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Zhang Y, Zhang Y, Wang C, Heo Y, Tumenbayar BI, Lee SH, Bae Y, Chin Heo S. Epigenetic Dynamics in Meniscus Cell Migration and its Zonal Dependency in Response to Inflammatory Conditions: Implications for Regeneration Strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604178. [PMID: 39091842 PMCID: PMC11291020 DOI: 10.1101/2024.07.22.604178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Meniscus injuries pose significant challenges in clinical settings, primarily due to the intrinsic heterogeneity of the tissue and the limited efficacy of current treatments. Endogenous cell migration is crucial for the healing process, yet the regulatory mechanisms of meniscus cell migration and its zonal dependency within the meniscus are not fully understood. Thus, this study investigates the role of epigenetic mechanisms in governing meniscus cell migration under inflammatory conditions, with a focus on their implications for injury healing and regeneration. Here, we discovered that a proinflammatory cytokine, TNF-α treatment significantly impedes the migration speed of inner meniscus cells, while outer meniscus cells are unaffected, underscoring a zonal-dependent response within the meniscus. Our analysis identified distinct histone modification patterns and chromatin dynamics between inner and outer meniscus cells during migration, highlighting the necessity to consider these zonal-dependent properties in devising repair strategies. Specifically, we found that TNF-α differentially influences histone modifications, particularly H3K27me3, between the two cell types. Transcriptome analysis further revealed that TNF-α treatment induces substantial gene expression changes, with inner meniscus cells exhibiting more pronounced alterations than outer cells. Gene cluster analysis pointed to distinct responses in chromatin remodeling, extracellular matrix assembly, and wound healing processes between the zonal cell populations. Moreover, we identified potential therapeutic targets by employing existing epigenetic drugs, GSKJ4 (a histone demethylase inhibitor) and C646 (a histone acetyltransferase inhibitor), to successfully restore the migration speed of inner meniscus cells under inflammatory conditions. This highlights their potential utility in treating meniscus tear injuries. Overall, our findings elucidate the intricate interplay between epigenetic mechanisms and meniscus cell migration, along with its meniscus zonal dependency. This study provides insights into potential targets for enhancing meniscus repair and regeneration, which may lead to improved clinical outcomes for patients with meniscus injuries and osteoarthritis.
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Affiliation(s)
- Yize Zhang
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Yujia Zhang
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine Wang
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuna Heo
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Bat-Ider Tumenbayar
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Se-Hwan Lee
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yongho Bae
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biomedical Engineering, School of Engineering and Applied Sciences, University at Buffalo, Buffalo, NY, USA
| | - Su Chin Heo
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
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Serra-Bardenys G, Blanco E, Escudero-Iriarte C, Serra-Camprubí Q, Querol J, Pascual-Reguant L, Morancho B, Escorihuela M, Tissera NS, Sabé A, Martín L, Segura-Bayona S, Verde G, Aiese Cigliano R, Millanes-Romero A, Jerónimo C, Cebrià-Costa JP, Nuciforo P, Simonetti S, Viaplana C, Dienstmann R, Oliveira M, Peg V, Stracker TH, Arribas J, Canals F, Villanueva J, Di Croce L, García de Herreros A, Tian TV, Peiró S. LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells. FEBS J 2024; 291:2423-2448. [PMID: 38451841 DOI: 10.1111/febs.17112] [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: 06/01/2023] [Revised: 01/02/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Oxidation of histone H3 at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase homolog 2 (LOXL2). This histone modification is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells and has been linked to the maintenance of compacted chromatin. However, the molecular mechanism underlying this maintenance is still unknown. Here, we show that LOXL2 interacts with RuvB-Like 1 (RUVBL1), RuvB-Like 2 (RUVBL2), Actin-like protein 6A (ACTL6A), and DNA methyltransferase 1associated protein 1 (DMAP1), a complex involved in the incorporation of the histone variant H2A.Z. Our experiments indicate that this interaction and the active form of RUVBL2 are required to maintain LOXL2-dependent chromatin compaction. Genome-wide experiments showed that H2A.Z, RUVBL2, and H3K4ox colocalize in heterochromatin regions. In the absence of LOXL2 or RUVBL2, global levels of the heterochromatin histone mark H3K9me3 were strongly reduced, and the ATAC-seq signal in the H3K9me3 regions was increased. Finally, we observed that the interplay between these series of events is required to maintain H3K4ox-enriched heterochromatin regions, which in turn is key for maintaining the oncogenic properties of the TNBC cell line tested (MDA-MB-231).
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Affiliation(s)
- Gemma Serra-Bardenys
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institut Bonanova FP Sanitaria, Consorci Mar Parc de Salut de Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | | | - Anna Sabé
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Luna Martín
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Gaetano Verde
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Alba Millanes-Romero
- Institute for Research in Biomedicine (IRB Barcelona) and Barcelona Institute of Science and Technology, Spain
| | - Celia Jerónimo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institut de Recherches Cliniques de Montréal, Canada
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sara Simonetti
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Travis H Stracker
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Joaquín Arribas
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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3
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De la Fuente IM, Carrasco-Pujante J, Camino-Pontes B, Fedetz M, Bringas C, Pérez-Samartín A, Pérez-Yarza G, López JI, Malaina I, Cortes JM. Systemic cellular migration: The forces driving the directed locomotion movement of cells. PNAS NEXUS 2024; 3:pgae171. [PMID: 38706727 PMCID: PMC11067954 DOI: 10.1093/pnasnexus/pgae171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/11/2024] [Indexed: 05/07/2024]
Abstract
Directional motility is an essential property of cells. Despite its enormous relevance in many fundamental physiological and pathological processes, how cells control their locomotion movements remains an unresolved question. Here, we have addressed the systemic processes driving the directed locomotion of cells. Specifically, we have performed an exhaustive study analyzing the trajectories of 700 individual cells belonging to three different species (Amoeba proteus, Metamoeba leningradensis, and Amoeba borokensis) in four different scenarios: in absence of stimuli, under an electric field (galvanotaxis), in a chemotactic gradient (chemotaxis), and under simultaneous galvanotactic and chemotactic stimuli. All movements were analyzed using advanced quantitative tools. The results show that the trajectories are mainly characterized by coherent integrative responses that operate at the global cellular scale. These systemic migratory movements depend on the cooperative nonlinear interaction of most, if not all, molecular components of cells.
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Affiliation(s)
- Ildefonso M De la Fuente
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa 48940, Spain
- Department of Nutrition, CEBAS-CSIC Institute, Espinardo University Campus, Murcia 30100, Spain
| | - Jose Carrasco-Pujante
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa 48940, Spain
| | | | - Maria Fedetz
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada 18016, Spain
| | - Carlos Bringas
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa 48940, Spain
| | - Alberto Pérez-Samartín
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa 48940, Spain
| | - Gorka Pérez-Yarza
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa 48940, Spain
| | - José I López
- Biobizkaia Health Research Institute, Barakaldo 48903, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa 48940, Spain
| | - Jesus M Cortes
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa 48940, Spain
- Biobizkaia Health Research Institute, Barakaldo 48903, Spain
- IKERBASQUE: The Basque Foundation for Science, Bilbao 48009, Spain
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Otsuka A, Minami K, Higashi K, Kawaguchi A, Tamura S, Ide S, Hendzel MJ, Kurokawa K, Maeshima K. Chromatin organization and behavior in HRAS-transformed mouse fibroblasts. Chromosoma 2024; 133:135-148. [PMID: 38400910 DOI: 10.1007/s00412-024-00817-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/26/2024]
Abstract
In higher eukaryotic cells, a string of nucleosomes, where long genomic DNA is wrapped around core histones, are rather irregularly folded into a number of condensed chromatin domains, which have been revealed by super-resolution imaging and Hi-C technologies. Inside these domains, nucleosomes fluctuate and locally behave like a liquid. The behavior of chromatin may be highly related to DNA transaction activities such as transcription and repair, which are often upregulated in cancer cells. To investigate chromatin behavior in cancer cells and compare those of cancer and non-cancer cells, we focused on oncogenic-HRAS (Gly12Val)-transformed mouse fibroblasts CIRAS-3 cells and their parental 10T1/2 cells. CIRAS-3 cells are tumorigenic and highly metastatic. First, we found that HRAS-induced transformation altered not only chromosome structure, but also nuclear morphology in the cell. Using single-nucleosome imaging/tracking in live cells, we demonstrated that nucleosomes are locally more constrained in CIRAS-3 cells than in 10T1/2 cells. Consistently, heterochromatin marked with H3K27me3 was upregulated in CIRAS-3 cells. Finally, Hi-C analysis showed enriched interactions of the B-B compartment in CIRAS-3 cells, which likely represents transcriptionally inactive chromatin. Increased heterochromatin may play an important role in cell migration, as they have been reported to increase during metastasis. Our study also suggests that single-nucleosome imaging provides new insights into how local chromatin is structured in living cells.
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Affiliation(s)
- Aoi Otsuka
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Koichi Higashi
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Akane Kawaguchi
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Michael J Hendzel
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ken Kurokawa
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.
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5
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Panahipour L, Croci R, Guarnieri S, Gruber R. PRF Lysates Enhance the Proliferation and Migration of Oral Squamous Carcinoma Cell Lines. Dent J (Basel) 2023; 11:242. [PMID: 37886927 PMCID: PMC10605502 DOI: 10.3390/dj11100242] [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: 07/20/2023] [Revised: 09/20/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Platelet-rich fibrin (PRF) is an autologous fibrin-rich matrix where activated platelets and leucocytes accumulate. PRF has a wide spectrum of clinical indications with the overall aim of supporting tissue regeneration which in dentistry includes the healing of healthy oral mucosa with epithelial cells. In oral squamous cell carcinoma lesions, however, epithelial cells undergo malignant transformation, indicated by their unrestricted proliferation and migration potential, which should not be further enhanced by a wound-healing formula. Yet, little is known about how oral squamous cell carcinomas respond to PRF lysates. The aim of the present study was, therefore, to test the capacity of PRF lysates to change the transcriptome of HSC2 oral squamous carcinoma cells and perform bioassays to support the findings. Based on the RNAseq analysis, PRF lysates caused an increase in the genes functionally linked to cell replication and migration. In support of this screening approach, PRF lysates enhanced the proliferation of HSC2 oral squamous carcinoma cells, as indicated by 3[H]-thymidine incorporation, cell counting, and the expression of proliferation-related genes. Moreover, PRF lysates sped up cell migration in a scratch assay requiring actin polymerization. Taken together, our data showing that PRF lysates are mitogenic and stimulate motility of oral squamous carcinoma cell lines could be an indication that treatment with PRF in cases of oral carcinoma should be carefully considered.
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Affiliation(s)
- Layla Panahipour
- Department of Oral Biology, University Clinic of Dentistry, Medical University of Vienna, 1090 Vienna, Austria; (L.P.); (R.C.); (S.G.)
| | - Rebecca Croci
- Department of Oral Biology, University Clinic of Dentistry, Medical University of Vienna, 1090 Vienna, Austria; (L.P.); (R.C.); (S.G.)
| | - Sara Guarnieri
- Department of Oral Biology, University Clinic of Dentistry, Medical University of Vienna, 1090 Vienna, Austria; (L.P.); (R.C.); (S.G.)
| | - Reinhard Gruber
- Department of Oral Biology, University Clinic of Dentistry, Medical University of Vienna, 1090 Vienna, Austria; (L.P.); (R.C.); (S.G.)
- Department of Periodontology, School of Dental Medicine, University of Bern, 3010 Bern, Switzerland
- Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
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Tortora MMC, Brennan LD, Karpen G, Jost D. HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation. Proc Natl Acad Sci U S A 2023; 120:e2211855120. [PMID: 37549295 PMCID: PMC10438847 DOI: 10.1073/pnas.2211855120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 06/28/2023] [Indexed: 08/09/2023] Open
Abstract
The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid-liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1-chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.
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Affiliation(s)
- Maxime M. C. Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
| | - Lucy D. Brennan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Gary Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of BioEngineering and BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
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Ksovreli M, Kachlishvili T, Mtiulishvili T, Dzmanashvili G, Batsatsashvili T, Zurabiani K, Tughushi D, Kantaria T, Nadaraia L, Rusishvili L, Piot O, Terryn C, Tchelidze P, Katsarava R, Kulikova N. Leucine-Based Pseudo-Proteins (LPPs) as Promising Biomaterials: A Study of Cell-Supporting Properties. Polymers (Basel) 2023; 15:3328. [PMID: 37571222 PMCID: PMC10422583 DOI: 10.3390/polym15153328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Scaffold-based systems have become essential in biomedical research, providing the possibility of building in vitro models that can better mimic tissue/organic physiology. A relatively new family of biomimetics-pseudo-proteins (PPs)-can therefore be considered especially promising in this context. Three different artificial leucine-based LPP films were tested in vitro as potential scaffolding materials. In vitro experiments were performed using two types of cells: primary mouse skin fibroblasts and a murine monocyte/macrophages cell line, RAW264.7. Cell adhesion and cell spreading were evaluated according to morphological parameters via scanning electron microscopy (SEM), and they were assessed according to actin cytoskeleton distribution, which was studied via confocal laser microscopy. Cell proliferation was evaluated via an MTT assay. Cell migration was studied using time-lapse microscopy. SEM images for both types of cells demonstrated prominent adhesion and perfect cell spreading on all three LPPs. Analyses of actin cytoskeleton organization revealed a high number of focal adhesions and prominent motility-associated structures. A certain stimulation of cell proliferation was detected in the cases of all three LPPs, and two of them promoted macrophage migration. Overall, our data suggest that the LPPs used in the study can be considered potential cell-friendly scaffolding materials.
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Affiliation(s)
- Mariam Ksovreli
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Tinatin Kachlishvili
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Tevdore Mtiulishvili
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Giorgi Dzmanashvili
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Tatuli Batsatsashvili
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Knarita Zurabiani
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - David Tughushi
- Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Temur Kantaria
- Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Lili Nadaraia
- Institute of Physical Material Science and Materials Technologies, Technical University of Georgia, 0159 Tbilisi, Georgia
- Carl Zeiss Scientific and Education Center, New Vision University, 0159 Tbilisi, Georgia
| | - Levan Rusishvili
- Department of Morphology, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, 0159 Tbilisi, Georgia
| | - Olivier Piot
- BioSpecT Unit, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Christine Terryn
- BioSpecT Unit, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Pavel Tchelidze
- Carl Zeiss Scientific and Education Center, New Vision University, 0159 Tbilisi, Georgia
- Faculty of Healthcare, East European University, 0159 Tbilisi, Georgia
| | - Ramaz Katsarava
- Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Nina Kulikova
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
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8
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Nishino M, Imaizumi H, Yokoyama Y, Katahira J, Kimura H, Matsuura N, Matsumura M. Histone methyltransferase SUV39H1 regulates the Golgi complex via the nuclear envelope-spanning LINC complex. PLoS One 2023; 18:e0283490. [PMID: 37437070 DOI: 10.1371/journal.pone.0283490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
Cell motility is related to the higher-order structure of chromatin. Stimuli that induce cell migration change chromatin organization; such stimuli include elevated histone H3 lysine 9 trimethylation (H3K9me3). We previously showed that depletion of histone H3 lysine 9 methyltransferase, SUV39H1, suppresses directional cell migration. However, the molecular mechanism underlying this association between chromatin and cell migration remains elusive. The Golgi apparatus is a cell organelle essential for cell motility. In this study, we show that loss of H3K9 methyltransferase SUV39H1 but not SETDB1 or SETDB2 causes dispersion of the Golgi apparatus throughout the cytoplasm. The Golgi dispersion triggered by SUV39H1 depletion is independent of transcription, centrosomes, and microtubule organization, but is suppressed by depletion of any of the following three proteins: LINC complex components SUN2, nesprin-2, or microtubule plus-end-directed kinesin-like protein KIF20A. In addition, SUN2 is closely localized to H3K9me3, and SUV39H1 affects the mobility of SUN2 in the nuclear envelope. Further, inhibition of cell motility caused by SUV39H1 depletion is restored by suppression of SUN2, nesprin-2, or KIF20A. In summary, these results show the functional association between chromatin organization and cell motility via the Golgi organization regulated by the LINC complex.
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Affiliation(s)
- Miyu Nishino
- Graduate School of Health Sciences, Ehime Prefectural University of Health Sciences, Ehime, Japan
| | - Hiromasa Imaizumi
- Graduate School of Medicine and Health Science, Osaka University, Osaka, Japan
- Department of Radiological Technology, Faculty of Health Science and Technology, Kawasaki University of Medical Welfare, Okayama, Japan
| | - Yuhki Yokoyama
- Graduate School of Medicine and Health Science, Osaka University, Osaka, Japan
| | - Jun Katahira
- Laboratories of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, Osaka, Japan
| | - Hiroshi Kimura
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Nariaki Matsuura
- Graduate School of Medicine and Health Science, Osaka University, Osaka, Japan
- Osaka International Cancer Institute, Osaka, Japan
| | - Miki Matsumura
- Graduate School of Health Sciences, Ehime Prefectural University of Health Sciences, Ehime, Japan
- Graduate School of Medicine and Health Science, Osaka University, Osaka, Japan
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9
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Hsia CR, Melters DP, Dalal Y. The Force is Strong with This Epigenome: Chromatin Structure and Mechanobiology. J Mol Biol 2023; 435:168019. [PMID: 37330288 PMCID: PMC10567996 DOI: 10.1016/j.jmb.2023.168019] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
All life forms sense and respond to mechanical stimuli. Throughout evolution, organisms develop diverse mechanosensing and mechanotransduction pathways, leading to fast and sustained mechanoresponses. Memory and plasticity characteristics of mechanoresponses are thought to be stored in the form of epigenetic modifications, including chromatin structure alterations. These mechanoresponses in the chromatin context share conserved principles across species, such as lateral inhibition during organogenesis and development. However, it remains unclear how mechanotransduction mechanisms alter chromatin structure for specific cellular functions, and if altered chromatin structure can mechanically affect the environment. In this review, we discuss how chromatin structure is altered by environmental forces via an outside-in pathway for cellular functions, and the emerging concept of how chromatin structure alterations can mechanically affect nuclear, cellular, and extracellular environments. This bidirectional mechanical feedback between chromatin of the cell and the environment can potentially have important physiological implications, such as in centromeric chromatin regulation of mechanobiology in mitosis, or in tumor-stroma interactions. Finally, we highlight the current challenges and open questions in the field and provide perspectives for future research.
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Affiliation(s)
- Chieh-Ren Hsia
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/JeremiahHsia
| | - Daniël P Melters
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/dpmelters
| | - Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States. https://twitter.com/NCIYaminiDalal
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10
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Bozzuto G, Colone M, Toccacieli L, Molinari A, Calcabrini A, Stringaro A. Interaction of Drug-Sensitive and -Resistant Human Melanoma Cells with HUVEC Cells: A Label-Free Cell-Based Impedance Study. Biomedicines 2023; 11:1544. [PMID: 37371639 DOI: 10.3390/biomedicines11061544] [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: 04/24/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Cancer cell extravasation is a crucial step in cancer metastasis. However, many of the mechanisms involved in this process are only now being elucidated. Thus, in the present study we analysed the trans-endothelial invasion of melanoma cells by a high throughput label-free cell impedance assay applied to transwell chamber invasion assay. This technique monitors and quantifies in real-time the invasion of endothelial cells by malignant tumour cells, for a long time, avoiding artefacts due to preparation of the end point measurements. Results obtained by impedance analysis were compared with endpoint measurements. In this study, we used human melanoma M14 wild type (WT) cells and their drug resistant counterparts, M14 multidrug resistant (ADR) melanoma cells, selected by prolonged exposure to doxorubicin (DOX). Tumour cells were co-cultured with monolayers of human umbilical vein endothelial cells (HUVEC). Results herein reported demonstrated that: (i) the trans-endothelial migration of resistant melanoma cells was faster than sensitive ones; (ii) the endothelial cells appeared to be strongly affected by the transmigration of melanoma cells which showed the ability to degrade their cytoplasm; (iii) resistant cells preferentially adopted the transcellular invasion vs. the paracellular one; (iv) the endothelial damage mediated by tumour metalloproteinases seemed to be reversible.
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Affiliation(s)
- Giuseppina Bozzuto
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marisa Colone
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Laura Toccacieli
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Agnese Molinari
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Annarica Calcabrini
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Annarita Stringaro
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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11
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Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023; 186:1493-1511.e40. [PMID: 37001506 PMCID: PMC10074325 DOI: 10.1016/j.cell.2023.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 02/10/2023] [Indexed: 04/03/2023]
Abstract
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.
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Affiliation(s)
- Joel Rozowsky
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiahao Gao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Beatrice Borsari
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Yucheng T Yang
- Institute of Science and Technology for Brain-Inspired Intelligence; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence; MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Gamze Gürsoy
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Kun Xiong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Tianxiao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jason Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Keyang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ana Berthel
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Zhanlin Chen
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA
| | - Fabio Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Maxwell S Sun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Justin Chang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Christopher J F Cameron
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Noam Shoresh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jorg Drenkow
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jessika Adrian
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sergey Aganezov
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | | | - Sora Chee
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Gabriel Conte Cortez Martins
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cassidy Danyko
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Carrie A Davis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Daniel Farid
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Idan Gabdank
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Yoel Gofin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David U Gorkin
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Mengting Gu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vivian Hecht
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin C Hitz
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Robbyn Issner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Melanie Kirsche
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xiangmeng Kong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Bonita R Lam
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Shantao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Bian Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Xiqi Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Khine Zin Lin
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, CHN
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan Mudge
- European Bioinformatics Institute, Cambridge, Cambridgeshire, GB
| | | | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ioann Popov
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Srividya Ramakrishnan
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Joe Raymond
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Leonidas Salichos
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
| | - Alexandra Scavelli
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jacob M Schreiber
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Fritz J Sedlazeck
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Lei Hoon See
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rachel M Sherman
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xu Shi
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Minyi Shi
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Cricket Alicia Sloan
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - J Seth Strattan
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Zhen Tan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Forrest Y Tanaka
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Anna Vlasova
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Comparative Genomics Group, Life Science Programme, Barcelona Supercomputing Centre, Barcelona, Spain; Institute of Research in Biomedicine, Barcelona, Spain
| | - Jun Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathan Werner
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Min Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Chengfei Yan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lu Yu
- Institute of Cancer Research, London, UK
| | - Christopher Zaleski
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA, USA
| | | | - J Michael Cherry
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Morgan E Levine
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Alexander Dobin
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Jesse Gillis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | | | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Roderic Guigó
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Mark Gerstein
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA.
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12
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Hernandez‐Vicens R, Singh J, Pernicone N, Listovsky T, Gerlitz G. SETDB1 regulates microtubule dynamics. Cell Prolif 2022; 55:e13348. [DOI: 10.1111/cpr.13348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Jagreeti Singh
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
| | - Nomi Pernicone
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
| | - Tamar Listovsky
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
- Ariel Center for Applied Cancer Research Ariel University Ariel Israel
- Adelson School of Medicine Ariel University Ariel Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Life Sciences Ariel University Ariel Israel
- Ariel Center for Applied Cancer Research Ariel University Ariel Israel
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13
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Hsia CR, McAllister J, Hasan O, Judd J, Lee S, Agrawal R, Chang CY, Soloway P, Lammerding J. Confined migration induces heterochromatin formation and alters chromatin accessibility. iScience 2022; 25:104978. [PMID: 36117991 PMCID: PMC9474860 DOI: 10.1016/j.isci.2022.104978] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 01/17/2023] Open
Abstract
During migration, cells often squeeze through small constrictions, requiring extensive deformation. We hypothesized that nuclear deformation associated with such confined migration could alter chromatin organization and function. By studying cells migrating through microfluidic devices that mimic interstitial spaces in vivo, we found that confined migration results in increased H3K9me3 and H3K27me3 heterochromatin marks that persist for days. This "confined migration-induced heterochromatin" (CMiH) was distinct from heterochromatin formation during migration initiation. Confined migration decreased chromatin accessibility at intergenic regions near centromeres and telomeres, suggesting heterochromatin spreading from existing sites. Consistent with the overall decrease in accessibility, global transcription was decreased during confined migration. Intriguingly, we also identified increased accessibility at promoter regions of genes linked to chromatin silencing, tumor invasion, and DNA damage response. Inhibiting CMiH reduced migration speed, suggesting that CMiH promotes confined migration. Together, our findings indicate that confined migration induces chromatin changes that regulate cell migration and other functions.
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Affiliation(s)
- Chieh-Ren Hsia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jawuanna McAllister
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ovais Hasan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seoyeon Lee
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Richa Agrawal
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chao-Yuan Chang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Paul Soloway
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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14
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Kalukula Y, Stephens AD, Lammerding J, Gabriele S. Mechanics and functional consequences of nuclear deformations. Nat Rev Mol Cell Biol 2022; 23:583-602. [PMID: 35513718 PMCID: PMC9902167 DOI: 10.1038/s41580-022-00480-z] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 02/08/2023]
Abstract
As the home of cellular genetic information, the nucleus has a critical role in determining cell fate and function in response to various signals and stimuli. In addition to biochemical inputs, the nucleus is constantly exposed to intrinsic and extrinsic mechanical forces that trigger dynamic changes in nuclear structure and morphology. Emerging data suggest that the physical deformation of the nucleus modulates many cellular and nuclear functions. These functions have long been considered to be downstream of cytoplasmic signalling pathways and dictated by gene expression. In this Review, we discuss an emerging perspective on the mechanoregulation of the nucleus that considers the physical connections from chromatin to nuclear lamina and cytoskeletal filaments as a single mechanical unit. We describe key mechanisms of nuclear deformations in time and space and provide a critical review of the structural and functional adaptive responses of the nucleus to deformations. We then consider the contribution of nuclear deformations to the regulation of important cellular functions, including muscle contraction, cell migration and human disease pathogenesis. Collectively, these emerging insights shed new light on the dynamics of nuclear deformations and their roles in cellular mechanobiology.
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Affiliation(s)
- Yohalie Kalukula
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Sylvain Gabriele
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
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15
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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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16
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Mikolajczyk A, Khosrawipour V, Lau H, Li S, Migdal P, Labbé MK, Kielan W, Nicpon J, Stieglitz S, Khosrawipour T. Exploring the potential of taurolidine in inducing mobilization and detachment of colon cancer cells: a preliminary in-vitro study. BMC Pharmacol Toxicol 2022; 23:38. [PMID: 35698168 PMCID: PMC9195453 DOI: 10.1186/s40360-022-00572-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
Background Recently, taurolidine has been intensively studied on a variety of in-vitro cancer cell-lines and first data exhibit encouraging antitumoral effects. While the clinical use of taurolidine is considered, some studies with in-vivo experiments contradict this beneficial effect and even indicate advanced cancer growth. The aim of this study is to further investigate this paradox in-vivo effect by taurolidine and closely analyze the interaction of cancer cells with the surrounding environment following taurolidine exposure. Methods HT-29 (ATCC® HTB-38™) cells were treated with taurolidine at different concentrations and oxaliplatin using an in-vitro model. Morphological changes with respect to increasing taurolidine dosage were visualized and monitored using electron microscopy. Cytotoxicity of the agents as well as extent of cellular detachment by mechanical stress was measured for each substance using a colorimetric MTS assay. Results Both taurolidine and oxaliplatin exhibit cell toxicity on colon cancer cells. Taurolidine reshapes colon cancer cells from round into spheric cells and further induces cluster formation. When exposed to mechanical stress, taurolidine significantly enhances detachment of adherent colon carcinoma cells compared to the control (p < 0.05) and the oxaliplatin group (p < 0.05). This effect is dose dependent. Conclusions Beside its cytotoxic effects, taurolidine could also change mechanical interactions of cancer cells with their environment. Local cancer cell conglomerates could be mechanically mobilized and may cause metastatic growth further downstream. The significance of changes in cellular morphology caused by taurolidine as well as its interaction with the microenvironment must be further addressed in clinical cancer therapies. Further clinical studies are needed to evaluate both the safety and efficacy of taurolidine for the treatment of peritoneal surface malignancies.
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Affiliation(s)
- Agata Mikolajczyk
- Department of Biochemistry and Molecular Biology, Wroclaw University of Environmental and Life Sciences, 50-375, Wroclaw, Wroclaw, Poland
| | - Veria Khosrawipour
- 2nd Department of General Surgery and Surgical Oncology, Wroclaw Medical University, 50-556, Wroclaw, Wroclaw, Poland.,Department of Surgery, University of California Irvine (UCI), Orange, CA, 92868, USA
| | - Hien Lau
- Department of Surgery, University of California Irvine (UCI), Orange, CA, 92868, USA
| | - Shiri Li
- Department of Surgery, Weill Cornell Medical College New York Presbyterian Hospital, New York, 10065, USA
| | - Pawel Migdal
- Department of Environment, Hygiene and Animal Welfare, Wroclaw University of Environmental and Life Sciences, 50-375, Wroclaw, Wroclaw, Poland
| | - Maya Karine Labbé
- School of Dentistry, Wroclaw Medical University, 50-367, Wroclaw, Poland
| | - Wojciech Kielan
- 2nd Department of General Surgery and Surgical Oncology, Wroclaw Medical University, 50-556, Wroclaw, Wroclaw, Poland
| | - Jakub Nicpon
- Department of Surgery, Faculty of Veterinary Sciences, Wroclaw University of Environmental and Life Sciences, 50-375, Wroclaw, Wroclaw, Poland
| | - Sven Stieglitz
- Department Pulmonary Medicine, Petrus-Hospital Wuppertal, University of Witten-Herdecke, 42283, Wuppertal, Wuppertal, Germany
| | - Tanja Khosrawipour
- Department of Surgery (A), University-Hospital Düsseldorf, Moorenstrasse 5, 40225, Düsseldorf, Düsseldorf, Germany. .,Medical faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.
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17
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Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements. Cells 2022; 11:cells11050761. [PMID: 35269383 PMCID: PMC8909793 DOI: 10.3390/cells11050761] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar portion of the genomes. The phenomenon of TE enrichment in constitutive heterochromatin has been proposed to be the consequence of a progressive accumulation of transposable elements caused by both reduced recombination and lack of functional genes in constitutive heterochromatin. However, this view does not take into account classical genetics studies and most recent evidence derived by genomic analyses of heterochromatin in Drosophila and other species. In particular, the lack of functional genes does not seem to be any more a general feature of heterochromatin. Sequencing and annotation of Drosophila melanogaster constitutive heterochromatin have shown that this peculiar genomic compartment contains hundreds of transcriptionally active genes, generally larger in size than that of euchromatic ones. Together, these genes occupy a significant fraction of the genomic territory of heterochromatin. Moreover, transposable elements have been suggested to drive the formation of heterochromatin by recruiting HP1 and repressive chromatin marks. In addition, there are several pieces of evidence that transposable elements accumulation in the heterochromatin might be important for centromere and telomere structure. Thus, there may be more complexity to the relationship between transposable elements and constitutive heterochromatin, in that different forces could drive the dynamic of this phenomenon. Among those forces, preferential transposition may be an important factor. In this article, we present an overview of experimental findings showing cases of transposon enrichment into the heterochromatin and their positive evolutionary interactions with an impact to host genomes.
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18
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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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19
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Chitosan Micro-Grooved Membranes with Increased Asymmetry for the Improvement of the Schwann Cell Response in Nerve Regeneration. Int J Mol Sci 2021; 22:ijms22157901. [PMID: 34360664 PMCID: PMC8348329 DOI: 10.3390/ijms22157901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 01/14/2023] Open
Abstract
Peripheral nerve injuries are a common condition in which a nerve is damaged, affecting more than one million people every year. There are still no efficient therapeutic treatments for these injuries. Artificial scaffolds can offer new opportunities for nerve regeneration applications; in this framework, chitosan is emerging as a promising biomaterial. Here, we set up a simple and effective method for the production of micro-structured chitosan films by solvent casting, with high fidelity in the micro-pattern reproducibility. Three types of chitosan directional micro-grooved patterns, presenting different levels of symmetricity, were developed for application in nerve regenerative medicine: gratings (GR), isosceles triangles (ISO) and scalene triangles (SCA). The directional patterns were tested with a Schwann cell line. The most asymmetric topography (SCA), although it polarized the cell shaping less efficiently, promoted higher cell proliferation and a faster cell migration, both individually and collectively, with a higher directional persistence of motion. Overall, the use of micro-structured asymmetrical directional topographies may be exploited to enhance the nerve regeneration process mediated by chitosan scaffolds.
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20
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Ehlinger C, Mathieu E, Rabineau M, Ball V, Lavalle P, Haikel Y, Vautier D, Kocgozlu L. Insensitivity of dental pulp stem cells migration to substrate stiffness. Biomaterials 2021; 275:120969. [PMID: 34157563 DOI: 10.1016/j.biomaterials.2021.120969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022]
Abstract
Dental pulp stem cells (DPSCs) are a promising cell source for regeneration of dental pulp. Migration is a key event but influence of the microenvironment rigidity (5 kPa at the center of dental pulp to 20 GPa for the dentin) is largely unknown. Mechanical signals are transmitted from the extracellular matrix to the cytoskeleton, to the nuclei, and to the chromatin, potentially regulating gene expression. To identify the microenvironmental influence on migration, we analyzed motility on PDMS substrates with stiffness increasing from 1.5 kPa up to 2.5 MPa. We found that migration speed slightly increases as substrate stiffness decreases in correlation with decreasing focal adhesion size. Motility is relatively insensitive to substrate stiffness, even on a bi-rigidity PDMS substrate where DPSCs migrate without preferential direction. Migration is independent of both myosin II activity and YAP translocation after myosin II inhibition. Additionally, inhibition of Arp2/3 complex leads to significant speed decrease for all rigidities, suggesting contribution of the lamellipodia in the migration. Interestingly, the chromatin architecture remains stable after a 7-days exposure on the PDMS substrates for all rigidity. To design scaffold mimicking dental pulp environment, similar DPSCs migration for all rigidity, leaves field open to choose this mechanical parameter.
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Affiliation(s)
- Claire Ehlinger
- Inserm UMR-S1121, Centre de Recherche en Biomédecine de Strasbourg (CRBS), 1 rue Eugène Boeckel, 67084, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67000, Strasbourg, France; Fédération de Médecine Translationnelle, Strasbourg, France
| | - Eric Mathieu
- Inserm UMR-S1121, Centre de Recherche en Biomédecine de Strasbourg (CRBS), 1 rue Eugène Boeckel, 67084, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67000, Strasbourg, France; Fédération de Médecine Translationnelle, Strasbourg, France
| | - Morgane Rabineau
- Inserm UMR-S1121, Centre de Recherche en Biomédecine de Strasbourg (CRBS), 1 rue Eugène Boeckel, 67084, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67000, Strasbourg, France; Fédération de Médecine Translationnelle, Strasbourg, France
| | - Vincent Ball
- Inserm UMR-S1121, Centre de Recherche en Biomédecine de Strasbourg (CRBS), 1 rue Eugène Boeckel, 67084, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67000, Strasbourg, France; Fédération de Médecine Translationnelle, Strasbourg, France
| | - Philippe Lavalle
- Inserm UMR-S1121, Centre de Recherche en Biomédecine de Strasbourg (CRBS), 1 rue Eugène Boeckel, 67084, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67000, Strasbourg, France; Fédération de Médecine Translationnelle, Strasbourg, France
| | - Youssef Haikel
- Inserm UMR-S1121, Centre de Recherche en Biomédecine de Strasbourg (CRBS), 1 rue Eugène Boeckel, 67084, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67000, Strasbourg, France; Fédération de Médecine Translationnelle, Strasbourg, France
| | - Dominique Vautier
- Inserm UMR-S1121, Centre de Recherche en Biomédecine de Strasbourg (CRBS), 1 rue Eugène Boeckel, 67084, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67000, Strasbourg, France; Fédération de Médecine Translationnelle, Strasbourg, France.
| | - Leyla Kocgozlu
- Inserm UMR-S1121, Centre de Recherche en Biomédecine de Strasbourg (CRBS), 1 rue Eugène Boeckel, 67084, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, 8 rue Sainte Elisabeth, 67000, Strasbourg, France; Fédération de Médecine Translationnelle, Strasbourg, France.
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21
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Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Ritland Politz JC, Tait LJ, Scalzo D, Telling A, Groudine M, Brangwynne CP, Marko JF, Stephens AD. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. eLife 2021; 10:e63972. [PMID: 34106828 PMCID: PMC8233041 DOI: 10.7554/elife.63972] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation controls nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1α (CBX5) is unknown. We used a novel HP1α auxin-inducible degron human cell line to rapidly degrade HP1α. Degradation did not alter transcription, local chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1α is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1αI165E indicate that chromatin crosslinking via HP1α dimerization is critical, while polymer simulations demonstrate the importance of chromatin-chromatin crosslinkers in mechanics. In mitotic chromosomes, HP1α similarly bolsters stiffness while aiding in mitotic alignment and faithful segregation. HP1α is therefore a critical chromatin-crosslinking protein that provides mechanical strength to chromosomes and the nucleus throughout the cell cycle and supports cellular functions.
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Affiliation(s)
- Amy R Strom
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Ronald J Biggs
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Katherine Chiu
- Biology Department, University of Massachusetts AmherstAmherstUnited States
| | - Cameron Herman
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Jimena Collado
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | | | - Leah J Tait
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - David Scalzo
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Agnes Telling
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Mark Groudine
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Clifford P Brangwynne
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Department of Physics and Astronomy, Northwestern UniversityEvanstonUnited States
| | - Andrew D Stephens
- Biology Department, University of Massachusetts AmherstAmherstUnited States
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