1
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Murad HY, Sabol RA, Nyiramana J, Twizeyimana A, Bortz EP, Matossian MD, Hong S, Kelly CA, Burow ME, Bunnell BA, Khismatullin DB. Mechanical Disruption by Focused Ultrasound Re-sensitizes ER+ Breast Cancer Cells to Hormone Therapy. ULTRASOUND IN MEDICINE & BIOLOGY 2024; 50:1885-1892. [PMID: 39277462 DOI: 10.1016/j.ultrasmedbio.2024.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 09/17/2024]
Abstract
OBJECTIVE Tamoxifen is the most used agent to treat estrogen receptor-positive (ER+) breast cancer (BC). While it decreases the risk of cancer recurrence by 50%, many patients develop resistance to this treatment, culminating in highly aggressive disease. Tamoxifen resistance comes from the repression of ER transcriptional activity that switches the cancer cells to proliferation via nonhormonal signaling pathways. Here, we evaluate a potential strategy to overcome tamoxifen resistance by focused ultrasound (FUS), a noninvasive approach for the mechanical excitation of cancer cells. METHODS Resistant and nonresistant ER+ BC cells and xenografts from patients with ER+ BC were treated with tamoxifen, FUS or their combination. The apoptosis, proliferation rate, gene expression and activity of estrogen receptor, and morphological changes were measured in treated cells and tissues. RESULTS FUS caused the mechanical disruption of tamoxifen-resistant BC cells that in turn led to the upregulation of ERα-encoding gene expression and long-term re-sensitization of the cells to tamoxifen. Patient-derived xenografts treated with Tamoxifen and FUS demonstrated a significant reduction in tumor viability and proliferation and a strong structural damage to tumor cells and extracellular matrix. CONCLUSION FUS can improve ER+ BC treatment by re-sensitizing the cancer cells to tamoxifen.
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Affiliation(s)
- Hakm Y Murad
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA, USA
| | - Rachel A Sabol
- Tulane Center for Stem Cell Research and Regenerative Medicine, New Orleans, LA, USA
| | - Jeannette Nyiramana
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA, USA
| | - Aimee Twizeyimana
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA, USA
| | - Emma P Bortz
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA, USA
| | - Margarite D Matossian
- Department of Medicine, Section of Hematology & Medical Oncology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Shirley Hong
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA, USA
| | - Charles A Kelly
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA, USA
| | - Matthew E Burow
- Department of Medicine, Section of Hematology & Medical Oncology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Bruce A Bunnell
- Tulane Center for Stem Cell Research and Regenerative Medicine, New Orleans, LA, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Damir B Khismatullin
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA, USA.
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2
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Trouth A, Veronezi GMB, Ramachandran S. The impact of cell states on heterochromatin dynamics. Biochem J 2024; 481:1519-1533. [PMID: 39422321 DOI: 10.1042/bcj20240139] [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: 08/09/2024] [Revised: 10/04/2024] [Accepted: 10/07/2024] [Indexed: 10/19/2024]
Abstract
Establishing, maintaining, and removing histone post-translational modifications associated with heterochromatin is critical for shaping genomic structure and function as a cell navigates different stages of development, activity, and disease. Dynamic regulation of the repressive chromatin landscape has been documented in several key cell states - germline cells, activated immune cells, actively replicating, and quiescent cells - with notable variations in underlying mechanisms. Here, we discuss the role of cell states of these diverse contexts in directing and maintaining observed chromatin landscapes. These investigations reveal heterochromatin architectures that are highly responsive to the functional context of a cell's existence and, in turn, their contribution to the cell's stable identity.
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Affiliation(s)
- Abby Trouth
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, U.S.A
| | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, U.S.A
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, U.S.A
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, U.S.A
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3
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Pletenev I, Bazarevich M, Zagirova D, Kononkova A, Cherkasov A, Efimova O, Tiukacheva E, Morozov K, Ulianov K, Komkov D, Tvorogova A, Golimbet V, Kondratyev N, Razin S, Khaitovich P, Ulianov S, Khrameeva E. Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome. Nucleic Acids Res 2024; 52:6234-6252. [PMID: 38647066 PMCID: PMC11194087 DOI: 10.1093/nar/gkae271] [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: 11/07/2023] [Revised: 03/21/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024] Open
Abstract
Chromatin architecture regulates gene expression and shapes cellular identity, particularly in neuronal cells. Specifically, polycomb group (PcG) proteins enable establishment and maintenance of neuronal cell type by reorganizing chromatin into repressive domains that limit the expression of fate-determining genes and sustain distinct gene expression patterns in neurons. Here, we map the 3D genome architecture in neuronal and non-neuronal cells isolated from the Wernicke's area of four human brains and comprehensively analyze neuron-specific aspects of chromatin organization. We find that genome segregation into active and inactive compartments is greatly reduced in neurons compared to other brain cells. Furthermore, neuronal Hi-C maps reveal strong long-range interactions, forming a specific network of PcG-mediated contacts in neurons that is nearly absent in other brain cells. These interacting loci contain developmental transcription factors with repressed expression in neurons and other mature brain cells. But only in neurons, they are rich in bivalent promoters occupied by H3K4me3 histone modification together with H3K27me3, which points to a possible functional role of PcG contacts in neurons. Importantly, other layers of chromatin organization also exhibit a distinct structure in neurons, characterized by an increase in short-range interactions and a decrease in long-range ones.
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Affiliation(s)
- Ilya A Pletenev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maria Bazarevich
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Diana R Zagirova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Moscow 127051, Russia
| | - Anna D Kononkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Alexander V Cherkasov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Olga I Efimova
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Eugenia A Tiukacheva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow 141700, Russia
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- CNRS UMR9018, Institut Gustave Roussy, Villejuif 94805, France
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Kirill V Morozov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Kirill A Ulianov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitriy Komkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna V Tvorogova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Vera E Golimbet
- Laboratory of Clinical Genetics, Mental Health Research Center, Moscow 115522, Russia
| | - Nikolay V Kondratyev
- Laboratory of Clinical Genetics, Mental Health Research Center, Moscow 115522, Russia
| | - Sergey V Razin
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Philipp Khaitovich
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Sergey V Ulianov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Ekaterina E Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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4
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Pasternak T, Kircher S, Palme K, Pérez-Pérez JM. Regulation of early seedling establishment and root development in Arabidopsis thaliana by light and carbohydrates. PLANTA 2023; 258:76. [PMID: 37670114 PMCID: PMC10480265 DOI: 10.1007/s00425-023-04226-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/11/2023] [Indexed: 09/07/2023]
Abstract
MAIN CONCLUSION Root development is regulated by sucrose and light during early seedling establishment through changes in the auxin response and chromatin topology. Light is a key environmental signal that regulates plant growth and development. The impact of light on development is primarily analyzed in the above-ground tissues, but little is known about the mechanisms by which light shapes the architecture of underground roots. Our study shows that carbohydrate starvation during skotomorphogenesis is accompanied by compaction of nuclei in the root apical meristem, which prevents cell cycle progression and leads to irreversible root differentiation in the absence of external carbohydrates, as evidenced by the lack of DNA replication and increased numbers of nuclei with specific chromatin characteristics. In these conditions, induction of photomorphogenesis was unable to restore seedling growth, as overall root growth was compromised. The addition of carbohydrates, either locally or systemically by transferring seedlings to sugar-containing medium, led to the induction of adventitious root formation with rapid recovery of seedling growth. Conversely, transferring in vitro carbohydrate-grown seedlings from light to dark transiently promoted cell elongation and significantly reduced root meristem size, but did not primarily affect cell cycle kinetics. We show that, in the presence of sucrose, dark incubation does not affect zonation in the root apical meristem but leads to shortening of the proliferative and transition zones. Sugar starvation led to a rapid increase in lysine demethylation of histone H3 at position K9, which preceded a rapid decline in cell cycle activity and activation of cell differentiation. In conclusion, carbohydrates are required for cell cycle activity, epigenetics reprogramming and for postmitotic cell elongation and auxin-regulated response in the root apical meristem.
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Affiliation(s)
- Taras Pasternak
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, University of Freiburg, 79104 Freiburg, Germany
| | - Stefan Kircher
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, University of Freiburg, 79104 Freiburg, Germany
| | - Klaus Palme
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, University of Freiburg, 79104 Freiburg, Germany
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- ScreenSYSGmbH, Engesserstr. 4a, Freiburg, 79108 Germany
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5
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Estève PO, Sen S, Vishnu US, Ruse C, Chin HG, Pradhan S. Poly ADP-ribosylation of SET8 leads to aberrant H4K20 methylation in mammalian nuclear genome. Commun Biol 2022; 5:1292. [PMID: 36434141 PMCID: PMC9700808 DOI: 10.1038/s42003-022-04241-8] [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: 05/14/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in a cell cycle-dependent manner. Poly ADP-ribosylation on SET8 renders it catalytically compromised, and degradation via ubiquitylation pathway. Knockdown of PARP1 led to an increase of SET8 protein levels, leading to aberrant H4K20me1 and H4K20me3 domains in the genome. H4K20me1 is associated with higher gene transcription levels while the increase of H4K20me3 levels was predominant in DNA repeat elements. Hence, SET8 mediated chromatin remodeling in mammalian cells are modulated by poly ADP-ribosylation by PARP1.
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Affiliation(s)
- Pierre-Olivier Estève
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
| | - Sagnik Sen
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
| | - Udayakumar S. Vishnu
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
| | - Cristian Ruse
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA ,grid.479574.c0000 0004 1791 3172Present Address: Moderna Therapeutics, 200 Technology Square, Cambridge, MA 02139 USA
| | - Hang Gyeong Chin
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
| | - Sriharsa Pradhan
- grid.273406.40000 0004 0376 1796New England Biolabs Inc, 240 County Road, Ipswich, MA 01938 USA
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6
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Karanja F, Sahu S, Weintraub S, Bhandari R, Jaszczak R, Sitt J, Halme A. Ecdysone exerts biphasic control of regenerative signaling, coordinating the completion of regeneration with developmental progression. Proc Natl Acad Sci U S A 2022; 119:e2115017119. [PMID: 35086929 PMCID: PMC8812538 DOI: 10.1073/pnas.2115017119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/13/2021] [Indexed: 12/12/2022] Open
Abstract
In Drosophila melanogaster, loss of regenerative capacity in wing imaginal discs coincides with an increase in systemic levels of the steroid hormone ecdysone, a key coordinator of their developmental progression. Regenerating discs release the relaxin hormone Dilp8 (Drosophila insulin-like peptide 8) to limit ecdysone synthesis and extend the regenerative period. Here, we describe how regenerating tissues produce a biphasic response to ecdysone levels: lower concentrations of ecdysone promote local and systemic regenerative signaling, whereas higher concentrations suppress regeneration through the expression of broad splice isoforms. Ecdysone also promotes the expression of wingless during both regeneration and normal development through a distinct regulatory pathway. This dual role for ecdysone explains how regeneration can still be completed successfully in dilp8- mutant larvae: higher ecdysone levels increase the regenerative activity of tissues, allowing regeneration to reach completion in a shorter time. From these observations, we propose that ecdysone hormone signaling functions to coordinate regeneration with developmental progression.
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Affiliation(s)
- Faith Karanja
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22902
| | - Subhshri Sahu
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22902
| | - Sara Weintraub
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22902
| | - Rajan Bhandari
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22902
| | - Rebecca Jaszczak
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22902
| | - Jason Sitt
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22902
| | - Adrian Halme
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22902
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7
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Impairment of human terminal erythroid differentiation by histone deacetylase 5 deficiency. Blood 2021; 138:1615-1627. [PMID: 34036344 DOI: 10.1182/blood.2020007401] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 04/22/2021] [Indexed: 11/20/2022] Open
Abstract
Histone deacetylases (HDACs) are a group of enzymes catalyzing the removal of acetyl groups from histone and non-histone proteins. HDACs have been shown to play diverse functions in a wide range of biological processes. However, their roles in mammalian erythropoiesis remain to be fully defined. We show here that of the eleven classic HDAC family members, six of them (HDAC 1,2,3 and HDAC 5,6,7) are expressed in human erythroid cells with HDAC5 most significantly up regulated during terminal erythroid differentiation. Knockdown of HDAC5 by either shRNA or siRNA in human CD34+ cells followed by erythroid cell culture led to increased apoptosis, decreased chromatin condensation, and impaired enucleation of erythroblasts. Biochemical analyses revealed that HDAC5 deficiency resulted in activation of p53 in association with increased acetylation of p53. Furthermore, while acetylation of histone 4 (H4) is decreased during normal terminal erythroid differentiation, HDAC5 deficiency led to increased acetylation of H4 (K12) in late stage erythroblasts. This increased acetylation was accompanied by decreased chromatin condensation, implying a role for H4 (K12) deacetylation in chromatin condensation. ATAC-seq and RNA-seq analyses revealed that HDAC5 knockdown leads to increased chromatin accessibility genome wide and global changes in gene expression. Moreover, pharmacological inhibition of HDAC5 by the inhibitor LMK235 also led to increased H4 acetylation, impaired chromatin condensation and enucleation. Taken together, our findings have uncovered previously unrecognized roles and molecular mechanisms of action for HDAC5 in human erythropoiesis. These results may provide insights into understanding the anemia associated with HDAC inhibitor treatment.
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8
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Muhr J, Hagey DW. The cell cycle and differentiation as integrated processes: Cyclins and CDKs reciprocally regulate Sox and Notch to balance stem cell maintenance. Bioessays 2021; 43:e2000285. [PMID: 34008221 DOI: 10.1002/bies.202000285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Development and maintenance of diverse organ systems require context-specific regulation of stem cell behaviour. We hypothesize that this is achieved via reciprocal regulation between the cell cycle machinery and differentiation factors. This idea is supported by the parallel evolutionary emergence of differentiation pathways, cell cycle components and complex multicellularity. In addition, the activities of different cell cycle phases have been found to bias cells towards stem cell maintenance or differentiation. Finally, several direct mechanistic links between these two processes have been established. Here, we focus on interactions between cyclin-CDK complexes and differentiation regulators of the Notch pathway and Sox family of transcription factors within the context of pluripotent and neural stem cells. Thus, this hypothesis formalizes the links between these two processes as an integrated network. Since such factors are common to all stem cells, better understanding their interconnections will help to explain their behaviour in health and disease.
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Affiliation(s)
- Jonas Muhr
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
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9
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Nicolini A, Rossi G, Ferrari P, Carpi A. Minimal residual disease in advanced or metastatic solid cancers: The G0-G1 state and immunotherapy are key to unwinding cancer complexity. Semin Cancer Biol 2020; 79:68-82. [PMID: 32201368 DOI: 10.1016/j.semcancer.2020.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/20/2020] [Accepted: 03/13/2020] [Indexed: 02/07/2023]
Abstract
In the last decade, a large amount of research has focused on elucidating the mechanisms that account for homing disseminated cancer cells (DCCs) from solid tumours to distant organs, which successively progress to overt metastatic disease; this is currently incurable. A better understanding of DCC behaviour is expected to allow detectable metastasis prevention by more effectively targeting 'metastatic seeds before they sprout'. As DCC biology co-evolved with that of the primary tumour, and due to the many similarities between them, the term 'niche' has been borrowed from normal adult stem cells (ASCs) to define the site of DCC metastatic colonisation. Moreover, heterogeneity, survival, protection, stemness and plasticity as well as the prolonged G0-G1 dormant state in the metastatic niche have been the main aspects of intense investigation. Consistent with these findings, in solid cancers with minimal residual disease (MRD), it has been proposed to prolong adjuvant therapy by targeting specific molecular pathway(s) involving DCC dormancy. However, so far, few disappointing clinical data have been reported. As an alternative strategy, because immune-surveillance contributes to the steady state of the DCC population and likely to the G0-G1 state of cancer cells, we have used prolonged immune-modulatory cytostatic chemotherapy, active immune stimulation with an INF-β/IL-2 sequence or drugs inhibiting myeloid-derived suppressor cell (MDSC)/Treg-mediated immune suppression. This strategy, mainly aimed at boosting the immune response, is based on recent findings suggesting the downregulation of immune escape mechanisms as well as other principal hallmarks during the G0-G1 state and/or in MRD. Preliminary clinical and/or laboratory data suggest the efficacy of this strategy in gastrointestinal and some endocrine-dependent cancers. Following this, we propose therapeutic schedules to prevent DCC activation and proliferation in solid cancers at a high risk of relapse or as maintenance therapy in metastatic patients after complete response (CR) to conventional treatment.
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Affiliation(s)
- Andrea Nicolini
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, Italy.
| | - Giuseppe Rossi
- National Research Council (CNR), Epidemiology and Biostatistics Unit, Institute of Clinical Physiology and G. Monasterio Foundation, Pisa, Italy
| | - Paola Ferrari
- Unit of Oncology 1, University Hospital of Pisa, Pisa, Italy
| | - Angelo Carpi
- Department of Clinical and Experimental Medicine, University of Pisa, Italy
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10
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Cheutin T, Cavalli G. The multiscale effects of polycomb mechanisms on 3D chromatin folding. Crit Rev Biochem Mol Biol 2019; 54:399-417. [PMID: 31698957 DOI: 10.1080/10409238.2019.1679082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022]
Abstract
Polycomb group (PcG) proteins silence master regulatory genes required to properly confer cell identity during the development of both Drosophila and mammals. They may act through chromatin compaction and higher-order folding of chromatin inside the cell nucleus. During the last decade, analysis on interphase chromosome architecture discovered self-interacting regions named topologically associated domains (TADs). TADs result from the 3D chromatin folding of a succession of transcribed and repressed epigenomic domains and from loop extrusion mediated by cohesin/CTCF in mammals. Polycomb silenced chromatin constitutes one type of repressed epigenomic domains which form compacted nano-compartments inside cell nuclei. Recruitment of canonical PcG proteins on chromatin relies on initial binding to discrete elements and further spreading into large chromatin domains covered with H3K27me3. Some of these discrete elements have a bivalent nature both in mammals and Drosophila and are dynamically regulated during development. Loops can occur between them, suggesting that their interaction plays both functional and structural roles. Formation of large chromatin domains covered by H3K27me3 seems crucial for PcG silencing and PcG proteins might exert their function through compaction of these domains in both mammals and flies, rather than by directly controlling the nucleosomal accessibility of discrete regulatory elements. In addition, PcG chromatin domains interact over long genomic distances, shaping a higher-order chromatin network. Therefore, PcG silencing might rely on multiscale chromatin folding to maintain cell identity during differentiation.
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Affiliation(s)
- Thierry Cheutin
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
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11
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Ma Y, McKay DJ, Buttitta L. Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells. PLoS Biol 2019; 17:e3000378. [PMID: 31479438 PMCID: PMC6743789 DOI: 10.1371/journal.pbio.3000378] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 09/13/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
During terminal differentiation, most cells exit the cell cycle and enter into a prolonged or permanent G0 in which they are refractory to mitogenic signals. Entry into G0 is usually initiated through the repression of cell cycle gene expression by formation of a transcriptional repressor complex called dimerization partner (DP), retinoblastoma (RB)-like, E2F and MuvB (DREAM). However, when DREAM repressive function is compromised during terminal differentiation, additional unknown mechanisms act to stably repress cycling and ensure robust cell cycle exit. Here, we provide evidence that developmentally programmed, temporal changes in chromatin accessibility at a small subset of critical cell cycle genes act to enforce cell cycle exit during terminal differentiation in the Drosophila melanogaster wing. We show that during terminal differentiation, chromatin closes at a set of pupal wing enhancers for the key rate-limiting cell cycle regulators Cyclin E (cycE), E2F transcription factor 1 (e2f1), and string (stg). This closing coincides with wing cells entering a robust postmitotic state that is strongly refractory to cell cycle reactivation, and the regions that close contain known binding sites for effectors of mitogenic signaling pathways such as Yorkie and Notch. When cell cycle exit is genetically disrupted, chromatin accessibility at cell cycle genes remains unaffected, and the closing of distal enhancers at cycE, e2f1, and stg proceeds independent of the cell cycling status. Instead, disruption of cell cycle exit leads to changes in accessibility and expression of a subset of hormone-induced transcription factors involved in the progression of terminal differentiation. Our results uncover a mechanism that acts as a cell cycle–independent timer to limit the response to mitogenic signaling and aberrant cycling in terminally differentiating tissues. In addition, we provide a new molecular description of the cross talk between cell cycle exit and terminal differentiation during metamorphosis. The longer a cell remains in G0, the more refractory it becomes to re-entering the cell cycle. This study shows that in terminally differentiated cells in vivo, regulatory elements at genes encoding just three key cell cycle regulators (cycE, e2f1 and stg) become inaccessible, limiting their aberrant activation and maintaining a prolonged, robust G0.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Daniel J McKay
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Laura Buttitta
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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12
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Shevelyov YY, Ulianov SV. The Nuclear Lamina as an Organizer of Chromosome Architecture. Cells 2019; 8:E136. [PMID: 30744037 PMCID: PMC6406483 DOI: 10.3390/cells8020136] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/20/2023] Open
Abstract
The nuclear lamina (NL) is a meshwork of lamins and lamin-associated proteins adjoining the inner side of the nuclear envelope. In early embryonic cells, the NL mainly suppresses background transcription, whereas, in differentiated cell types, its disruption affects gene expression more severely. Normally, the NL serves as a backbone for multiple chromatin anchoring sites, thus shaping the spatial organization of chromosomes in the interphase nucleus. However, upon cell senescence, aging, or in some types of terminally differentiated cells and lamin-associated diseases, the loss of NL-chromatin tethering causes drastic alterations in chromosome architecture. Here, we provide an overview of the recent advances in the field of NL-chromatin interactions, focusing on their impact on chromatin positioning, compaction, repression, and spatial organization.
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Affiliation(s)
- Yuri Y. Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia;
| | - Sergey V. Ulianov
- Division of the Regulation of Transcription and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia;
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Cremer T, Cremer M, Cremer C. The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context. BIOCHEMISTRY (MOSCOW) 2018; 83:313-325. [PMID: 29626919 DOI: 10.1134/s000629791804003x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.
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Affiliation(s)
- T Cremer
- Biocenter, Department of Biology II, Ludwig Maximilian University (LMU), Munich, Germany.
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