization. Our model provides a single framework connecting microenvironment mechanical history to cellular outcomes ranging from no memory to terminal differentiation. Predicting cellular memory of environmental changes can help engineer cellular dynamics through changes in culture environments.
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Affiliation(s)
- Christopher C Price
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jairaj Mathur
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, Missouri
| | - Joel D Boerckel
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amit Pathak
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, Missouri.
| | - Vivek B Shenoy
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania.
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39
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Liu L, Liu M, Xie D, Liu X, Yan H. Role of the extracellular matrix and YAP/TAZ in cell reprogramming. Differentiation 2021; 122:1-6. [PMID: 34768156 DOI: 10.1016/j.diff.2021.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 01/04/2023]
Abstract
Stem cells are crucial in the fields of regenerative medicine and cell therapy. Mechanical signals from the cellular microenvironment play an important role in inducing the reprogramming of somatic cells into stem cells in vitro, but the mechanisms of this process have yet to be fully explored. Mechanical signals may activate a physical pathway involving the focal adhesions-cytoskeleton-LINC complex axis, and a chemical pathway involving YAP/TAZ. ENH protein likely plays an important role in connecting and regulating these two pathways. Such mechanisms illustrate one way in which mechanical signals from the cellular microenvironment can induce reprogramming of somatic cells to stem cells, and lays the foundation for a new strategy for inducing and regulating such reprogramming in vitro by means of physical processes related to local mechanical forces.
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Affiliation(s)
- Lan Liu
- Department of Plastic and Burns Surgery, The Affiliated Hospital of Southwest Medical University, National Key Clinical Construction Specialty, Wound Repair and Regeneration Laboratory, Luzhou, Sichuan Province, 646000, China
| | - Mengchang Liu
- Department of Plastic and Burns Surgery, The Affiliated Hospital of Southwest Medical University, National Key Clinical Construction Specialty, Wound Repair and Regeneration Laboratory, Luzhou, Sichuan Province, 646000, China
| | - Defu Xie
- Department of Plastic and Burns Surgery, The Affiliated Hospital of Southwest Medical University, National Key Clinical Construction Specialty, Wound Repair and Regeneration Laboratory, Luzhou, Sichuan Province, 646000, China
| | - Xingke Liu
- Department of Plastic and Burns Surgery, The Affiliated Hospital of Southwest Medical University, National Key Clinical Construction Specialty, Wound Repair and Regeneration Laboratory, Luzhou, Sichuan Province, 646000, China
| | - Hong Yan
- Department of Plastic and Burns Surgery, The Affiliated Hospital of Southwest Medical University, National Key Clinical Construction Specialty, Wound Repair and Regeneration Laboratory, Luzhou, Sichuan Province, 646000, China.
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40
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Mohanta TK, Mishra AK, Al-Harrasi A. The 3D Genome: From Structure to Function. Int J Mol Sci 2021; 22:11585. [PMID: 34769016 PMCID: PMC8584255 DOI: 10.3390/ijms222111585] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/09/2023] Open
Abstract
The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding factor domains, cohesin, and chromatin structures are the prominent identified components that encode the 3D structure of the genome. Although TADs are the major contributors to 3D genome organization, they are absent in Arabidopsis. However, a few research groups have reported the presence of TAD-like structures in the plant kingdom.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Korea; or
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
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41
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Gravitational Force-Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells. Int J Mol Sci 2021; 22:ijms22179426. [PMID: 34502336 PMCID: PMC8430767 DOI: 10.3390/ijms22179426] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
The mechanisms underlying gravity perception in mammalian cells are unknown. We have recently discovered that the transcriptome of cells in the immune system, which is the most affected system during a spaceflight, responds rapidly and broadly to altered gravity. To pinpoint potential underlying mechanisms, we compared gene expression and three-dimensional (3D) chromosomal conformational changes in human Jurkat T cells during the short-term gravitational changes in parabolic flight and suborbital ballistic rocket flight experiments. We found that differential gene expression in gravity-responsive chromosomal regions, but not differentially regulated single genes, are highly conserved between different real altered gravity comparisons. These coupled gene expression effects in chromosomal regions could be explained by underlying chromatin structures. Based on a high-throughput chromatin conformation capture (Hi-C) analysis in altered gravity, we found that small chromosomes (chr16–22, with the exception of chr18) showed increased intra- and interchromosomal interactions in altered gravity, whereby large chromosomes showed decreased interactions. Finally, we detected a nonrandom overlap between Hi-C-identified chromosomal interacting regions and gravity-responsive chromosomal regions (GRCRs). We therefore demonstrate the first evidence that gravitational force-induced 3D chromosomal conformational changes are associated with rapid transcriptional response in human T cells. We propose a general model of cellular sensitivity to gravitational forces, where gravitational forces acting on the cellular membrane are rapidly and mechanically transduced through the cytoskeleton into the nucleus, moving chromosome territories to new conformation states and their genes into more expressive or repressive environments, finally resulting in region-specific differential gene expression.
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42
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Abstract
Membrane-bound organelles provide physical and functional compartmentalization of biological processes in eukaryotic cells. The characteristic shape and internal organization of these organelles is determined by a combination of multiple internal and external factors. The maintenance of the shape of nucleus, which houses the genetic material within a double membrane bilayer, is crucial for a seamless spatio-temporal control over nuclear and cellular functions. Dynamic morphological changes in the shape of nucleus facilitate various biological processes. Chromatin packaging, nuclear and cytosolic protein organization, and nuclear membrane lipid homeostasis are critical determinants of overall nuclear morphology. As such, a multitude of molecular players and pathways act together to regulate the nuclear shape. Here, we review the known mechanisms governing nuclear shape in various unicellular and multicellular organisms, including the non-spherical nuclei and non-lamin-related structural determinants. The review also touches upon cellular consequences of aberrant nuclear morphologies.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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43
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Wagh K, Ishikawa M, Garcia DA, Stavreva DA, Upadhyaya A, Hager GL. Mechanical Regulation of Transcription: Recent Advances. Trends Cell Biol 2021; 31:457-472. [PMID: 33712293 PMCID: PMC8221528 DOI: 10.1016/j.tcb.2021.02.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/01/2023]
Abstract
Mechanotransduction is the ability of a cell to sense mechanical cues from its microenvironment and convert them into biochemical signals to elicit adaptive transcriptional and other cellular responses. Here, we describe recent advances in the field of mechanical regulation of transcription, highlight mechanical regulation of the epigenome as a key novel aspect of mechanotransduction, and describe recent technological advances that could further elucidate the link between mechanical stimuli and gene expression. In this review, we emphasize the importance of mechanotransduction as one of the governing principles of cancer progression, underscoring the need to conduct further studies of the molecular mechanisms involved in sensing mechanical cues and coordinating transcriptional responses.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Momoko Ishikawa
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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44
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Vajrala VS, Alric B, Laborde A, Colin C, Suraniti E, Temple-Boyer P, Arbault S, Delarue M, Launay J. Microwell Array Based Opto-Electrochemical Detections Revealing Co-Adaptation of Rheological Properties and Oxygen Metabolism in Budding Yeast. Adv Biol (Weinh) 2021; 5:e2100484. [PMID: 33969641 DOI: 10.1002/adbi.202100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/29/2021] [Indexed: 11/08/2022]
Abstract
Microdevices composed of microwell arrays integrating nanoelectrodes (OptoElecWell) are developed to achieve dual high-resolution optical and electrochemical detections on single Saccharomyces cerevisiae yeast cells. Each array consists of 1.6 × 105 microwells measuring 8 µm in diameter and 5 µm height, with a platinum nanoring electrode for in situ electrochemistry, all integrated on a transparent thin wafer for further high-resolution live-cell imaging. After optimizing the filling rate, 32% of cells are effectively trapped within microwells. This allows to analyse S. cerevisiae metabolism associated with basal respiration while simultaneously measuring optically other cellular parameters. In this study, the impact of glucose concentration on respiration and intracellular rheology is focused. It is found that while the oxygen uptake rate decreases with increasing glucose concentration, diffusion of tracer nanoparticles increases. The OptoElecWell-based respiration methodology provides similar results compared to the commercial gold-standard Seahorse XF analyzer, while using 20 times fewer biological samples, paving the way to achieve single cell metabolomics. In addition, it facilitates an optical route to monitor the contents within single cells. The proposed device, in combination with the dual detection analysis, opens up new avenues for measuring cellular metabolism, and relating it to cellular physiological indicators at single cell level.
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Affiliation(s)
| | - Baptiste Alric
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse, F-31400, France.,Université de Toulouse, UPS, LAAS, Toulouse, F-31400, France
| | - Adrian Laborde
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse, F-31400, France.,Université de Toulouse, UPS, LAAS, Toulouse, F-31400, France
| | - Camille Colin
- Univ. Bordeaux, ISM, CNRS UMR 5255, INP Bordeaux, Pessac, 33607, France
| | - Emmanuel Suraniti
- Univ. Bordeaux, ISM, CNRS UMR 5255, INP Bordeaux, Pessac, 33607, France
| | | | - Stephane Arbault
- Univ. Bordeaux, ISM, CNRS UMR 5255, INP Bordeaux, Pessac, 33607, France
| | - Morgan Delarue
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse, F-31400, France
| | - Jérôme Launay
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse, F-31400, France.,Université de Toulouse, UPS, LAAS, Toulouse, F-31400, France
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45
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Abdeen AA, Cosgrove BD, Gersbach CA, Saha K. Integrating Biomaterials and Genome Editing Approaches to Advance Biomedical Science. Annu Rev Biomed Eng 2021; 23:493-516. [PMID: 33909475 DOI: 10.1146/annurev-bioeng-122019-121602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The recent discovery and subsequent development of the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat-CRISPR-associated protein 9) platform as a precise genome editing tool have transformed biomedicine. As these CRISPR-based tools have matured, multiple stages of the gene editing process and the bioengineering of human cells and tissues have advanced. Here, we highlight recent intersections in the development of biomaterials and genome editing technologies. These intersections include the delivery of macromolecules, where biomaterial platforms have been harnessed to enable nonviral delivery of genome engineering tools to cells and tissues in vivo. Further, engineering native-like biomaterial platforms for cell culture facilitates complex modeling of human development and disease when combined with genome engineering tools. Deeper integration of biomaterial platforms in these fields could play a significant role in enabling new breakthroughs in the application of gene editing for the treatment of human disease.
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Affiliation(s)
- Amr A Abdeen
- Department of Biomedical Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Brian D Cosgrove
- Department of Biomedical Engineering and Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA;
| | - Charles A Gersbach
- Department of Biomedical Engineering and Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA; .,Department of Surgery, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Krishanu Saha
- Department of Biomedical Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA.,McPherson Eye Research Institute, Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA;
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46
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Li M, Zhao Q, Belloli R, Duffy CR, Cai HN. Insulator foci distance correlates with cellular and nuclear morphology in early Drosophila embryos. Dev Biol 2021; 476:189-199. [PMID: 33844976 DOI: 10.1016/j.ydbio.2021.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/16/2021] [Accepted: 03/26/2021] [Indexed: 11/25/2022]
Abstract
The three-dimensional (3D) organization of the genome is highly dynamic, changing during development and varying across different tissues and cell types. Recent studies indicate that these changes alter regulatory interactions, leading to changes in gene expression. Despite its importance, the mechanisms that influence genomic organization remain poorly understood. We have previously identified a network of chromatin boundary elements, or insulators, in the Drosophila Antennapedia homeotic complex (ANT-C). These genomic elements interact with one another to tether chromatin loops that could block or promote enhancer-promoter interactions. To understand the function of these insulators, we assessed their interactions by measuring their 3D nuclear distance in developing animal tissues. Our data suggest that the ANT-C Hox complex might be in a folded or looped configuration rather than in a random or extended form. The architecture of the ANT-C complex, as read out by the pair-wise distance between insulators, undergoes a strong compression during late embryogenesis, coinciding with the reduction of cell and nuclear diameters due to continued cell divisions in post-cleavage cells. Our results suggest that genomic architecture and gene regulation may be influenced by cellular morphology and movement during development.
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Affiliation(s)
- Mo Li
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA
| | - Qing Zhao
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA
| | - Ryan Belloli
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA
| | - Carly R Duffy
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA
| | - Haini N Cai
- Department of Cellular Biology, University of Georgia, Athens GA, 30602, USA.
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47
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Liu K, Patteson AE, Banigan EJ, Schwarz JM. Dynamic Nuclear Structure Emerges from Chromatin Cross-Links and Motors. PHYSICAL REVIEW LETTERS 2021; 126:158101. [PMID: 33929233 DOI: 10.1103/physrevlett.126.158101] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The cell nucleus houses the chromosomes, which are linked to a soft shell of lamin protein filaments. Experiments indicate that correlated chromosome dynamics and nuclear shape fluctuations arise from motor activity. To identify the physical mechanisms, we develop a model of an active, cross-linked Rouse chain bound to a polymeric shell. System-sized correlated motions occur but require both motor activity and cross-links. Contractile motors, in particular, enhance chromosome dynamics by driving anomalous density fluctuations. Nuclear shape fluctuations depend on motor strength, cross-linking, and chromosome-lamina binding. Therefore, complex chromosome dynamics and nuclear shape emerge from a minimal, active chromosome-lamina system.
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Affiliation(s)
- Kuang Liu
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, New York 13244, USA
| | - Alison E Patteson
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, New York 13244, USA
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, MIT, Cambridge, Massachusetts 02139, USA
| | - J M Schwarz
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, New York 13244, USA
- Indian Creek Farm, Ithaca, New York 14850, USA
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Iyer KV, Taubenberger A, Zeidan SA, Dye NA, Eaton S, Jülicher F. Apico-basal cell compression regulates Lamin A/C levels in epithelial tissues. Nat Commun 2021; 12:1756. [PMID: 33767161 PMCID: PMC7994818 DOI: 10.1038/s41467-021-22010-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023] Open
Abstract
The levels of nuclear protein Lamin A/C are crucial for nuclear mechanotransduction. Lamin A/C levels are known to scale with tissue stiffness and extracellular matrix levels in mesenchymal tissues. But in epithelial tissues, where cells lack a strong interaction with the extracellular matrix, it is unclear how Lamin A/C is regulated. Here, we show in epithelial tissues that Lamin A/C levels scale with apico-basal cell compression, independent of tissue stiffness. Using genetic perturbations in Drosophila epithelial tissues, we show that apico-basal cell compression regulates the levels of Lamin A/C by deforming the nucleus. Further, in mammalian epithelial cells, we show that nuclear deformation regulates Lamin A/C levels by modulating the levels of phosphorylation of Lamin A/C at Serine 22, a target for Lamin A/C degradation. Taken together, our results reveal a mechanism of Lamin A/C regulation which could provide key insights for understanding nuclear mechanotransduction in epithelial tissues.
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Affiliation(s)
- K. Venkatesan Iyer
- grid.419537.d0000 0001 2113 4567Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany ,grid.419560.f0000 0001 2154 3117Max Planck Institute for the Physics of Complex Systems, Dresden, Germany ,grid.34980.360000 0001 0482 5067Present Address: Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India
| | - Anna Taubenberger
- grid.4488.00000 0001 2111 7257Biotechnology Center TU Dresden, Dresden, Germany
| | - Salma Ahmed Zeidan
- grid.419537.d0000 0001 2113 4567Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Natalie A. Dye
- grid.419537.d0000 0001 2113 4567Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany ,grid.4488.00000 0001 2111 7257Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Suzanne Eaton
- grid.419537.d0000 0001 2113 4567Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany ,grid.4488.00000 0001 2111 7257Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Frank Jülicher
- grid.419560.f0000 0001 2154 3117Max Planck Institute for the Physics of Complex Systems, Dresden, Germany ,grid.4488.00000 0001 2111 7257Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany ,grid.495510.cCenter for Systems Biology Dresden, Dresden, Germany
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49
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The Long Linker Region of Telomere-Binding Protein TRF2 Is Responsible for Interactions with Lamins. Int J Mol Sci 2021; 22:ijms22073293. [PMID: 33804854 PMCID: PMC8036907 DOI: 10.3390/ijms22073293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/15/2022] Open
Abstract
Telomere-binding factor 2 (TRF2) is part of the shelterin protein complex found at chromosome ends. Lamin A/C interacts with TRF2 and influences telomere position. TRF2 has an intrinsically disordered region between the ordered dimerization and DNA-binding domains. This domain is referred to as the long linker region of TRF2, or udTRF2. We suggest that udTRF2 might be involved in the interaction between TRF2 and lamins. The recombinant protein corresponding to the udTRF2 region along with polyclonal antibodies against this region were used in co-immunoprecipitation with purified lamina and nuclear extracts. Co-immunoprecipitation followed by Western blots and mass spectrometry indicated that udTRF2 interacts with lamins, preferably lamins A/C. The interaction did not involve any lamin-associated proteins, was not dependent on the post-translation modification of lamins, nor did it require their higher-order assembly. Besides lamins, a number of other udTRF2-interacting proteins were identified by mass spectrometry, including several heterogeneous nuclear ribonucleoproteins (hnRNP A2/B1, hnRNPA1, hnRNP A3, hnRNP K, hnRNP L, hnRNP M), splicing factors (SFPQ, NONO, SRSF1, and others), helicases (DDX5, DHX9, and Eif4a3l1), topoisomerase I, and heat shock protein 71, amongst others. Some of the identified interactors are known to be involved in telomere biology; the roles of the others remain to be investigated. Thus, the long linker region of TRF2 (udTRF2) is a regulatory domain responsible for the association between TRF2 and lamins and is involved in interactions with other proteins.
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dos Santos Á, Toseland CP. Regulation of Nuclear Mechanics and the Impact on DNA Damage. Int J Mol Sci 2021; 22:3178. [PMID: 33804722 PMCID: PMC8003950 DOI: 10.3390/ijms22063178] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
In eukaryotic cells, the nucleus houses the genomic material of the cell. The physical properties of the nucleus and its ability to sense external mechanical cues are tightly linked to the regulation of cellular events, such as gene expression. Nuclear mechanics and morphology are altered in many diseases such as cancer and premature ageing syndromes. Therefore, it is important to understand how different components contribute to nuclear processes, organisation and mechanics, and how they are misregulated in disease. Although, over the years, studies have focused on the nuclear lamina-a mesh of intermediate filament proteins residing between the chromatin and the nuclear membrane-there is growing evidence that chromatin structure and factors that regulate chromatin organisation are essential contributors to the physical properties of the nucleus. Here, we review the main structural components that contribute to the mechanical properties of the nucleus, with particular emphasis on chromatin structure. We also provide an example of how nuclear stiffness can both impact and be affected by cellular processes such as DNA damage and repair.
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Affiliation(s)
- Ália dos Santos
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Christopher P. Toseland
- Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
- Insigneo Institute for in Silico Medicine, University of Sheffield, Sheffield S10 2RX, UK
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