1
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Hodkinson LJ, Gross J, Schmidt CA, Diaz-Saldana PP, Aoki T, Rieder LE. Sequence reliance of the Drosophila context-dependent transcription factor CLAMP. Genetics 2024; 227:iyae060. [PMID: 38775472 DOI: 10.1093/genetics/iyae060] [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: 01/03/2024] [Accepted: 03/19/2024] [Indexed: 06/04/2024] Open
Abstract
Despite binding similar cis elements in multiple locations, a single transcription factor (TF) often performs context-dependent functions at different loci. How factors integrate cis sequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. The Drosophila context-dependent TF chromatin-linked adaptor for male-specific lethal proteins (CLAMP) targets similar GA-rich cis elements on the X-chromosome and at the histone gene locus but recruits very different, locus-specific factors. We discover that CLAMP leverages information from both cis element and local sequence to perform context-specific functions. Our observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors.
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Affiliation(s)
- Lauren J Hodkinson
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Julia Gross
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Casey A Schmidt
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Tsutomo Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Leila E Rieder
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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2
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Velazquez-Caldelas TE, Zamora-Fuentes JM, Hernandez-Lemus E. Coordinated inflammation and immune response transcriptional regulation in breast cancer molecular subtypes. Front Immunol 2024; 15:1357726. [PMID: 38983850 PMCID: PMC11231215 DOI: 10.3389/fimmu.2024.1357726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
Breast cancer, characterized by its complexity and diversity, presents significant challenges in understanding its underlying biology. In this study, we employed gene co-expression network analysis to investigate the gene composition and functional patterns in breast cancer subtypes and normal breast tissue. Our objective was to elucidate the detailed immunological features distinguishing these tumors at the transcriptional level and to explore their implications for diagnosis and treatment. The analysis identified nine distinct gene module clusters, each representing unique transcriptional signatures within breast cancer subtypes and normal tissue. Interestingly, while some clusters exhibited high similarity in gene composition between normal tissue and certain subtypes, others showed lower similarity and shared traits. These clusters provided insights into the immune responses within breast cancer subtypes, revealing diverse immunological functions, including innate and adaptive immune responses. Our findings contribute to a deeper understanding of the molecular mechanisms underlying breast cancer subtypes and highlight their unique characteristics. The immunological signatures identified in this study hold potential implications for diagnostic and therapeutic strategies. Additionally, the network-based approach introduced herein presents a valuable framework for understanding the complexities of other diseases and elucidating their underlying biology.
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Affiliation(s)
| | | | - Enrique Hernandez-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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3
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Raimer Young HM, Hou PC, Bartosik AR, Atkin ND, Wang L, Wang Z, Ratan A, Zang C, Wang YH. DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity. Nucleic Acids Res 2024; 52:3837-3855. [PMID: 38452213 DOI: 10.1093/nar/gkae164] [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: 08/15/2023] [Revised: 02/03/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding sites in five human cell types. Energetically favorable alternative DNA secondary structures underlie strong CTCF binding sites. These structures coincided with the location of topoisomerase II (TOP2) cleavage complex, suggesting that DNA secondary structure acts as a recognition sequence for TOP2 binding and cleavage at CTCF binding sites. Furthermore, CTCF knockdown significantly increased DSBs at strong CTCF binding sites and at CTCF sites that are located at topologically associated domain (TAD) boundaries. TAD boundary-associated CTCF sites that lost CTCF upon knockdown displayed increased DSBs when compared to the gained sites, and those lost sites are overrepresented with G-quadruplexes, suggesting that the structures act as boundary insulators in the absence of CTCF, and contribute to increased DSBs. These results model how alternative DNA secondary structures facilitate recruitment of TOP2 to CTCF binding sites, providing mechanistic insight into DNA fragility at CTCF binding sites.
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Affiliation(s)
- Heather M Raimer Young
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Pei-Chi Hou
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Anna R Bartosik
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908-0717, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0733, USA
- University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
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4
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Kozlenkov A, Vadukapuram R, Zhou P, Fam P, Wegner M, Dracheva S. Novel method of isolating nuclei of human oligodendrocyte precursor cells reveals substantial developmental changes in gene expression and H3K27ac histone modification. Glia 2024; 72:69-89. [PMID: 37712493 PMCID: PMC10697634 DOI: 10.1002/glia.24462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Oligodendrocyte precursor cells (OPCs) generate differentiated mature oligodendrocytes (MOs) during development. In adult brain, OPCs replenish MOs in adaptive plasticity, neurodegenerative disorders, and after trauma. The ability of OPCs to differentiate to MOs decreases with age and is compromised in disease. Here we explored the cell specific and age-dependent differences in gene expression and H3K27ac histone mark in these two cell types. H3K27ac is indicative of active promoters and enhancers. We developed a novel flow-cytometry-based approach to isolate OPC and MO nuclei from human postmortem brain and profiled gene expression and H3K27ac in adult and infant OPCs and MOs genome-wide. In adult brain, we detected extensive H3K27ac differences between the two cell types with high concordance between gene expression and epigenetic changes. Notably, the expression of genes that distinguish MOs from OPCs appears to be under a strong regulatory control by the H3K27ac modification in MOs but not in OPCs. Comparison of gene expression and H3K27ac between infants and adults uncovered numerous developmental changes in each cell type, which were linked to several biological processes, including cell proliferation and glutamate signaling. A striking example was a subset of histone genes that were highly active in infant samples but fully lost activity in adult brain. Our findings demonstrate a considerable rearrangement of the H3K27ac landscape that occurs during the differentiation of OPCs to MOs and during postnatal development of these cell types, which aligned with changes in gene expression. The uncovered regulatory changes justify further in-depth epigenetic studies of OPCs and MOs in development and disease.
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Affiliation(s)
- Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ramu Vadukapuram
- James J. Peters VA Medical Center, Bronx, NY, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ping Zhou
- James J. Peters VA Medical Center, Bronx, NY, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Fam
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY, USA
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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5
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Hodkinson LJ, Gross J, Schmidt CA, Diaz-Saldana PP, Aoki T, Rieder LE. Sequence reliance of a Drosophila context-dependent transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570650. [PMID: 38106168 PMCID: PMC10723421 DOI: 10.1101/2023.12.07.570650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Despite binding similar cis elements in multiple locations, a single transcription factor often performs context-dependent functions at different loci. How factors integrate cis sequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. The Drosophila context-dependent transcription factor CLAMP targets similar GA-rich cis elements on the X-chromosome and at the histone gene locus but recruits very different, loci-specific factors. We discover that CLAMP leverages information from both cis element and local sequence to perform context-specific functions. Our observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors.
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Affiliation(s)
- Lauren J. Hodkinson
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322 USA
| | - Julia Gross
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, GA 30322 USA
| | | | | | - Tsutomo Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540 USA
| | - Leila E. Rieder
- Department of Biology Emory University, Atlanta, GA 30322 USA
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6
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Geisler MS, Kemp JP, Duronio RJ. Histone locus bodies: a paradigm for how nuclear biomolecular condensates control cell cycle regulated gene expression. Nucleus 2023; 14:2293604. [PMID: 38095604 PMCID: PMC10730174 DOI: 10.1080/19491034.2023.2293604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Histone locus bodies (HLBs) are biomolecular condensates that assemble at replication-dependent (RD) histone genes in animal cells. These genes produce unique mRNAs that are not polyadenylated and instead end in a conserved 3' stem loop critical for coordinated production of histone proteins during S phase of the cell cycle. Several evolutionarily conserved factors necessary for synthesis of RD histone mRNAs concentrate only in the HLB. Moreover, because HLBs are present throughout the cell cycle even though RD histone genes are only expressed during S phase, changes in HLB composition during cell cycle progression drive much of the cell cycle regulation of RD histone gene expression. Thus, HLBs provide a powerful opportunity to determine the cause-and-effect relationships between nuclear body formation and cell cycle regulated gene expression. In this review, we focus on progress during the last five years that has advanced our understanding of HLB biology.
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Affiliation(s)
- Mark S. Geisler
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - James P. Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J. Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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7
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Ghule PN, Boyd JR, Kabala F, Fritz AJ, Bouffard NA, Gao C, Bright K, Macfarlane J, Seward DJ, Pegoraro G, Misteli T, Lian JB, Frietze S, Stein JL, van Wijnen AJ, Stein GS. Spatiotemporal higher-order chromatin landscape of human histone gene clusters at histone locus bodies during the cell cycle in breast cancer progression. Gene 2023; 872:147441. [PMID: 37094694 PMCID: PMC10370284 DOI: 10.1016/j.gene.2023.147441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
Human Histone Locus Bodies (HLBs) are nuclear subdomains comprised of clustered histone genes that are coordinately regulated throughout the cell cycle. We addressed temporal-spatial higher-order genome organization for time-dependent chromatin remodeling at HLBs that supports control of cell proliferation. Proximity distances of specific genomic contacts within histone gene clusters exhibit subtle changes during the G1 phase in MCF10 breast cancer progression model cell lines. This approach directly demonstrates that the two principal histone gene regulatory proteins, HINFP (H4 gene regulator) and NPAT, localize at chromatin loop anchor-points, denoted by CTCF binding, supporting the stringent requirement for histone biosynthesis to package newly replicated DNA as chromatin. We identified a novel enhancer region located ∼ 2 MB distal to histone gene sub-clusters on chromosome 6 that consistently makes genomic contacts with HLB chromatin and is bound by NPAT. During G1 progression the first DNA loops form between one of three histone gene sub-clusters bound by HINFP and the distal enhancer region. Our findings are consistent with a model that the HINFP/NPAT complex controls the formation and dynamic remodeling of higher-order genomic organization of histone gene clusters at HLBs in early to late G1 phase to support transcription of histone mRNAs in S phase.
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Affiliation(s)
- Prachi N Ghule
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Joseph R Boyd
- Department of Biomedical and Health Sciences and University of Vermont Cancer Center, College of Nursing and Health Sciences, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Fleur Kabala
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Nicole A Bouffard
- Microscopy Imaging Center, Center for Biomedical Shared Resources at the University of Vermont, 150 Firestone Building, 149 Beaumont Ave, Burlington, VT 05405, USA
| | - Cong Gao
- Department of Biomedical and Health Sciences and University of Vermont Cancer Center, College of Nursing and Health Sciences, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Kathleen Bright
- Department of Biomedical and Health Sciences and University of Vermont Cancer Center, College of Nursing and Health Sciences, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Jill Macfarlane
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - David J Seward
- Department of Pathology and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, Center for Cancer Research (CCR), National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Seth Frietze
- Department of Biomedical and Health Sciences and University of Vermont Cancer Center, College of Nursing and Health Sciences, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Andre J van Wijnen
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, Larner College of Medicine at the University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.
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Alonso-Gil D, Cuadrado A, Giménez-Llorente D, Rodríguez-Corsino M, Losada A. Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2. Nat Commun 2023; 14:1326. [PMID: 36898992 PMCID: PMC10006224 DOI: 10.1038/s41467-023-36900-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Cohesin organizes the genome through the formation of chromatin loops. NIPBL activates cohesin's ATPase and is essential for loop extrusion, but its requirement for cohesin loading is unclear. Here we have examined the effect of reducing NIPBL levels on the behavior of the two cohesin variants carrying STAG1 or STAG2 by combining a flow cytometry assay to measure chromatin-bound cohesin with analyses of its genome-wide distribution and genome contacts. We show that NIPBL depletion results in increased cohesin-STAG1 on chromatin that further accumulates at CTCF positions while cohesin-STAG2 diminishes genome-wide. Our data are consistent with a model in which NIPBL may not be required for chromatin association of cohesin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 binds chromatin and becomes stabilized at CTCF sites even under low NIPBL levels, but genome folding is severely impaired.
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Affiliation(s)
- Dácil Alonso-Gil
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Daniel Giménez-Llorente
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miriam Rodríguez-Corsino
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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9
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Raths F, Karimzadeh M, Ing N, Martinez A, Yang Y, Qu Y, Lee TY, Mulligan B, Devkota S, Tilley WT, Hickey TE, Wang B, Giuliano AE, Bose S, Goodarzi H, Ray EC, Cui X, Knott SR. The molecular consequences of androgen activity in the human breast. CELL GENOMICS 2023; 3:100272. [PMID: 36950379 PMCID: PMC10025454 DOI: 10.1016/j.xgen.2023.100272] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/20/2022] [Accepted: 01/30/2023] [Indexed: 03/24/2023]
Abstract
Estrogen and progesterone have been extensively studied in the mammary gland, but the molecular effects of androgen remain largely unexplored. Transgender men are recorded as female at birth but identify as male and may undergo gender-affirming androgen therapy to align their physical characteristics and gender identity. Here we perform single-cell-resolution transcriptome, chromatin, and spatial profiling of breast tissues from transgender men following androgen therapy. We find canonical androgen receptor gene targets are upregulated in cells expressing the androgen receptor and that paracrine signaling likely drives sex-relevant androgenic effects in other cell types. We also observe involution of the epithelium and a spatial reconfiguration of immune, fibroblast, and vascular cells, and identify a gene regulatory network associated with androgen-induced fat loss. This work elucidates the molecular consequences of androgen activity in the human breast at single-cell resolution.
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Affiliation(s)
- Florian Raths
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mehran Karimzadeh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Vector Institute, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan Ing
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Martinez
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yoona Yang
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ying Qu
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tian-Yu Lee
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brianna Mulligan
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Suzanne Devkota
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wayne T. Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
| | - Theresa E. Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Bo Wang
- Vector Institute, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | | | - Shikha Bose
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Edward C. Ray
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Transgender Surgery and Health Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiaojiang Cui
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon R.V. Knott
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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10
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Boyd JR, Gao C, Quinn K, Fritz A, Stein J, Stein G, Glass K, Frietze S. peaksat: an R package for ChIP-seq peak saturation analysis. BMC Genomics 2023; 24:43. [PMID: 36698077 PMCID: PMC9878872 DOI: 10.1186/s12864-023-09109-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/02/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Epigenomic profiling assays such as ChIP-seq have been widely used to map the genome-wide enrichment profiles of chromatin-associated proteins and posttranslational histone modifications. Sequencing depth is a key parameter in experimental design and quality control. However, due to variable sequencing depth requirements across experimental conditions, it can be challenging to determine optimal sequencing depth, particularly for projects involving multiple targets or cell types. RESULTS We developed the peaksat R package to provide target read depth estimates for epigenomic experiments based on the analysis of peak saturation curves. We applied peaksat to establish the distinctive read depth requirements for ChIP-seq studies of histone modifications in different cell lines. Using peaksat, we were able to estimate the target read depth required per library to obtain high-quality peak calls for downstream analysis. In addition, peaksat was applied to other sequence-enrichment methods including CUT&RUN and ATAC-seq. CONCLUSION peaksat addresses a need for researchers to make informed decisions about whether their sequencing data has been generated to an adequate depth and subsequently sufficient meaningful peaks, and failing that, how many more reads would be required per library. peaksat is applicable to other sequence-based methods that include calling peaks in their analysis.
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Affiliation(s)
- Joseph R Boyd
- Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA
| | - Kathleen Quinn
- Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA
| | - Andrew Fritz
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Janet Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
- University of Vermont Cancer Center, Burlington, VT, USA
| | - Gary Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
- University of Vermont Cancer Center, Burlington, VT, USA
- Department of Surgery, University of Vermont, Burlington, VT, USA
| | - Karen Glass
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
- University of Vermont Cancer Center, Burlington, VT, USA
- Department of Pharmacology, University of Vermont, Burlington, VT, USA
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, 106 Carrigan Drive, 302 Rowell, VT, 04505, Burlington, USA.
- Department of Biochemistry, University of Vermont, Burlington, VT, USA.
- University of Vermont Cancer Center, Burlington, VT, USA.
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11
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Fritz AJ, Ghule PN, Toor R, Dillac L, Perelman J, Boyd J, Lian JB, Gordon JA, Frietze S, Van Wijnen A, Stein JL, Stein GS. Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle. Crit Rev Eukaryot Gene Expr 2023; 33:85-97. [PMID: 37017672 PMCID: PMC10826887 DOI: 10.1615/critreveukaryotgeneexpr.2022046190] [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] [Indexed: 12/23/2022]
Abstract
Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.
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Affiliation(s)
- Andrew J. Fritz
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Prachi N. Ghule
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Rabail Toor
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Louis Dillac
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Jonah Perelman
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Joseph Boyd
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Johnathan A.R. Gordon
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Seth Frietze
- University of Vermont Cancer Center, Burlington, Vermont, USA
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Andre Van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
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12
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HMGA1 Regulates the Expression of Replication-Dependent Histone Genes and Cell-Cycle in Breast Cancer Cells. Int J Mol Sci 2022; 24:ijms24010594. [PMID: 36614035 PMCID: PMC9820469 DOI: 10.3390/ijms24010594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022] Open
Abstract
Breast cancer (BC) is the primary cause of cancer mortality in women and the triple-negative breast cancer (TNBC) is the most aggressive subtype characterized by poor differentiation and high proliferative properties. High mobility group A1 (HMGA1) is an oncogenic factor involved in the onset and progression of the neoplastic transformation in BC. Here, we unraveled that the replication-dependent-histone (RD-HIST) gene expression is enriched in BC tissues and correlates with HMGA1 expression. We explored the role of HMGA1 in modulating the RD-HIST genes expression in TNBC cells and show that MDA-MB-231 cells, depleted of HMGA1, express low levels of core histones. We show that HMGA1 participates in the activation of the HIST1H4H promoter and that it interacts with the nuclear protein of the ataxia-telangiectasia mutated locus (NPAT), the coordinator of the transcription of the RD-HIST genes. Moreover, we demonstrate that HMGA1 silencing increases the percentage of cells in G0/G1 phase both in TNBC and epirubicin resistant TNBC cells. Moreover, HMGA1 silencing causes an increase in epirubicin IC50 both in parental and epirubicin resistant cells thus suggesting that targeting HMGA1 could affect the efficacy of epirubicin treatment.
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13
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Barutcu AR, Elizalde G, Gonzalez AE, Soni K, Rinn JL, Wagers AJ, Almada AE. Prolonged FOS activity disrupts a global myogenic transcriptional program by altering 3D chromatin architecture in primary muscle progenitor cells. Skelet Muscle 2022; 12:20. [PMID: 35971133 PMCID: PMC9377060 DOI: 10.1186/s13395-022-00303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The AP-1 transcription factor, FBJ osteosarcoma oncogene (FOS), is induced in adult muscle satellite cells (SCs) within hours following muscle damage and is required for effective stem cell activation and muscle repair. However, why FOS is rapidly downregulated before SCs enter cell cycle as progenitor cells (i.e., transiently expressed) remains unclear. Further, whether boosting FOS levels in the proliferating progeny of SCs can enhance their myogenic properties needs further evaluation. METHODS We established an inducible, FOS expression system to evaluate the impact of persistent FOS activity in muscle progenitor cells ex vivo. We performed various assays to measure cellular proliferation and differentiation, as well as uncover changes in RNA levels and three-dimensional (3D) chromatin interactions. RESULTS Persistent FOS activity in primary muscle progenitor cells severely antagonizes their ability to differentiate and form myotubes within the first 2 weeks in culture. RNA-seq analysis revealed that ectopic FOS activity in muscle progenitor cells suppressed a global pro-myogenic transcriptional program, while activating a stress-induced, mitogen-activated protein kinase (MAPK) transcriptional signature. Additionally, we observed various FOS-dependent, chromosomal re-organization events in A/B compartments, topologically associated domains (TADs), and genomic loops near FOS-regulated genes. CONCLUSIONS Our results suggest that elevated FOS activity in recently activated muscle progenitor cells perturbs cellular differentiation by altering the 3D chromosome organization near critical pro-myogenic genes. This work highlights the crucial importance of tightly controlling FOS expression in the muscle lineage and suggests that in states of chronic stress or disease, persistent FOS activity in muscle precursor cells may disrupt the muscle-forming process.
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Affiliation(s)
- A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Present address: Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Gabriel Elizalde
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alfredo E Gonzalez
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kartik Soni
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Present address: BioFrontiers and Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Albert E Almada
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA.
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA.
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14
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Lebeau B, Zhao K, Jangal M, Zhao T, Guerra M, Greenwood CMT, Witcher M. Single base-pair resolution analysis of DNA binding motif with MoMotif reveals an oncogenic function of CTCF zinc-finger 1 mutation. Nucleic Acids Res 2022; 50:8441-8458. [PMID: 35947648 PMCID: PMC9410893 DOI: 10.1093/nar/gkac658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
Defining the impact of missense mutations on the recognition of DNA motifs is highly dependent on bioinformatic tools that define DNA binding elements. However, classical motif analysis tools remain limited in their capacity to identify subtle changes in complex binding motifs between distinct conditions. To overcome this limitation, we developed a new tool, MoMotif, that facilitates a sensitive identification, at the single base-pair resolution, of complex, or subtle, alterations to core binding motifs, discerned from ChIP-seq data. We employed MoMotif to define the previously uncharacterized recognition motif of CTCF zinc-finger 1 (ZF1), and to further define the impact of CTCF ZF1 mutation on its association with chromatin. Mutations of CTCF ZF1 are exclusive to breast cancer and are associated with metastasis and therapeutic resistance, but the underlying mechanisms are unclear. Using MoMotif, we identified an extension of the CTCF core binding motif, necessitating a functional ZF1 to bind appropriately. Using a combination of ChIP-Seq and RNA-Seq, we discover that the inability to bind this extended motif drives an altered transcriptional program associated with the oncogenic phenotypes observed clinically. Our study demonstrates that MoMotif is a powerful new tool for comparative ChIP-seq analysis and characterising DNA-protein contacts.
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Affiliation(s)
| | | | - Maika Jangal
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Tiejun Zhao
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Maria Guerra
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
| | - Celia M T Greenwood
- Correspondence may also be addressed to Celia Greenwood. Tel: +1 514 340 8222 (Ext 28397);
| | - Michael Witcher
- To whom correspondence should be addressed. Tel: +1 514 340 8222 (Ext 23363);
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15
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Fritz AJ, El Dika M, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Cell and Tissue Structure, Function, and Phenotype. Results Probl Cell Differ 2022; 70:339-373. [PMID: 36348114 PMCID: PMC9753575 DOI: 10.1007/978-3-031-06573-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epigenetic gene regulatory mechanisms play a central role in the biological control of cell and tissue structure, function, and phenotype. Identification of epigenetic dysregulation in cancer provides mechanistic into tumor initiation and progression and may prove valuable for a variety of clinical applications. We present an overview of epigenetically driven mechanisms that are obligatory for physiological regulation and parameters of epigenetic control that are modified in tumor cells. The interrelationship between nuclear structure and function is not mutually exclusive but synergistic. We explore concepts influencing the maintenance of chromatin structures, including phase separation, recognition signals, factors that mediate enhancer-promoter looping, and insulation and how these are altered during the cell cycle and in cancer. Understanding how these processes are altered in cancer provides a potential for advancing capabilities for the diagnosis and identification of novel therapeutic targets.
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Affiliation(s)
- Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
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16
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Johnson KS, Hussein S, Chakraborty P, Muruganantham A, Mikhail S, Gonzalez G, Song S, Jolly MK, Toneff MJ, Benton ML, Lin YC, Taube JH. CTCF Expression and Dynamic Motif Accessibility Modulates Epithelial-Mesenchymal Gene Expression. Cancers (Basel) 2022; 14:cancers14010209. [PMID: 35008373 PMCID: PMC8750563 DOI: 10.3390/cancers14010209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) and its reversal, mesenchymal-epithelial transition (MET) drive tissue reorganization critical for early development. In carcinomas, processing through EMT, MET, or partial states promotes migration, invasion, dormancy, and metastatic colonization. As a reversible process, EMT is inherently regulated at epigenetic and epigenomic levels. To understand the epigenomic nature of reversible EMT and its partial states, we characterized chromatin accessibility dynamics, transcriptomic output, protein expression, and cellular phenotypes during stepwise reversible EMT. We find that the chromatin insulating protein machinery, including CTCF, is suppressed and re-expressed, coincident with broad alterations in chromatin accessibility, during EMT/MET, and is lower in triple-negative breast cancer cell lines with EMT features. Through an analysis of chromatin accessibility using ATAC-seq, we identify that early phases of EMT are characterized by enrichment for AP-1 family member binding motifs, but also by a diminished enrichment for CTCF binding motifs. Through a loss-of-function analysis, we demonstrate that the suppression of CTCF alters cellular plasticity, strengthening the epithelial phenotype via the upregulation of epithelial markers E-cadherin/CDH1 and downregulation of N-cadherin/CDH2. Conversely, the upregulation of CTCF leads to the upregulation of EMT gene expression and an increase in mesenchymal traits. These findings are indicative of a role of CTCF in regulating epithelial-mesenchymal plasticity and gene expression.
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Affiliation(s)
- Kelsey S. Johnson
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Shaimaa Hussein
- Baylor Institute for Immunology Research, Baylor Scott & White, Dallas, TX 75246, USA; (S.H.); (Y.C.L.)
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (P.C.); (M.K.J.)
| | - Arvind Muruganantham
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Sheridan Mikhail
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Giovanny Gonzalez
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Shuxuan Song
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (P.C.); (M.K.J.)
| | | | | | - Yin C. Lin
- Baylor Institute for Immunology Research, Baylor Scott & White, Dallas, TX 75246, USA; (S.H.); (Y.C.L.)
| | - Joseph H. Taube
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
- Dan L. Duncan Cancer Center, Houston, TX 76706, USA
- Correspondence:
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17
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Shao Z, Wang T, Zhang M, Jiang Z, Huang S, Zeng P. IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA. PLoS Comput Biol 2021; 17:e1009250. [PMID: 34464378 PMCID: PMC8437300 DOI: 10.1371/journal.pcbi.1009250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/13/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023] Open
Abstract
Effective and powerful survival mediation models are currently lacking. To partly fill such knowledge gap, we particularly focus on the mediation analysis that includes multiple DNA methylations acting as exposures, one gene expression as the mediator and one survival time as the outcome. We proposed IUSMMT (intersection-union survival mixture-adjusted mediation test) to effectively examine the existence of mediation effect by fitting an empirical three-component mixture null distribution. With extensive simulation studies, we demonstrated the advantage of IUSMMT over existing methods. We applied IUSMMT to ten TCGA cancers and identified multiple genes that exhibited mediating effects. We further revealed that most of the identified regions, in which genes behaved as active mediators, were cancer type-specific and exhibited a full mediation from DNA methylation CpG sites to the survival risk of various types of cancers. Overall, IUSMMT represents an effective and powerful alternative for survival mediation analysis; our results also provide new insights into the functional role of DNA methylation and gene expression in cancer progression/prognosis and demonstrate potential therapeutic targets for future clinical practice.
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Affiliation(s)
- Zhonghe Shao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Meng Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhou Jiang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shuiping Huang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, China
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18
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Dozmorov MG, Tyc KM, Sheffield NC, Boyd DC, Olex AL, Reed J, Harrell JC. Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines. Gigascience 2021; 10:6242846. [PMID: 33880552 DOI: 10.1093/gigascience/giab022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/14/2021] [Accepted: 03/09/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Sequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined. RESULTS We evaluated the effect of mouse read removal on the quality of Hi-C data using in silico created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated 2 experimental PDX Hi-C datasets using different library preparation strategies. We evaluated 3 alignment strategies (Direct, Xenome, Combined) and 3 pipelines (Juicer, HiC-Pro, HiCExplorer) on Hi-C data quality. CONCLUSIONS Removal of mouse reads had little-to-no effect on data quality as compared with the results obtained with the Direct alignment strategy. Juicer extracted more valid chromatin interactions for Hi-C matrices, regardless of the mouse read removal strategy. However, the pipeline effect was minimal, while the library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Katarzyna M Tyc
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - David C Boyd
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA.,Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jason Reed
- Virginia Commonwealth University, Massey Cancer Center, Richmond, VA, 23298, USA.,Department of Physics, Virginia Commonwealth University, Richmond, VA 23220, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA
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19
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Du G, Li H, Ding Y, Jiang S, Hong H, Gan J, Wang L, Yang Y, Li Y, Huang X, Sun Y, Tao H, Li Y, Xu X, Zheng Y, Wang J, Bai X, Xu K, Li Y, Jiang Q, Li C, Chen H, Bo X. The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers. Comput Struct Biotechnol J 2021; 19:1684-1693. [PMID: 33897976 PMCID: PMC8050718 DOI: 10.1016/j.csbj.2021.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
The hierarchical levels of TAD boundaries were tissue- and cell type-specific. The TAD nesting level of genes in tumors is different from that in normal tissue. Hierarchical TAD level of genes is related to abnormal transcription and prognosis in cancers.
Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD) structures in cancers and defined a “TAD hierarchical score (TH score)” for genes, which allowed us to assess the TAD nesting level of all genes in a simplified way. We demonstrated that the TAD nesting levels of genes in a tumor differ from those in normal tissue. Furthermore, the hierarchical TAD level dynamics were related to transcriptional changes in cancer, and some of the genes in which the hierarchical level was altered were significantly related to the prognosis of cancer patients. Overall, the results of this study suggest that the folding dynamics of TADs are closely related to transcriptional abnormalities in cancers, emphasizing that the function of hierarchical chromatin organization goes beyond simple chromatin packaging efficiency.
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Affiliation(s)
- Guifang Du
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hao Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yang Ding
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shuai Jiang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hao Hong
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Jingbo Gan
- Center for Statistical Science, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Longteng Wang
- Center for Statistical Science, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuanping Yang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Yinyin Li
- Department of Liver Disease, Fifth Medical Center, Chinese People's Liberation Army General Hospital, Beijing 100069, China
| | - Xin Huang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yu Sun
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Huan Tao
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yaru Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiang Xu
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yang Zheng
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Junting Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xuemei Bai
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Kang Xu
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yaoshen Li
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Qi Jiang
- Tongfang Cloud (Beijing) Technology Co., Ltd, Beijing 100083, China
| | - Cheng Li
- Center for Statistical Science, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hebing Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing 100850, China
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20
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Lee BH, Rhie SK. Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Epigenetics Chromatin 2021; 14:14. [PMID: 33741028 PMCID: PMC7980343 DOI: 10.1186/s13072-021-00390-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetic marks do not change the sequence of DNA but affect gene expression in a cell-type specific manner by altering the activities of regulatory elements. Development of new molecular biology assays, sequencing technologies, and computational approaches enables us to profile the human epigenome in three-dimensional structure genome-wide. Here we describe various molecular biology techniques and bioinformatic tools that have been developed to measure the activities of regulatory elements and their chromatin interactions. Moreover, we list currently available three-dimensional epigenomic data sets that are generated in various human cell types and tissues to assist in the design and analysis of research projects.
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Affiliation(s)
- Beoung Hun Lee
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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21
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Ponte I, Andrés M, Jordan A, Roque A. Towards understanding the Regulation of Histone H1 Somatic Subtypes with OMICs. J Mol Biol 2020; 433:166734. [PMID: 33279581 DOI: 10.1016/j.jmb.2020.166734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
Histone H1 is involved in the regulation of chromatin higher-order structure and compaction. In humans, histone H1 is a multigene family with seven subtypes differentially expressed in somatic cells. Which are the regulatory mechanisms that determine the variability of the H1 complement is a long-standing biological question regarding histone H1. We have used a new approach based on the integration of OMICs data to address this issue. We have examined the 3D-chromatin structure, the binding of transcription factors (TFs), and the expression of somatic H1 genes in human cell lines, using data from public repositories, such as ENCODE. Analysis of Hi-C, ChIP-seq, and RNA-seq data, have revealed that transcriptional control has a greater impact on H1 regulation than previously thought. Somatic H1 genes located in topologically associated domains (TADs) show higher expression than in boundary regions. H1 genes are targeted by a variable number of transcription factors including cell cycle-related TFs, and tissue-specific TFs, suggesting a fine-tuned, subtype-specific transcriptional control. We describe, for the first time, that all H1 somatic subtypes are under transcriptional co-regulation. The replication-independent subtypes, which are encoded in different chromosomes isolated from other histone genes, are also co-regulated with the rest of the somatic H1 genes, indicating that transcriptional co-regulation extends beyond the histone cluster. Transcriptional control and transcriptional co-regulation explain, at least in part, the variability of H1 complement, the fluctuations of H1 subtypes during development, and also the compensatory effects observed, in model systems, after perturbation of one or more H1 subtypes.
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Affiliation(s)
- Inma Ponte
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain
| | - Marta Andrés
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Alicia Roque
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain.
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22
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Fritz AJ, Hong D, Boyd J, Kost J, Finstaad KH, Fitzgerald MP, Hanna S, Abuarqoub AH, Malik M, Bushweller J, Tye C, Ghule P, Gordon J, Zaidi SK, Frietze S, Lian JB, Stein JL, Stein GS. RUNX1 and RUNX2 transcription factors function in opposing roles to regulate breast cancer stem cells. J Cell Physiol 2020; 235:7261-7272. [PMID: 32180230 PMCID: PMC7415511 DOI: 10.1002/jcp.29625] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
Breast cancer stem cells (BCSCs) are competent to initiate tumor formation and growth and refractory to conventional therapies. Consequently BCSCs are implicated in tumor recurrence. Many signaling cascades associated with BCSCs are critical for epithelial-to-mesenchymal transition (EMT). We developed a model system to mechanistically examine BCSCs in basal-like breast cancer using MCF10AT1 FACS sorted for CD24 (negative/low in BCSCs) and CD44 (positive/high in BCSCs). Ingenuity Pathway Analysis comparing RNA-seq on the CD24-/low versus CD24+/high MCF10AT1 indicates that the top activated upstream regulators include TWIST1, TGFβ1, OCT4, and other factors known to be increased in BCSCs and during EMT. The top inhibited upstream regulators include ESR1, TP63, and FAS. Consistent with our results, many genes previously demonstrated to be regulated by RUNX factors are altered in BCSCs. The RUNX2 interaction network is the top significant pathway altered between CD24-/low and CD24+/high MCF10AT1. RUNX1 is higher in expression at the RNA level than RUNX2. RUNX3 is not expressed. While, human-specific quantitative polymerase chain reaction primers demonstrate that RUNX1 and CDH1 decrease in human MCF10CA1a cells that have grown tumors within the murine mammary fat pad microenvironment, RUNX2 and VIM increase. Treatment with an inhibitor of RUNX binding to CBFβ for 5 days followed by a 7-day recovery period results in EMT suggesting that loss of RUNX1, rather than increase in RUNX2, is a driver of EMT in early stage breast cancer. Increased understanding of RUNX regulation on BCSCs and EMT will provide novel insight into therapeutic strategies to prevent recurrence.
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Affiliation(s)
- Andrew J. Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Deli Hong
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Joseph Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Jason Kost
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Kristiaan H. Finstaad
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Mark P. Fitzgerald
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Sebastian Hanna
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Alqassem H. Abuarqoub
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Miles Malik
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - John Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville VA
| | - Coralee Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Prachi Ghule
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Jonathan Gordon
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Sayyed K. Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Seth Frietze
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences
| | - Jane B. Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Janet L. Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Gary S. Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
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23
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Fumagalli MR, Font-Clos F, Milan S, Zapperi S, La Porta CAM. Comparative analysis of metabolic and transcriptomic features of Nothobranchius furzeri. J R Soc Interface 2020; 17:20200217. [PMID: 32603650 PMCID: PMC7423413 DOI: 10.1098/rsif.2020.0217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Some species have a longer lifespan than others, but usually lifespan is correlated with typical body weight. Here, we study the lifetime evolution of the metabolic behaviour of Nothobranchius furzeri, a killifish with an extremely short lifespan with respect to other fishes, even when taking into account rescaling by body weight. Comparison of the gene expression patterns of N. furzeri with those of zebrafish Danio rerio and mouse (Mus musculus) shows that a broad set of metabolic genes and pathways are affected in N. furzeri during ageing in a way that is consistent with a global deregulation of chromatin. Computational analysis of the glycolysis pathway for the three species highlights a rapid increase in the metabolic activity during the lifetime of N. furzeri with respect to the other species. Our results highlight that the unusually short lifespan of N. furzeri is associated with peculiar patterns in the metabolic activities and in chromatin dynamics.
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Affiliation(s)
- Maria Rita Fumagalli
- CNR - Consiglio Nazionale delle Ricerche, Biophysics Institute, Via De Marini 6, Genova, Italy
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Francesc Font-Clos
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
| | - Simone Milan
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Stefano Zapperi
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica della Materia Condensata e di Tecnologie per l’Energia, Via R. Cozzi 53, 20125 Milano, Italy
| | - Caterina A. M. La Porta
- CNR - Consiglio Nazionale delle Ricerche, Biophysics Institute, Via De Marini 6, Genova, Italy
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133 Milano, Italy
- Innovation for Well-Being and Environment (CR-I-WE), University of Milan, Milan, Italy
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24
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Kim JH, Pegoraro AF, Das A, Koehler SA, Ujwary SA, Lan B, Mitchel JA, Atia L, He S, Wang K, Bi D, Zaman MH, Park JA, Butler JP, Lee KH, Starr JR, Fredberg JJ. Unjamming and collective migration in MCF10A breast cancer cell lines. Biochem Biophys Res Commun 2020; 521:706-715. [PMID: 31699371 PMCID: PMC6937379 DOI: 10.1016/j.bbrc.2019.10.188] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/28/2019] [Indexed: 02/08/2023]
Abstract
Each cell comprising an intact, healthy, confluent epithelial layer ordinarily remains sedentary, firmly adherent to and caged by its neighbors, and thus defines an elemental constituent of a solid-like cellular collective [1,2]. After malignant transformation, however, the cellular collective can become fluid-like and migratory, as evidenced by collective motions that arise in characteristic swirls, strands, ducts, sheets, or clusters [3,4]. To transition from a solid-like to a fluid-like phase and thereafter to migrate collectively, it has been recently argued that cells comprising the disordered but confluent epithelial collective can undergo changes of cell shape so as to overcome geometric constraints attributable to the newly discovered phenomenon of cell jamming and the associated unjamming transition (UJT) [1,2,5-9]. Relevance of the jamming concept to carcinoma cells lines of graded degrees of invasive potential has never been investigated, however. Using classical in vitro cultures of six breast cancer model systems, here we investigate structural and dynamical signatures of cell jamming, and the relationship between them [1,2,10,11]. In order of roughly increasing invasive potential as previously reported, model systems examined included MCF10A, MCF10A.Vector; MCF10A.14-3-3ζ; MCF10.ErbB2, MCF10AT; and MCF10CA1a [12-15]. Migratory speed depended on the particular cell line. Unsurprisingly, for example, the MCF10CA1a cell line exhibited much faster migratory speed relative to the others. But unexpectedly, across different cell lines higher speeds were associated with enhanced size of cooperative cell packs in a manner reminiscent of a peloton [9]. Nevertheless, within each of the cell lines evaluated, cell shape and shape variability from cell-to-cell conformed with predicted structural signatures of cell layer unjamming [1]. Moreover, both structure and migratory dynamics were compatible with previous theoretical descriptions of the cell jamming mechanism [2,10,11,16,17]. As such, these findings demonstrate the richness of the cell jamming mechanism, which is now seen to apply across these cancer cell lines but remains poorly understood.
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Affiliation(s)
| | | | - Amit Das
- Northeastern University, MA, USA
| | | | | | - Bo Lan
- Harvard School of Public Health, MA, USA
| | | | - Lior Atia
- Harvard School of Public Health, MA, USA
| | - Shijie He
- Mass General Hospital and Harvard Medical School, USA
| | | | | | | | | | - James P Butler
- Harvard School of Public Health, MA, USA; Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kyu Ha Lee
- The Forsyth Institute, Cambridge, MA, USA
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25
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Zhang CY, Calvo EL, Yang CQ, Liu J, Sang XY, Lin SX. Transcriptome of 17β-hydroxysteroid dehydrogenase type 2 plays both hormone-dependent and hormone-independent roles in MCF-7 breast cancer cells. J Steroid Biochem Mol Biol 2019; 195:105471. [PMID: 31513846 DOI: 10.1016/j.jsbmb.2019.105471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 12/11/2022]
Abstract
Breast cancer is a major cause of cancer-related death for women in western countries. 17β-Hydroxysteroid dehydrogenases (17β-HSDs) play important roles in the last step of sex-hormone activation and the first step of sex-hormone inactivation. 17β-HSD2 is responsible for oxidizing the sex hormones. We used microarray technology to analyze the effect of 17β-HSD2 on the MCF-7 cell transcript profile after knocking down 17β-HSD2. Five hundred forty-two genes were regulated 1.5-fold or higher after treatment with 17β-HSD2 siRNA. Knocking down 17β-HSD2 interrupted nucleosome assembly. Pathway-Act-Network analysis showed that the MAPK and apoptosis signaling pathways were most regulated. In the gene-gene interaction network analysis, UGT2B15, which is involved in hormone metabolism, was the most regulated core gene. FOS, GREB1, and CXCL12 were the most regulated genes, and CXCL12 was related to tumor migration. Following 17β-HSD2 knock-down, the cell viability decreased to 75.9%. The S-phase percentage decreased by 19.4%, the Q2-phase percentage in cell apoptosis testing increased by 1.5 times, and cell migration decreased to 66.0%. These results were consistent with our gene chip analysis and indicated that 17β-HSD2 plays both hormone-dependent and hormone-independent enzymatic roles. In-depth investigations of this enzyme on the genomic level will help clarify its related molecular mechanisms.
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Affiliation(s)
- Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China; Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL) and Department of Molecular Medicine, Québec G1V 4G2, Canada
| | - Ezequiel-Luis Calvo
- Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL) and Department of Molecular Medicine, Québec G1V 4G2, Canada
| | - Chang-Qing Yang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Jie Liu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Xiao-Ye Sang
- Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL) and Department of Molecular Medicine, Québec G1V 4G2, Canada
| | - Sheng-Xiang Lin
- Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL) and Department of Molecular Medicine, Québec G1V 4G2, Canada.
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26
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Garciaz S, N'guyen Dasi L, Finetti P, Chevalier C, Vernerey J, Poplineau M, Platet N, Audebert S, Pophillat M, Camoin L, Bertucci F, Calmels B, Récher C, Birnbaum D, Chabannon C, Vey N, Duprez E. Epigenetic down-regulation of the HIST1 locus predicts better prognosis in acute myeloid leukemia with NPM1 mutation. Clin Epigenetics 2019; 11:141. [PMID: 31606046 PMCID: PMC6790061 DOI: 10.1186/s13148-019-0738-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The epigenetic machinery is frequently altered in acute myeloid leukemia. Focusing on cytogenetically normal (CN) AML, we previously described an abnormal H3K27me3 enrichment covering 70 kb on the HIST1 cluster (6.p22) in CN-AML patient blasts. Here, we further investigate the molecular, functional, and prognosis significance of this epigenetic alteration named H3K27me3 HIST1 in NPM1-mutated (NPM1mut) CN-AML. RESULTS We found that three quarter of the NPM1mut CN-AML patients were H3K27me3 HIST1high. H3K27me3 HIST1high group of patients was associated with a favorable outcome independently of known molecular risk factors. In gene expression profiling, the H3K27me3 HIST1high mark was associated with lower expression of the histone genes HIST1H1D, HIST1H2BG, HIST1H2AE, and HIST1H3F and an upregulation of genes involved in myelomonocytic differentiation. Mass spectrometry analyses confirmed that the linker histone protein H1d, but not the other histone H1 subtypes, was downregulated in the H3K27me3 HIST1high group of patients. H1d knockdown primed ATRA-mediated differentiation of OCI-AML3 and U937 AML cell lines, as assessed on CD11b/CD11c markers, morphological and gene expression analyses. CONCLUSIONS Our data suggest that NPM1mut AML prognosis depends on the epigenetic silencing of the HIST1 cluster and that, among the H3K27me3 silenced histone genes, HIST1H1D plays a role in AML blast differentiation.
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Affiliation(s)
- Sylvain Garciaz
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Lia N'guyen Dasi
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Pascal Finetti
- Predictive Oncology Laboratory, CRCM, Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Christine Chevalier
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France.,Institut Pasteur, G5 Chromatin and Infection, Paris, France
| | - Julien Vernerey
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Nadine Platet
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France
| | - Stéphane Audebert
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Matthieu Pophillat
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Luc Camoin
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - François Bertucci
- Predictive Oncology Laboratory, CRCM, Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Boris Calmels
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Centre d'Investigations Cliniques en Biothérapies, Marseille, France
| | - Christian Récher
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France Université Toulouse III Paul Sabatier, Cancer Research Center of Toulouse, UMR1037-INSERM, ERL5294 CNRS, Toulouse, France
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, CRCM, Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Christian Chabannon
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Centre d'Investigations Cliniques en Biothérapies, Marseille, France
| | - Norbert Vey
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 27 Boulevard Lei Roure, 13273, Marseille Cedex 09, France.
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27
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Dong S, Li W, Wang L, Hu J, Song Y, Zhang B, Ren X, Ji S, Li J, Xu P, Liang Y, Chen G, Lou JT, Yu W. Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker. Cancer Res 2019; 79:6101-6112. [PMID: 31575549 DOI: 10.1158/0008-5472.can-19-1019] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/24/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Cytologic examination is the current "gold standard" for lung cancer diagnosis, however, this has low sensitivity. Here, we identified a typical methylation signature of histone genes in lung cancer by whole-genome DNA methylation analysis, which was validated by The Cancer Genome Atlas (TCGA) lung cancer cohort (n = 907) and was further confirmed in 265 bronchoalveolar lavage fluid samples with specificity and sensitivity of 96.7% and 87.0%, respectively. More importantly, HIST1H4F was universally hypermethylated in all 17 tumor types from TCGA datasets (n = 7,344), which was further validated in nine different types of cancer (n = 243). These results demonstrate that HIST1H4F can function as a universal-cancer-only methylation (UCOM) marker, which may aid in understanding general tumorigenesis and improve screening for early cancer diagnosis. SIGNIFICANCE: These findings identify a new biomarker for cancer detection and show that hypermethylation of histone-related genes seems to persist across cancers.
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Affiliation(s)
- Shihua Dong
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Li
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lin Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baolong Zhang
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoguang Ren
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shimeng Ji
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin Li
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peng Xu
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Liang
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gang Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Tao Lou
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Wenqiang Yu
- Shanghai Public Health Clinical Center and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
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28
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Kent IA, Zhang Q, Katiyar A, Li Y, Pathak S, Dickinson RB, Lele TP. Apical cell protrusions cause vertical deformation of the soft cancer nucleus. J Cell Physiol 2019; 234:20675-20684. [PMID: 31006858 DOI: 10.1002/jcp.28672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 03/21/2019] [Indexed: 01/17/2023]
Abstract
Breast cancer nuclei have highly irregular shapes, which are diagnostic and prognostic markers of breast cancer progression. The mechanisms by which irregular cancer nuclear shapes develop are not well understood. Here we report the existence of vertical, apical cell protrusions in cultured MDA-MB-231 breast cancer cells. Once formed, these protrusions persist over time scales of hours and are associated with vertically upward nuclear deformations. They are absent in normal mammary epithelial cells (MCF-10A cells). Microtubule disruption enriched these protrusions preferentially in MDA-MB-231 cells compared with MCF-10A cells, whereas inhibition of nonmuscle myosin II (NMMII) abolished this enrichment. Dynamic confocal imaging of the vertical cell and nuclear shape revealed that the apical cell protrusions form first, and in response, the nucleus deforms and/or subsequently gets vertically extruded into the apical protrusion. Overexpression of lamin A/C in MDA-MB-231 cells reduced nuclear deformation in apical protrusions. These data highlight the role of mechanical stresses generated by moving boundaries, as well as abnormal nuclear mechanics in the development of abnormal nuclear shapes in breast cancer cells.
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Affiliation(s)
- Ian A Kent
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Qiao Zhang
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Aditya Katiyar
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, Florida
| | - Yuan Li
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Shreya Pathak
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Richard B Dickinson
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Tanmay P Lele
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
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29
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Fritz AJ, Gillis NE, Gerrard DL, Rodriguez PD, Hong D, Rose JT, Ghule PN, Bolf EL, Gordon JA, Tye CE, Boyd JR, Tracy KM, Nickerson JA, van Wijnen AJ, Imbalzano AN, Heath JL, Frietze SE, Zaidi SK, Carr FE, Lian JB, Stein JL, Stein GS. Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer. Genes Chromosomes Cancer 2019; 58:484-499. [PMID: 30873710 DOI: 10.1002/gcc.22731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022] Open
Abstract
Cells establish and sustain structural and functional integrity of the genome to support cellular identity and prevent malignant transformation. In this review, we present a strategic overview of epigenetic regulatory mechanisms including histone modifications and higher order chromatin organization (HCO) that are perturbed in breast cancer onset and progression. Implications for dysfunctions that occur in hormone regulation, cell cycle control, and mitotic bookmarking in breast cancer are considered, with an emphasis on epithelial-to-mesenchymal transition and cancer stem cell activities. The architectural organization of regulatory machinery is addressed within the contexts of translating cancer-compromised genomic organization to advances in breast cancer risk assessment, diagnosis, prognosis, and identification of novel therapeutic targets with high specificity and minimal off target effects.
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Affiliation(s)
- A J Fritz
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - N E Gillis
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - D L Gerrard
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - P D Rodriguez
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - D Hong
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - J T Rose
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - P N Ghule
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - E L Bolf
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J A Gordon
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - C E Tye
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J R Boyd
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - K M Tracy
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J A Nickerson
- Division of Genes and Development of the Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts
| | - A J van Wijnen
- Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic Minnesota, Rochester, Minnesota
| | - A N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - J L Heath
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pediatrics, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - S E Frietze
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - S K Zaidi
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - F E Carr
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J B Lian
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J L Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - G S Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
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30
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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31
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Smith PJ, Darzynkiewicz Z, Errington RJ. Nuclear cytometry and chromatin organization. Cytometry A 2018; 93:771-784. [PMID: 30144297 DOI: 10.1002/cyto.a.23521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022]
Abstract
The nuclear-targeting chemical probe, for the detection and quantification of DNA within cells, has been a mainstay of cytometry-from the colorimetric Feulgen stain to smart fluorescent agents with tuned functionality. The level of nuclear structure and function at which the probe aims to readout, or indeed at which a DNA-targeted drug acts, is shadowed by a wide range of detection modalities and analytical methods. These methods are invariably limited in terms of the resolution attainable versus the volume occupied by targeted chromatin structures. The scalar challenge arises from the need to understand the extent and different levels of compaction of genomic DNA and how such structures can be re-modeled, reported, or even perturbed by both probes and drugs. Nuclear cytometry can report on the complex levels of chromatin order, disorder, disassembly, and even active disruption by probes and drugs. Nuclear probes can report defining features of clinical and therapeutic interest as in NETosis and other cell death processes. New cytometric approaches continue to bridge the scalar challenges of analyzing chromatin organization. Advances in super-resolution microscopy address the resolution and depth of analysis issues in cellular systems. Typical of recent insights into chromatin organization enabled by exploiting a DNA interacting probe is ChromEM tomography (ChromEMT). ChromEMT uses the unique properties of the anthraquinone-based cytometric dye DRAQ5™ to reveal that local and global 3D chromatin structures effect differences in compaction. The focus of this review is nuclear and chromatin cytometry, with linked reference to DNA targeting probes and drugs as exemplified by the anthracenediones.
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Affiliation(s)
- Paul J Smith
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Zbigniew Darzynkiewicz
- Department of Pathology, Brander Cancer Research Institute, New York Medical College, Valhalla, New York, 10595
| | - Rachel J Errington
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
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32
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Zaidi SK, Fritz AJ, Tracy KM, Gordon JA, Tye CE, Boyd J, Van Wijnen AJ, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS. Nuclear organization mediates cancer-compromised genetic and epigenetic control. Adv Biol Regul 2018; 69:1-10. [PMID: 29759441 PMCID: PMC6102062 DOI: 10.1016/j.jbior.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/13/2018] [Accepted: 05/02/2018] [Indexed: 12/19/2022]
Abstract
Nuclear organization is functionally linked to genetic and epigenetic regulation of gene expression for biological control and is modified in cancer. Nuclear organization supports cell growth and phenotypic properties of normal and cancer cells by facilitating physiologically responsive interactions of chromosomes, genes and regulatory complexes at dynamic three-dimensional microenvironments. We will review nuclear structure/function relationships that include: 1. Epigenetic bookmarking of genes by phenotypic transcription factors to control fidelity and plasticity of gene expression as cells enter and exit mitosis; 2. Contributions of chromatin remodeling to breast cancer nuclear morphology, metabolism and effectiveness of chemotherapy; 3. Relationships between fidelity of nuclear organization and metastasis of breast cancer to bone; 4. Dynamic modifications of higher-order inter- and intra-chromosomal interactions in breast cancer cells; 5. Coordinate control of cell growth and phenotype by tissue-specific transcription factors; 6. Oncofetal epigenetic control by bivalent histone modifications that are functionally related to sustaining the stem cell phenotype; and 7. Noncoding RNA-mediated regulation in the onset and progression of breast cancer. The discovery of components to nuclear organization that are functionally related to cancer and compromise gene expression have the potential for translation to innovative cancer diagnosis and targeted therapy.
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Affiliation(s)
- Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Jonathan A Gordon
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Joseph Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Andre J Van Wijnen
- Departments of Orthopedic Surgery, Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Jeffrey A Nickerson
- Department of Pediatrics, UMass Medical School, Worcester, MA, United States
| | - Antony N Imbalzano
- Graduate Program in Cell Biology and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, United States
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
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33
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Sawyer IA, Bartek J, Dundr M. Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing. Semin Cell Dev Biol 2018; 90:94-103. [PMID: 30017905 DOI: 10.1016/j.semcdb.2018.07.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/03/2018] [Indexed: 01/01/2023]
Abstract
Proteins and RNAs inside the cell nucleus are organized into distinct phases, also known as liquid-liquid phase separated (LLPS) droplet organelles or nuclear bodies. These regions exist within the spaces between chromatin-rich regions but their function is tightly linked to gene activity. They include major microscopically-observable structures such as the nucleolus, paraspeckle and Cajal body. The biochemical and assembly factors enriched inside these microenvironments regulate chromatin structure, transcription, and RNA processing, and other important cellular functions. Here, we describe published evidence that suggests nuclear bodies are bona fide LLPS droplet organelles and major regulators of the processes listed above. We also outline an updated "Supply or Sequester" model to describe nuclear body function, in which proteins or RNAs are supplied to surrounding genomic regions or sequestered away from their sites of activity. Finally, we describe recent evidence that suggests these microenvironments are both reflective and drivers of diverse pathophysiological states.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, United States; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jiri Bartek
- Danish Cancer, Society Research Center, Genome Integrity Unit, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, United States.
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34
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Ghule PN, Seward DJ, Fritz AJ, Boyd JR, van Wijnen AJ, Lian JB, Stein JL, Stein GS. Higher order genomic organization and regulatory compartmentalization for cell cycle control at the G1/S-phase transition. J Cell Physiol 2018; 233:6406-6413. [PMID: 29744889 DOI: 10.1002/jcp.26741] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 01/19/2023]
Abstract
Fidelity of histone gene regulation, and ultimately of histone protein biosynthesis, is obligatory for packaging of newly replicated DNA into chromatin. Control of histone gene expression within the 3-dimensional context of nuclear organization is reflected by two well documented observations. DNA replication-dependent histone mRNAs are synthesized at specialized subnuclear domains designated histone locus bodies (HLBs), in response to activation of the growth factor dependent Cyclin E/CDK2/HINFP/NPAT pathway at the G1/S transition in mammalian cells. Complete loss of the histone gene regulatory factors HINFP or NPAT disrupts HLB integrity that is necessary for coordinate control of DNA replication and histone gene transcription. Here we review the molecular histone-related requirements for G1/S-phase progression during the cell cycle. Recently developed experimental strategies, now enable us to explore mechanisms involved in dynamic control of histone gene expression in the context of the temporal (cell cycle) and spatial (HLBs) remodeling of the histone gene loci.
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Affiliation(s)
- Prachi N Ghule
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - David J Seward
- Department of Pathology, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Joseph R Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Andre J van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
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35
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Arias Escayola D, Neugebauer KM. Dynamics and Function of Nuclear Bodies during Embryogenesis. Biochemistry 2018; 57:2462-2469. [PMID: 29473743 DOI: 10.1021/acs.biochem.7b01262] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Nuclear bodies are RNA-rich membraneless organelles in the cell nucleus that concentrate specific sets of nuclear proteins and RNA-protein complexes. Nuclear bodies such as the nucleolus, Cajal body (CB), and the histone locus body (HLB) concentrate factors required for nuclear steps of RNA processing. Formation of these nuclear bodies occurs on genomic loci and is frequently associated with active sites of transcription. Whether nuclear body formation is dependent on a particular gene element, an active process such as transcription, or the nascent RNA present at gene loci is a topic of debate. Recently, this question has been addressed through studies in model organisms and their embryos. The switch from maternally provided RNA and protein to zygotic gene products in early embryos has been well characterized in a variety of organisms. This process, termed maternal-to-zygotic transition, provides an excellent model for studying formation of nuclear bodies before, during, and after the transcriptional activation of the zygotic genome. Here, we review findings in embryos that reveal key principles in the study of the formation and function of nucleoli, CBs, and HLBs. We propose that while particular gene elements may contribute to formation of these nuclear bodies, active transcription promotes maturation of nuclear bodies and efficient RNA processing within them.
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Affiliation(s)
- Dahyana Arias Escayola
- Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
| | - Karla M Neugebauer
- Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
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