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Wu M, Bian X, Hu S, Huang B, Shen J, Du Y, Wang Y, Xu M, Xu H, Yang M, Wu S. A gradient of the HD-Zip regulator Woolly regulates multicellular trichome morphogenesis in tomato. THE PLANT CELL 2024; 36:2375-2392. [PMID: 38470570 PMCID: PMC11132899 DOI: 10.1093/plcell/koae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/02/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Homeodomain (HD) proteins regulate embryogenesis in animals such as the fruit fly (Drosophila melanogaster), often in a concentration-dependent manner. HD-leucine zipper (Zip) IV family genes are unique to plants and often function in the L1 epidermal cell layer. However, our understanding of the roles of HD-Zip IV family genes in plant morphogenesis is limited. In this study, we investigated the morphogenesis of tomato (Solanum lycopersicum) multicellular trichomes, a type of micro-organ in plants. We found that a gradient of the HD-Zip IV regulator Woolly (Wo) coordinates spatially polarized cell division and cell expansion in multicellular trichomes. Moreover, we identified a TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTOR (TCP) transcription factor-encoding gene, SlBRANCHED2a (SlBRC2a), as a key downstream target of Wo that regulates the transition from cell division to cell expansion. High levels of Wo promote cell division in apical trichome cells, whereas in basal trichome cells, Wo mediates a negative feedback loop with SlBRC2a that forces basal cells to enter endoreduplication. The restricted high and low activities of Wo pattern the morphogenesis of tomato multicellular trichomes. These findings provide insights into the functions of HD-Zip IV genes during plant morphogenesis.
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Affiliation(s)
- MinLiang Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - XinXin Bian
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - ShouRong Hu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - BenBen Huang
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - JingYuan Shen
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - YaDi Du
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - YanLi Wang
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - MengYuan Xu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - HuiMin Xu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - MeiNa Yang
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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2
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Koizumi T, Fujimoto A, Kawaguchi H, Kurosaki T, Kitamura A. Stress Granule Dysfunction via Chromophore-Associated Light Inactivation. ACS OMEGA 2024; 9:21298-21306. [PMID: 38764671 PMCID: PMC11097178 DOI: 10.1021/acsomega.4c01469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/21/2024]
Abstract
Stress granules (SGs) are cytoplasmic condensates composed of various proteins and RNAs that protect translation-associated machinery from harmful conditions during stress. However, the method of spatiotemporal inactivation of condensates such as SGs in live cells to study cellular phenotypes is still in the process of being demonstrated. Here, we show that the inactivation of SGs by chromophore-associated light inactivation (CALI) using a genetically encoded red fluorescence protein (SuperNova-Red) as a photosensitizer leads to differences in cell viability during recovery from hyperosmotic stress. CALI delayed the disassembly kinetics of SGs during recovery from hyperosmotic stress. Consequently, CALI could inactivate the SGs, and the cellular fate due to SGs could be analyzed. Furthermore, CALI is an effective spatiotemporal knockdown method for intracellular condensates/aggregates and would contribute to the elucidation of importance of such condensates/aggregates.
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Affiliation(s)
- Takumi Koizumi
- Laboratory
of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Ai Fujimoto
- Laboratory
of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Haruka Kawaguchi
- Laboratory
of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Tsumugi Kurosaki
- Laboratory
of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Akira Kitamura
- Laboratory
of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
- PRIME, Japan
Agency for Medical Research and Development, Chiyoda-ku, Tokyo 100-004, Japan
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3
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Vicars H, Karg T, Mills A, Sullivan W. Acentric chromosome congression and alignment on the metaphase plate via kinetochore-independent forces in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567057. [PMID: 38798431 PMCID: PMC11118298 DOI: 10.1101/2023.11.14.567057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Chromosome congression and alignment on the metaphase plate involves lateral and microtubule plus-end interactions with the kinetochore. Here we take advantage of our ability to efficiently generate a GFP-marked acentric X chromosome fragment in Drosophila neuroblasts to identify forces acting on chromosome arms that drive congression and alignment. We find acentrics efficiently align on the metaphase plate, often more rapidly than kinetochore-bearing chromosomes. Unlike intact chromosomes, the paired sister acentrics oscillate as they move to and reside on the metaphase plate in a plane distinct and significantly further from the main mass of intact chromosomes. Consequently, at anaphase onset acentrics are oriented either parallel or perpendicular to the spindle. Parallel-oriented sisters separate by sliding while those oriented perpendicularly separate via unzipping. This oscillation, together with the fact that in monopolar spindles acentrics are rapidly shunted away from the poles, indicates that distributed plus-end directed forces are primarily responsible for acentric migration. This conclusion is supported by the observation that reduction of EB1 preferentially disrupts acentric alignment. In addition, reduction of Klp3a activity, a gene required for the establishment of pole-to-pole microtubules, preferentially disrupts acentric alignment. Taken together these studies suggest that plus-end forces mediated by the outer pole-to-pole microtubules are primarily responsible for acentric metaphase alignment. Surprisingly, we find that a small fraction of sister acentrics are anti-parallel aligned indicating that the kinetochore is required to ensure parallel alignment of sister chromatids. Finally, we find induction of acentric chromosome fragments results in a global reorganization of the congressed chromosomes into a torus configuration. Article Summary The kinetochore serves as a site for attaching microtubules and allows for successful alignment, separation, and segregation of replicated sister chromosomes during cell division. However, previous studies have revealed that sister chromosomes without kinetochores (acentrics) often align to the metaphase plate, undergo separation and segregation, and are properly transmitted to daughter cells. In this study, we discuss the forces acting on chromosomes, independent of the kinetochore, underlying their successful alignment in early mitosis.
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Flores Cortes E, Saddoris SM, Owens AK, Gibeault R, Depledge DP, Schang LM. Histone H2A variant H2A.B is enriched in transcriptionally active and replicating HSV-1 lytic chromatin. J Virol 2024; 98:e0201523. [PMID: 38451083 PMCID: PMC11019955 DOI: 10.1128/jvi.02015-23] [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: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections but the precise mechanisms are not fully defined. Nucleosomes are dynamic: they slide, breathe, assemble, and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent, whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X, and macroH2A were enhanced in infected cells, whereas those of H2A.B were uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, as well as ectopic and endogenous H2B were assembled into HSV-1 chromatin evenly throughout the genome but canonical H2A was relatively depleted whereas H2A.B was enriched, particularly in the most dynamic viral chromatin. When viral transcription and DNA replication were restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants. IMPORTANCE Herpes simplex virus 1 (HSV-1) transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed epigenetic mechanisms of regulation of HSV-1 transcription have not been fully characterized and may differ from those regulating cellular transcription. Whereas lytic HSV-1 chromatin is unusually dynamic, latent silenced HSV-1 chromatin is not. The mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment of the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding of its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
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Affiliation(s)
- Esteban Flores Cortes
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Sarah M. Saddoris
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Arryn K. Owens
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Rebecca Gibeault
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel P. Depledge
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
| | - Luis M. Schang
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Wu M, Bian X, Huang B, Du Y, Hu S, Wang Y, Shen J, Wu S. HD-Zip proteins modify floral structures for self-pollination in tomato. Science 2024; 384:124-130. [PMID: 38574141 DOI: 10.1126/science.adl1982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024]
Abstract
Cleistogamy is a type of self-pollination that relies on the formation of a stigma-enclosing floral structure. We identify three homeodomain-leucine zipper IV (HD-Zip IV) genes that coordinately promote the formation of interlocking trichomes at the anther margin to unite neighboring anthers, generating a closed anther cone and cleistogamy (flower morphology necessitating strict self-pollination). These HD-Zip IV genes also control style length by regulating the transition from cell division to endoreduplication. The expression of these HD-Zip IV genes and their downstream gene, Style 2.1, was sequentially modified to shape the cleistogamy morphology during tomato evolution and domestication. Our results provide insights into the molecular basis of cleistogamy in modern tomato and suggest targets for improving fruit set and preventing pollen contamination in genetically modified crops.
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Affiliation(s)
- Minliang Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinxin Bian
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Benben Huang
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yadi Du
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shourong Hu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanli Wang
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingyuan Shen
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Wu
- College of Horticulture, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
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Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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7
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Petito V, Di Vincenzo F, Putignani L, Abreu MT, Regenberg B, Gasbarrini A, Scaldaferri F. Extrachromosomal Circular DNA: An Emerging Potential Biomarker for Inflammatory Bowel Diseases? Genes (Basel) 2024; 15:414. [PMID: 38674347 PMCID: PMC11049804 DOI: 10.3390/genes15040414] [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: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Inflammatory bowel disease (IBD) comprising ulcerative colitis and Crohn's disease is a chronic immune-mediated disease which affects the gastrointestinal tract with a relapsing and remitting course, causing lifelong morbidity. IBD pathogenesis is determined by multiple factors including genetics, immune and microbial factors, and environmental factors. Although therapy options are expanding, remission rates are unsatisfiable, and together with the disease course, response to therapy remains unpredictable. Therefore, the identification of biomarkers that are predictive for the disease course and response to therapy is a significant challenge. Extrachromosomal circular DNA (eccDNA) fragments exist in all tissue tested so far. These fragments, ranging in length from a few hundreds of base pairs to mega base pairs, have recently gained more interest due to technological advances. Until now, eccDNA has mainly been studied in relation to cancer due to its ability to act as an amplification site for oncogenes and drug resistance genes. However, eccDNA could also play an important role in inflammation, expressed both locally in the- involved tissue and at distant sites. Here, we review the current evidence on the molecular mechanisms of eccDNA and its role in inflammation and IBD. Additionally, the potential of eccDNA as a tissue or plasma marker for disease severity and/or response to therapy is evaluated.
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Affiliation(s)
- Valentina Petito
- Digestive Disease Center-CEMAD, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Federica Di Vincenzo
- Digestive Disease Center-CEMAD, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Lorenza Putignani
- UOS Microbiomica, UOC Microbiologia e Diagnostica di Immunologia, Dipartimento di Medicina Diagnostica e di Laboratorio, Ospedale Pediatrico “Bambino Gesù” IRCCS, 00146 Rome, Italy
| | - Maria T. Abreu
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Birgitte Regenberg
- Department of Biology, Section for Ecology and Evolution, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Antonio Gasbarrini
- Digestive Disease Center-CEMAD, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Franco Scaldaferri
- Digestive Disease Center-CEMAD, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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8
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Buss JH, Begnini KR, Lenz G. The contribution of asymmetric cell division to phenotypic heterogeneity in cancer. J Cell Sci 2024; 137:jcs261400. [PMID: 38334041 DOI: 10.1242/jcs.261400] [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: 02/10/2024] Open
Abstract
Cells have evolved intricate mechanisms for dividing their contents in the most symmetric way during mitosis. However, a small proportion of cell divisions results in asymmetric segregation of cellular components, which leads to differences in the characteristics of daughter cells. Although the classical function of asymmetric cell division (ACD) in the regulation of pluripotency is the generation of one differentiated daughter cell and one self-renewing stem cell, recent evidence suggests that ACD plays a role in other physiological processes. In cancer, tumor heterogeneity can result from the asymmetric segregation of genetic material and other cellular components, resulting in cell-to-cell differences in fitness and response to therapy. Defining the contribution of ACD in generating differences in key features relevant to cancer biology is crucial to advancing our understanding of the causes of tumor heterogeneity and developing strategies to mitigate or counteract it. In this Review, we delve into the occurrence of asymmetric mitosis in cancer cells and consider how ACD contributes to the variability of several phenotypes. By synthesizing the current literature, we explore the molecular mechanisms underlying ACD, the implications of phenotypic heterogeneity in cancer, and the complex interplay between these two phenomena.
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Affiliation(s)
- Julieti Huch Buss
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
| | - Karine Rech Begnini
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
- Instituto do Cérebro (INSCER), Pontifícia Universidade Católica RS (PUCRS), Porto Alegre, RS 90610-000, Brazil
| | - Guido Lenz
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
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9
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Bueno C, García-Bernal D, Martínez S, Blanquer M, Moraleda JM. The nuclei of human adult stem cells can move within the cell and generate cellular protrusions to contact other cells. Stem Cell Res Ther 2024; 15:32. [PMID: 38321563 PMCID: PMC10848534 DOI: 10.1186/s13287-024-03638-y] [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: 10/03/2023] [Accepted: 01/17/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND The neuronal transdifferentiation of adult bone marrow cells (BMCs) is still considered an artifact based on an alternative explanation of experimental results supporting this phenomenon obtained over decades. However, recent studies have shown that following neural induction, BMCs enter an intermediate cellular state before adopting neural-like morphologies by active neurite extension and that binucleated BMCs can be formed independent of any cell fusion events. These findings provide evidence to reject the idea that BMC neural transdifferentiation is merely an experimental artifact. Therefore, understanding the intermediate states that cells pass through during transdifferentiation is crucial given their potential application in regenerative medicine and disease modelling. METHODS In this study, we examined the functional significance of the variety of morphologies and positioning that cell nuclei of human bone marrow-derived mesenchymal stem cells (hBM-MSCs) can adopt during neural-like differentiation using live-cell nuclear fluorescence labelling, time-lapse microscopy, and confocal microscopy analysis. RESULTS Here, we showed that after neural induction, hBM-MSCs enter an intermediate cellular state in which the nuclei are able to move within the cells, switching shapes and positioning and even generating cellular protrusions as they attempt to contact the cells around them. These findings suggest that changes in nuclear positioning occur because human cell nuclei somehow sense their environment. In addition, we showed the process of direct interactions between cell nuclei, which opens the possibility of a new level of intercellular interaction. CONCLUSIONS The present study advances the understanding of the intermediate stage through which hBM-MSCs pass during neural transdifferentiation, which may be crucial to understanding the mechanisms of these cell conversion processes and eventually harness them for use in regenerative medicine. Importantly, our study provides for the first time evidence that the nuclei of hBM-MSC-derived intermediate cells somehow sense their environment, generating cellular protrusions to contact other cells. In summary, human mesenchymal stromal cells could not only help to increase our understanding of the mechanisms underlying cellular plasticity but also facilitate the exact significance of nuclear positioning in cellular function and in tissue physiology.
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Affiliation(s)
- Carlos Bueno
- Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Faculty of Medicine, Institute of Biomedical Research (IMIB), University of Murcia, 30120, Murcia, Spain.
| | - David García-Bernal
- Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Faculty of Medicine, Institute of Biomedical Research (IMIB), University of Murcia, 30120, Murcia, Spain
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Murcia, 30100, Murcia, Spain
| | - Salvador Martínez
- Instituto de Neurociencias de Alicante (UMH-CSIC), Universidad Miguel Hernandez, 03550, San Juan, Alicante, Spain
- Center of Biomedical Network Research on Mental Health (CIBERSAM), ISCIII, 28029, Madrid, Spain
- Alicante Institute for Health and Biomedical Research (ISABIAL), 03010, Alicante, Spain
| | - Miguel Blanquer
- Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Faculty of Medicine, Institute of Biomedical Research (IMIB), University of Murcia, 30120, Murcia, Spain
| | - José M Moraleda
- Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Faculty of Medicine, Institute of Biomedical Research (IMIB), University of Murcia, 30120, Murcia, Spain
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10
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Matsui S, Granitto M, Buckley M, Ludwig K, Koigi S, Shiley J, Zacharias WJ, Mayhew CN, Lim HW, Iwafuchi M. Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate. Mol Cell 2024; 84:476-489.e10. [PMID: 38211589 PMCID: PMC10872272 DOI: 10.1016/j.molcel.2023.12.007] [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: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Pioneer transcription factors (TFs) regulate cell fate by establishing transcriptionally primed and active states. However, cell fate control requires the coordination of both lineage-specific gene activation and repression of alternative-lineage programs, a process that is poorly understood. Here, we demonstrate that the pioneer TF FOXA coordinates with PRDM1 TF to recruit nucleosome remodeling and deacetylation (NuRD) complexes and Polycomb repressive complexes (PRCs), which establish highly occupied, accessible nucleosome conformation with bivalent epigenetic states, thereby preventing precocious and alternative-lineage gene expression during human endoderm differentiation. Similarly, the pioneer TF OCT4 coordinates with PRDM14 to form bivalent enhancers and repress cell differentiation programs in human pluripotent stem cells, suggesting that this may be a common and critical function of pioneer TFs. We propose that pioneer and PRDM TFs coordinate to safeguard cell fate through epigenetic repression mechanisms.
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Affiliation(s)
- Satoshi Matsui
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan Buckley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Katie Ludwig
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sandra Koigi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joseph Shiley
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - William J Zacharias
- Division of Pulmonary Biology and Pulmonary and Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| | - Makiko Iwafuchi
- Division of Developmental Biology, Center for Stem Cell & Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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11
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Flores E, Saddoris SM, Owens AK, Gibeault R, Depledge DP, Schang LM. Histone H2A variant H2A.B is enriched in transcriptionally active HSV-1 lytic chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573075. [PMID: 38187672 PMCID: PMC10769327 DOI: 10.1101/2023.12.22.573075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections, but the precise mechanisms are not fully defined. Nucleosomes are dynamic; they slide, breathe, assemble and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X and macroH2A were enhanced in infected cells, whereas those of H2A.B uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, ectopic, and endogenous H2B, were assembled into HSV-1 chromatin evenly throughout the genome, but canonical H2A was relatively depleted from the viral chromatin whereas H2A.B was enriched in the most dynamic viral chromatin. When viral transcription was restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency, and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants. Importance HSV-1 transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed mechanisms of regulation of HSV-1 transcription by epigenetics have not been fully characterized and may differ from those regulating cellular transcription. In particular, the lytic HSV-1 chromatin is unusually dynamic, whereas the latent silenced one is not, but the mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment on the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding for its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
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12
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Szelenyi ER, Navarrete JS, Murry AD, Zhang Y, Girven KS, Kuo L, Cline MM, Bernstein MX, Burdyniuk M, Bowler B, Goodwin NL, Juarez B, Zweifel LS, Golden SA. An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single-cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568319. [PMID: 38045271 PMCID: PMC10690249 DOI: 10.1101/2023.11.22.568319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
High-throughput volumetric fluorescent microscopy pipelines can spatially integrate whole-brain structure and function at the foundational level of single-cells. However, conventional fluorescent protein (FP) modifications used to discriminate single-cells possess limited efficacy or are detrimental to cellular health. Here, we introduce a synthetic and non-deleterious nuclear localization signal (NLS) tag strategy, called 'Arginine-rich NLS' (ArgiNLS), that optimizes genetic labeling and downstream image segmentation of single-cells by restricting FP localization near-exclusively in the nucleus through a poly-arginine mechanism. A single N-terminal ArgiNLS tag provides modular nuclear restriction consistently across spectrally separate FP variants. ArgiNLS performance in vivo displays functional conservation across major cortical cell classes, and in response to both local and systemic brain wide AAV administration. Crucially, the high signal-to-noise ratio afforded by ArgiNLS enhances ML-automated segmentation of single-cells due to rapid classifier training and enrichment of labeled cell detection within 2D brain sections or 3D volumetric whole-brain image datasets, derived from both staining-amplified and native signal. This genetic strategy provides a simple and flexible basis for precise image segmentation of genetically labeled single-cells at scale and paired with behavioral procedures.
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Affiliation(s)
- Eric R. Szelenyi
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Jovana S. Navarrete
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
- University of Washington, Graduate Program in Neuroscience, Seattle, WA, USA
| | - Alexandria D. Murry
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Yizhe Zhang
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Kasey S. Girven
- University of Washington, Department of Anesthesiology and Pain Medicine
| | - Lauren Kuo
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington Undergraduate Program in Biochemistry
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Marcella M. Cline
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Mollie X. Bernstein
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
| | | | - Bryce Bowler
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Nastacia L. Goodwin
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
- University of Washington, Graduate Program in Neuroscience, Seattle, WA, USA
| | - Barbara Juarez
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Psychiatry and Behavioral Sciences, Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
- University of Maryland School of Medicine, Department of Neurobiology, Baltimore, MD, USA
| | - Larry S. Zweifel
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Psychiatry and Behavioral Sciences, Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
| | - Sam A. Golden
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
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13
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Joest EF, Tampé R. Design principles for engineering light-controlled antibodies. Trends Biotechnol 2023; 41:1501-1517. [PMID: 37507295 DOI: 10.1016/j.tibtech.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023]
Abstract
Engineered antibodies are essential tools for research and advanced pharmacy. In the development of therapeutics, antibodies are excellent candidates as they offer both target recognition and modulation. Thanks to the latest advances in biotechnology, light-activated antibody fragments can be constructed to control spontaneous antigen interaction with high spatiotemporal precision. To implement conditional antigen binding, several optogenetic and optochemical engineering concepts have recently been developed. Here, we highlight the various strategies and discuss the features of opto-conditional antibodies. Each concept offers intrinsic advantages beneficial to different applications. In summary, the novel design approaches constitute a complementary toolset to promote current and upcoming antibody technologies with ultimate precision.
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Affiliation(s)
- Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany.
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14
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Baglamis S, Sheraton VM, Meijer D, Qian H, Hoebe RA, Lenos KJ, Betjes MA, Betjes MA, Tans S, van Zon J, Vermeulen L, Krawczyk PM. Using picoliter droplet deposition to track clonal competition in adherent and organoid cancer cell cultures. Sci Rep 2023; 13:18832. [PMID: 37914743 PMCID: PMC10620187 DOI: 10.1038/s41598-023-42849-w] [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: 02/12/2023] [Accepted: 09/15/2023] [Indexed: 11/03/2023] Open
Abstract
Clonal growth and competition underlie processes of key relevance in etiology, progression and therapy response across all cancers. Here, we demonstrate a novel experimental approach, based on multi-color, fluorescent tagging of cell nuclei, in combination with picoliter droplet deposition, to study the clonal dynamics in two- and three-dimensional cell cultures. The method allows for the simultaneous visualization and analysis of multiple clones in individual multi-clonal colonies, providing a powerful tool for studying clonal dynamics and identifying clonal populations with distinct characteristics. Results of our experiments validate the utility of the method in studying clonal dynamics in vitro, and reveal differences in key aspects of clonal behavior of different cancer cell lines in monoculture conditions, as well as in co-cultures with stromal fibroblasts.
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Affiliation(s)
- Selami Baglamis
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands
| | - Vivek M Sheraton
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands
- Institute for Advanced Study, University of Amsterdam, 1012 WX, Amsterdam, The Netherlands
| | - Debora Meijer
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Haibin Qian
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Ron A Hoebe
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands
| | - Max A Betjes
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands
| | | | | | | | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands.
- Oncode Institute, 3521 AL, Utrecht, The Netherlands.
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ, Amsterdam, The Netherlands.
| | - Przemek M Krawczyk
- Cancer Center Amsterdam, 1081 HV, Amsterdam, The Netherlands.
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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15
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Donà M, Bradamante G, Bogojevic Z, Gutzat R, Streubel S, Mosiolek M, Dolan L, Mittelsten Scheid O. A versatile CRISPR-based system for lineage tracing in living plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1169-1184. [PMID: 37403571 DOI: 10.1111/tpj.16378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Individual cells give rise to diverse cell lineages during the development of multicellular organisms. Understanding the contribution of these lineages to mature organisms is a central question of developmental biology. Several techniques to document cell lineages have been used, from marking single cells with mutations that express a visible marker to generating molecular bar codes by CRISPR-induced mutations and subsequent single-cell analysis. Here, we exploit the mutagenic activity of CRISPR to allow lineage tracing within living plants with a single reporter. Cas9-induced mutations are directed to correct a frameshift mutation that restores expression of a nuclear fluorescent protein, labelling the initial cell and all progenitor cells with a strong signal without modifying other phenotypes of the plants. Spatial and temporal control of Cas9 activity can be achieved using tissue-specific and/or inducible promoters. We provide proof of principle for the function of lineage tracing in two model plants. The conserved features of the components and the versatile cloning system, allowing for easy exchange of promoters, are expected to make the system widely applicable.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Gabriele Bradamante
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Zorana Bogojevic
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Susanna Streubel
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Liam Dolan
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
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16
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Bok S, Yallowitz AR, Sun J, McCormick J, Cung M, Hu L, Lalani S, Li Z, Sosa BR, Baumgartner T, Byrne P, Zhang T, Morse KW, Mohamed FF, Ge C, Franceschi RT, Cowling RT, Greenberg BH, Pisapia DJ, Imahiyerobo TA, Lakhani S, Ross ME, Hoffman CE, Debnath S, Greenblatt MB. A multi-stem cell basis for craniosynostosis and calvarial mineralization. Nature 2023; 621:804-812. [PMID: 37730988 PMCID: PMC10799660 DOI: 10.1038/s41586-023-06526-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/09/2023] [Indexed: 09/22/2023]
Abstract
Craniosynostosis is a group of disorders of premature calvarial suture fusion. The identity of the calvarial stem cells (CSCs) that produce fusion-driving osteoblasts in craniosynostosis remains poorly understood. Here we show that both physiologic calvarial mineralization and pathologic calvarial fusion in craniosynostosis reflect the interaction of two separate stem cell lineages; a previously identified cathepsin K (CTSK) lineage CSC1 (CTSK+ CSC) and a separate discoidin domain-containing receptor 2 (DDR2) lineage stem cell (DDR2+ CSC) that we identified in this study. Deletion of Twist1, a gene associated with craniosynostosis in humans2,3, solely in CTSK+ CSCs is sufficient to drive craniosynostosis in mice, but the sites that are destined to fuse exhibit an unexpected depletion of CTSK+ CSCs and a corresponding expansion of DDR2+ CSCs, with DDR2+ CSC expansion being a direct maladaptive response to CTSK+ CSC depletion. DDR2+ CSCs display full stemness features, and our results establish the presence of two distinct stem cell lineages in the sutures, with both populations contributing to physiologic calvarial mineralization. DDR2+ CSCs mediate a distinct form of endochondral ossification without the typical haematopoietic marrow formation. Implantation of DDR2+ CSCs into suture sites is sufficient to induce fusion, and this phenotype was prevented by co-transplantation of CTSK+ CSCs. Finally, the human counterparts of DDR2+ CSCs and CTSK+ CSCs display conserved functional properties in xenograft assays. The interaction between these two stem cell populations provides a new biologic interface for the modulation of calvarial mineralization and suture patency.
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Affiliation(s)
- Seoyeon Bok
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alisha R Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jun Sun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason McCormick
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Michelle Cung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lingling Hu
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Sarfaraz Lalani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zan Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Branden R Sosa
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tomas Baumgartner
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Paul Byrne
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Kyle W Morse
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Fatma F Mohamed
- Department of Periodontics, Prevention and Geriatrics, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Chunxi Ge
- Department of Periodontics, Prevention and Geriatrics, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Renny T Franceschi
- Department of Periodontics, Prevention and Geriatrics, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| | - Randy T Cowling
- Division of Cardiovascular Medicine, Department of Medicine, University of California, San Diego, CA, USA
| | - Barry H Greenberg
- Division of Cardiovascular Medicine, Department of Medicine, University of California, San Diego, CA, USA
| | - David J Pisapia
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Imahiyerobo
- Division of Plastic Surgery, Department of Surgery, New York-Presbyterian Hospital and Columbia University Medical Center, New York, NY, USA
| | - Shenela Lakhani
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - M Elizabeth Ross
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Caitlin E Hoffman
- Department of Neurological Surgery, Weill Cornell Medicine and New York-Presbyterian Hospital, New York, NY, USA
| | - Shawon Debnath
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Research Division, Hospital for Special Surgery, New York, NY, USA.
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17
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Ksovreli M, Kachlishvili T, Mtiulishvili T, Dzmanashvili G, Batsatsashvili T, Zurabiani K, Tughushi D, Kantaria T, Nadaraia L, Rusishvili L, Piot O, Terryn C, Tchelidze P, Katsarava R, Kulikova N. Leucine-Based Pseudo-Proteins (LPPs) as Promising Biomaterials: A Study of Cell-Supporting Properties. Polymers (Basel) 2023; 15:3328. [PMID: 37571222 PMCID: PMC10422583 DOI: 10.3390/polym15153328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Scaffold-based systems have become essential in biomedical research, providing the possibility of building in vitro models that can better mimic tissue/organic physiology. A relatively new family of biomimetics-pseudo-proteins (PPs)-can therefore be considered especially promising in this context. Three different artificial leucine-based LPP films were tested in vitro as potential scaffolding materials. In vitro experiments were performed using two types of cells: primary mouse skin fibroblasts and a murine monocyte/macrophages cell line, RAW264.7. Cell adhesion and cell spreading were evaluated according to morphological parameters via scanning electron microscopy (SEM), and they were assessed according to actin cytoskeleton distribution, which was studied via confocal laser microscopy. Cell proliferation was evaluated via an MTT assay. Cell migration was studied using time-lapse microscopy. SEM images for both types of cells demonstrated prominent adhesion and perfect cell spreading on all three LPPs. Analyses of actin cytoskeleton organization revealed a high number of focal adhesions and prominent motility-associated structures. A certain stimulation of cell proliferation was detected in the cases of all three LPPs, and two of them promoted macrophage migration. Overall, our data suggest that the LPPs used in the study can be considered potential cell-friendly scaffolding materials.
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Affiliation(s)
- Mariam Ksovreli
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Tinatin Kachlishvili
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Tevdore Mtiulishvili
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Giorgi Dzmanashvili
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Tatuli Batsatsashvili
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Knarita Zurabiani
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - David Tughushi
- Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Temur Kantaria
- Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Lili Nadaraia
- Institute of Physical Material Science and Materials Technologies, Technical University of Georgia, 0159 Tbilisi, Georgia
- Carl Zeiss Scientific and Education Center, New Vision University, 0159 Tbilisi, Georgia
| | - Levan Rusishvili
- Department of Morphology, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, 0159 Tbilisi, Georgia
| | - Olivier Piot
- BioSpecT Unit, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Christine Terryn
- BioSpecT Unit, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Pavel Tchelidze
- Carl Zeiss Scientific and Education Center, New Vision University, 0159 Tbilisi, Georgia
- Faculty of Healthcare, East European University, 0159 Tbilisi, Georgia
| | - Ramaz Katsarava
- Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, 0159 Tbilisi, Georgia
| | - Nina Kulikova
- Institute of Cellular and Molecular Biology, Agricultural University of Georgia, 0159 Tbilisi, Georgia
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18
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Hung KL, Jones MG, Wong ITL, Lange JT, Luebeck J, Scanu E, He BJ, Brückner L, Li R, González RC, Schmargon R, Dörr JR, Belk JA, Bafna V, Werner B, Huang W, Henssen AG, Mischel PS, Chang HY. Coordinated inheritance of extrachromosomal DNA species in human cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549597. [PMID: 37503111 PMCID: PMC10371175 DOI: 10.1101/2023.07.18.549597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The chromosomal theory of inheritance has dominated human genetics, including cancer genetics. Genes on the same chromosome segregate together while genes on different chromosomes assort independently, providing a fundamental tenet of Mendelian inheritance. Extrachromosomal DNA (ecDNA) is a frequent event in cancer that drives oncogene amplification, dysregulated gene expression and intratumoral heterogeneity, including through random segregation during cell division. Distinct ecDNA sequences, herein termed ecDNA species, can co-exist to facilitate intermolecular cooperation in cancer cells. However, how multiple ecDNA species within a tumor cell are assorted and maintained across somatic cell generations to drive cancer cell evolution is not known. Here we show that cooperative ecDNA species can be coordinately inherited through mitotic co-segregation. Imaging and single-cell analyses show that multiple ecDNAs encoding distinct oncogenes co-occur and are correlated in copy number in human cancer cells. EcDNA species are coordinately segregated asymmetrically during mitosis, resulting in daughter cells with simultaneous copy number gains in multiple ecDNA species prior to any selection. Computational modeling reveals the quantitative principles of ecDNA co-segregation and co-selection, predicting their observed distributions in cancer cells. Finally, we show that coordinated inheritance of ecDNAs enables co-amplification of specialized ecDNAs containing only enhancer elements and guides therapeutic strategies to jointly deplete cooperating ecDNA oncogenes. Coordinated inheritance of ecDNAs confers stability to oncogene cooperation and novel gene regulatory circuits, allowing winning combinations of epigenetic states to be transmitted across cell generations.
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Affiliation(s)
- King L. Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Matthew G. Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joshua T. Lange
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Elisa Scanu
- Department of Mathematics, Queen Mary University of London, London, UK
| | - Britney Jiayu He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Lotte Brückner
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Rocío Chamorro González
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Rachel Schmargon
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jan R. Dörr
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Julia A. Belk
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Weini Huang
- Department of Mathematics, Queen Mary University of London, London, UK
- Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Berlin Institute of Health, Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany
| | - Paul S. Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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19
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Kondratyev M, Pesic A, Ketela T, Stickle N, Beswick C, Shalev Z, Marastoni S, Samadian S, Dvorkin-Gheva A, Sayad A, Bashkurov M, Boasquevisque P, Datti A, Pugh TJ, Virtanen C, Moffat J, Grénman RA, Koritzinsky M, Wouters BG. Identification of acquired Notch3 dependency in metastatic Head and Neck Cancer. Commun Biol 2023; 6:538. [PMID: 37202533 DOI: 10.1038/s42003-023-04828-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 04/11/2023] [Indexed: 05/20/2023] Open
Abstract
During cancer development, tumor cells acquire changes that enable them to invade surrounding tissues and seed metastasis at distant sites. These changes contribute to the aggressiveness of metastatic cancer and interfere with success of therapy. Our comprehensive analysis of "matched" pairs of HNSCC lines derived from primary tumors and corresponding metastatic sites identified several components of Notch3 signaling that are differentially expressed and/or altered in metastatic lines and confer a dependency on this pathway. These components were also shown to be differentially expressed between early and late stages of tumors in a TMA constructed from over 200 HNSCC patients. Finally, we show that suppression of Notch3 improves survival in mice in both subcutaneous and orthotopic models of metastatic HNSCC. Novel treatments targeting components of this pathway may prove effective in targeting metastatic HNSCC cells alone or in combination with conventional therapies.
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Affiliation(s)
- Maria Kondratyev
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada.
| | - Aleksandra Pesic
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Troy Ketela
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Natalie Stickle
- Princess Margaret Cancer Center, Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Christine Beswick
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Zvi Shalev
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Stefano Marastoni
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Soroush Samadian
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Anna Dvorkin-Gheva
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Mikhail Bashkurov
- SMART High-Content Screening facility at Network Biology Collaborative Centre, Toronto, ON, Canada
| | - Pedro Boasquevisque
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Alessandro Datti
- SMART High-Content Screening facility at Network Biology Collaborative Centre, Toronto, ON, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Carl Virtanen
- Princess Margaret Cancer Center, Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | | | - Bradly G Wouters
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada.
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20
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Bedbrook CN, Nath RD, Nagvekar R, Deisseroth K, Brunet A. Rapid and precise genome engineering in a naturally short-lived vertebrate. eLife 2023; 12:80639. [PMID: 37191291 DOI: 10.7554/elife.80639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The African turquoise killifish is a powerful vertebrate system to study complex phenotypes at scale, including aging and age-related disease. Here, we develop a rapid and precise CRISPR/Cas9-mediated knock-in approach in the killifish. We show its efficient application to precisely insert fluorescent reporters of different sizes at various genomic loci in order to drive cell-type- and tissue-specific expression. This knock-in method should allow the establishment of humanized disease models and the development of cell-type-specific molecular probes for studying complex vertebrate biology.
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Affiliation(s)
- Claire N Bedbrook
- Department of Genetics, Stanford University, Stanford, United States
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Ravi D Nath
- Department of Genetics, Stanford University, Stanford, United States
| | - Rahul Nagvekar
- Department of Genetics, Stanford University, Stanford, United States
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, United States
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, United States
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, United States
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21
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Dupont C, Chahar D, Trullo A, Gostan T, Surcis C, Grimaud C, Fisher D, Feil R, Llères D. Evidence for low nanocompaction of heterochromatin in living embryonic stem cells. EMBO J 2023:e110286. [PMID: 37082862 DOI: 10.15252/embj.2021110286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/22/2023] Open
Abstract
Despite advances in the identification of chromatin regulators and genome interactions, the principles of higher-order chromatin structure have remained elusive. Here, we applied FLIM-FRET microscopy to analyse, in living cells, the spatial organisation of nanometre range proximity between nucleosomes, which we called "nanocompaction." Both in naive embryonic stem cells (ESCs) and in ESC-derived epiblast-like cells (EpiLCs), we find that, contrary to expectations, constitutive heterochromatin is much less compacted than bulk chromatin. The opposite was observed in fixed cells. HP1α knockdown increased nanocompaction in living ESCs, but this was overridden by loss of HP1β, indicating the existence of a dynamic HP1-dependent low compaction state in pluripotent cells. Depletion of H4K20me2/3 abrogated nanocompaction, while increased H4K20me3 levels accompanied the nuclear reorganisation during EpiLCs induction. Finally, the knockout of the nuclear cellular-proliferation marker Ki-67 strongly reduced both interphase and mitotic heterochromatin nanocompaction in ESCs. Our data indicate that, contrary to prevailing models, heterochromatin is not highly compacted at the nanoscale but resides in a dynamic low nanocompaction state that depends on H4K20me2/3, the balance between HP1 isoforms, and Ki-67.
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Affiliation(s)
- Claire Dupont
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - Dhanvantri Chahar
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - Antonio Trullo
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - Thierry Gostan
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - Caroline Surcis
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - Charlotte Grimaud
- Institute of Human Genetics (IGH), CNRS, University of Montpellier, Montpellier, France
| | - Daniel Fisher
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - David Llères
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, Montpellier, France
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22
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Hasani H, Sun J, Zhu SI, Rong Q, Willomitzer F, Amor R, McConnell G, Cossairt O, Goodhill GJ. Whole-brain imaging of freely-moving zebrafish. Front Neurosci 2023; 17:1127574. [PMID: 37139528 PMCID: PMC10150962 DOI: 10.3389/fnins.2023.1127574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
One of the holy grails of neuroscience is to record the activity of every neuron in the brain while an animal moves freely and performs complex behavioral tasks. While important steps forward have been taken recently in large-scale neural recording in rodent models, single neuron resolution across the entire mammalian brain remains elusive. In contrast the larval zebrafish offers great promise in this regard. Zebrafish are a vertebrate model with substantial homology to the mammalian brain, but their transparency allows whole-brain recordings of genetically-encoded fluorescent indicators at single-neuron resolution using optical microscopy techniques. Furthermore zebrafish begin to show a complex repertoire of natural behavior from an early age, including hunting small, fast-moving prey using visual cues. Until recently work to address the neural bases of these behaviors mostly relied on assays where the fish was immobilized under the microscope objective, and stimuli such as prey were presented virtually. However significant progress has recently been made in developing brain imaging techniques for zebrafish which are not immobilized. Here we discuss recent advances, focusing particularly on techniques based on light-field microscopy. We also draw attention to several important outstanding issues which remain to be addressed to increase the ecological validity of the results obtained.
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Affiliation(s)
- Hamid Hasani
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, IL, United States
| | - Jipeng Sun
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Shuyu I. Zhu
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Qiangzhou Rong
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Florian Willomitzer
- Wyant College of Optical Sciences, University of Arizona, Tucson, AZ, United States
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gail McConnell
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Oliver Cossairt
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Geoffrey J. Goodhill
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
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23
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McCarthy N, Tie G, Madha S, He R, Kraiczy J, Maglieri A, Shivdasani RA. Smooth muscle contributes to the development and function of a layered intestinal stem cell niche. Dev Cell 2023; 58:550-564.e6. [PMID: 36924771 PMCID: PMC10089980 DOI: 10.1016/j.devcel.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 03/17/2023]
Abstract
Wnt and Rspondin (RSPO) signaling drives proliferation, and bone morphogenetic protein inhibitors (BMPi) impede differentiation, of intestinal stem cells (ISCs). Here, we identify the mouse ISC niche as a complex, multi-layered structure that encompasses distinct mesenchymal and smooth muscle populations. In young and adult mice, diverse sub-cryptal cells provide redundant ISC-supportive factors; few of these are restricted to single cell types. Niche functions refine during postnatal crypt morphogenesis, in part to oppose the dense aggregation of differentiation-promoting BMP+ sub-epithelial myofibroblasts at crypt-villus junctions. Muscularis mucosae, a specialized muscle layer, first appears during this period and supplements neighboring RSPO and BMPi sources. Components of this developing niche are conserved in human fetuses. The in vivo ablation of mouse postnatal smooth muscle increases BMP signaling activity, potently limiting a pre-weaning burst of crypt fission. Thus, distinct and progressively specialized mesenchymal cells together create the milieu that is required to propagate crypts during rapid organ growth and to sustain adult ISCs.
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Affiliation(s)
- Neil McCarthy
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Guodong Tie
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shariq Madha
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Judith Kraiczy
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Adrianna Maglieri
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA.
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24
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Yu J, Vu Le QA, Kim YH, Min J. Detection of Salmonella dublin using the vitellogenin 2 promoter of Daphnia magna. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114735. [PMID: 36907088 DOI: 10.1016/j.ecoenv.2023.114735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/17/2022] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Salmonella is a well-known bacterium that causes waterborne diseases in humans and primates. The need for test models to detect such pathogens and study the responses of such organisms to induced toxic environments is vital. Daphnia magna has been ubiquitously used in aquatic life monitoring for decades because of outstanding properties, such as facile cultivation, short lifespan, and high reproductive capacity. In this study, the proteomic response of D. magna exposed to four Salmonella strains (Salmonella dublin, Salmonella enteritidis, Salmonella enterica, and Salmonella typhimurium) was characterized. As indicated by two-dimensional gel electrophoresis, vitellogenin fused with superoxide dismutase was completely suppressed under exposure to S. dublin. Thus, we evaluated the feasibility of using the vitellogenin 2 gene as a biomarker for S. dublin detection, particularly in providing rapid, visual detection through fluorescent signals. Accordingly, the applicability of the HeLa cells transfected with pBABE-Vtg2B-H2B-GFP as a biomarker for the detection of S. dublin was evaluated, and it was confirmed that the fluorescence signal decreased only when S. dublin was treated. Therefore, such HeLa cells can be utilized as a novel biomarker for detecting S. dublin.
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Affiliation(s)
- Jaeyoung Yu
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Republic of Korea.
| | - Quynh Anh Vu Le
- Department of Bioprocess Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Republic of Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju 28644, Republic of Korea.
| | - Jiho Min
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Republic of Korea; Department of Bioprocess Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Republic of Korea.
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25
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Fu Y, Jia X, Yuan J, Yang Y, Zhang T, Yu Q, Zhou J, Wang T. Fam72a functions as a cell-cycle-controlled gene during proliferation and antagonizes apoptosis through reprogramming PP2A substrates. Dev Cell 2023; 58:398-415.e7. [PMID: 36868233 DOI: 10.1016/j.devcel.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/28/2022] [Accepted: 02/09/2023] [Indexed: 03/05/2023]
Abstract
The cell cycle is key to life. After decades of research, it is unclear whether any parts of this process have yet to be identified. Fam72a is a poorly characterized gene and is evolutionarily conserved across multicellular organisms. Here, we have found that Fam72a is a cell-cycle-regulated gene that is transcriptionally and post-transcriptionally regulated by FoxM1 and APC/C, respectively. Functionally, Fam72a directly binds to tubulin and both the Aα and B56 subunits of PP2A-B56 to modulate tubulin and Mcl1 phosphorylation, which in turn affects the progression of the cell cycle and signaling of apoptosis. Moreover, Fam72a is involved in early responses to chemotherapy, and it efficiently antagonizes various anticancer compounds such as CDK and Bcl2 inhibitors. Thus, Fam72a switches the tumor-suppressive PP2A to be oncogenic by reprogramming its substrates. These findings identify a regulatory axis of PP2A and a protein member in the cell cycle and tumorigenesis regulatory network in human cells.
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Affiliation(s)
- Yuan Fu
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Department of Thoracic Oncology, Tianjin Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin Medical University, Tianjin 300070, China.
| | - Xiaofan Jia
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jinwei Yuan
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yuting Yang
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Teng Zhang
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qiujing Yu
- Department of Immunology and Key Laboratory of Immune Microenvironment and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jun Zhou
- Department of Genetics and Cell Biology, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ting Wang
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Department of Thoracic Oncology, Tianjin Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin Medical University, Tianjin 300070, China.
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26
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May D, Yun S, Gonzalez DG, Park S, Chen Y, Lathrop E, Cai B, Xin T, Zhao H, Wang S, Gonzalez LE, Cockburn K, Greco V. Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo. eLife 2023; 12:83444. [PMID: 36880644 PMCID: PMC10027315 DOI: 10.7554/elife.83444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/06/2023] [Indexed: 03/08/2023] Open
Abstract
Stem cell differentiation requires dramatic changes in gene expression and global remodeling of chromatin architecture. How and when chromatin remodels relative to the transcriptional, behavioral, and morphological changes during differentiation remain unclear, particularly in an intact tissue context. Here, we develop a quantitative pipeline which leverages fluorescently-tagged histones and longitudinal imaging to track large-scale chromatin compaction changes within individual cells in a live mouse. Applying this pipeline to epidermal stem cells, we reveal that cell-to-cell chromatin compaction heterogeneity within the stem cell compartment emerges independent of cell cycle status, and instead is reflective of differentiation status. Chromatin compaction state gradually transitions over days as differentiating cells exit the stem cell compartment. Moreover, establishing live imaging of Keratin-10 (K10) nascent RNA, which marks the onset of stem cell differentiation, we find that Keratin-10 transcription is highly dynamic and largely precedes the global chromatin compaction changes associated with differentiation. Together, these analyses reveal that stem cell differentiation involves dynamic transcriptional states and gradual chromatin rearrangement.
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Affiliation(s)
- Dennis May
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Sangwon Yun
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - David G Gonzalez
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Sangbum Park
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Institute for Quantitative Health Science & Engineering (IQ), Michigan State University, East Lansing, United States
- Division of Dermatology, Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, United States
- Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, East Lansing, United States
| | - Yanbo Chen
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Elizabeth Lathrop
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Biao Cai
- Department of Biostatistics, Yale University School of Public Health, New Haven, United States
| | - Tianchi Xin
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Department of Biostatistics, Yale University School of Public Health, New Haven, United States
| | - Siyuan Wang
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Deparment of Cell Biology, Yale University School of Medicine, New Haven, United States
| | - Lauren E Gonzalez
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Katie Cockburn
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Valentina Greco
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Division of Dermatology, Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, United States
- Departments of Cell Biology and Dermatology, Yale Stem Cell Center, Yale Cancer Center, Yale University School of Medicine, New Haven, United States
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27
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Chen Y, Qiu Q, She J, Yu J. Extrachromosomal circular DNA in colorectal cancer: biogenesis, function and potential as therapeutic target. Oncogene 2023; 42:941-951. [PMID: 36859558 PMCID: PMC10038807 DOI: 10.1038/s41388-023-02640-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
Extrachromosomal circular DNA (ecDNA) has gained renewed interest since its discovery more than half a century ago, emerging as critical driver of tumor evolution. ecDNA is highly prevalent in many types of cancers, including colorectal cancer (CRC), which is one of the most deadly cancers worldwide. ecDNAs play an essential role in regulating oncogene expression, intratumor heterogeneity, and resistance to therapy independently of canonical chromosomal alterations in CRC. Furthermore, the existence of ecDNAs is attributed to the patient's prognosis, since ecDNA-based oncogene amplification adversely affects clinical outcomes. Recent understanding of ecDNA put an extra layer of complexity in the pathogenesis of CRC. In this review, we will discuss the current understanding on mechanisms of biogenesis, and distinctive features of ecDNA in CRC. In addition, we will examine how ecDNAs mediate oncogene overexpression, gene regulation, and topological interactions with active chromatin, which facilitates genetic heterogeneity, accelerates CRC malignancy, and enhances rapid adaptation to therapy resistance. Finally, we will discuss the potential diagnostic and therapeutic implications of ecDNAs in CRC.
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Affiliation(s)
- Yinnan Chen
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Quanpeng Qiu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Junjun She
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Jun Yu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Actin-driven chromosome clustering facilitates fast and complete chromosome capture in mammalian oocytes. Nat Cell Biol 2023; 25:439-452. [PMID: 36732633 PMCID: PMC10014578 DOI: 10.1038/s41556-022-01082-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
Accurate chromosome segregation during meiosis is crucial for reproduction. Human and porcine oocytes transiently cluster their chromosomes before the onset of spindle assembly and subsequent chromosome segregation. The mechanism and function of chromosome clustering are unknown. Here we show that chromosome clustering is required to prevent chromosome losses in the long gap phase between nuclear envelope breakdown and the onset of spindle assembly, and to promote the rapid capture of all chromosomes by the acentrosomal spindle. The initial phase of chromosome clustering is driven by a dynamic network of Formin-2- and Spire-nucleated actin cables. The actin cables form in the disassembling nucleus and migrate towards the nuclear centre, moving the chromosomes centripetally by interacting with their arms and kinetochores as they migrate. A cage of stable microtubule loops drives the late stages of chromosome clustering. Together, our data establish a crucial role for chromosome clustering in accurate progression through meiosis.
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29
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Kho M, Hladyshau S, Tsygankov D, Nie S. Coordinated regulation of Cdc42ep1, actin, and septin filaments during neural crest cell migration. Front Cell Dev Biol 2023; 11:1106595. [PMID: 36923257 PMCID: PMC10009165 DOI: 10.3389/fcell.2023.1106595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
The septin cytoskeleton has been demonstrated to interact with other cytoskeletal components to regulate various cellular processes, including cell migration. However, the mechanisms of how septin regulates cell migration are not fully understood. In this study, we use the highly migratory neural crest cells of frog embryos to examine the role of septin filaments in cell migration. We found that septin filaments are required for the proper migration of neural crest cells by controlling both the speed and the direction of cell migration. We further determined that septin filaments regulate these features of cell migration by interacting with actin stress fibers. In neural crest cells, septin filaments co-align with actin stress fibers, and the loss of septin filaments leads to impaired stability and contractility of actin stress fibers. In addition, we showed that a partial loss of septin filaments leads to drastic changes in the orientations of newly formed actin stress fibers, suggesting that septin filaments help maintain the persistent orientation of actin stress fibers during directed cell migration. Lastly, our study revealed that these activities of septin filaments depend on Cdc42ep1, which colocalizes with septin filaments in the center of neural crest cells. Cdc42ep1 interacts with septin filaments in a reciprocal manner, with septin filaments recruiting Cdc42ep1 to the cell center and Cdc42ep1 supporting the formation of septin filaments.
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Affiliation(s)
- Mary Kho
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Siarhei Hladyshau
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States
| | - Shuyi Nie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States
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30
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Illuminating the Live-Cell Dynamics of Hepatitis B Virus Covalently Closed Circular DNA Using the CRISPR-Tag System. mBio 2023; 14:e0355022. [PMID: 36840581 PMCID: PMC10128046 DOI: 10.1128/mbio.03550-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is the major obstacle to curing chronic hepatitis B (CHB). Current cccDNA detection methods are mostly based on biochemical extraction and bulk measurements. They nevertheless generated a general sketch of its biological features. However, an understanding of the spatiotemporal features of cccDNA is still lacking. To achieve this, we established a system combining CRISPR-Tag and recombinant HBV minicircle technology to visualize cccDNA at single-cell level in real time. Using this system, we found that the observed recombinant cccDNA (rcccDNA) correlated quantitatively with its active transcripts when a low to medium number of foci (<20) are present, but this correlation was lost in cells harboring high copy numbers (≥20) of rcccDNA. The disruption of HBx expression seems to displace cccDNA from the dCas9-accessible region, while HBx complementation restored the number of observable cccDNA foci. This indicated regulation of cccDNA accessibility by HBx. Second, observable HBV and duck HBV (DHBV) cccDNA molecules are substantially lost during cell division, and the remaining ones were distributed randomly to daughter cells. In contrast, Kaposi's sarcoma-associated herpesvirus (KSHV)-derived episomes can be retained in a LANA (latency-associated nuclear antigen)-dependent manner. Last, the dynamics of rcccDNA episomes in nuclei displayed confined diffusion at short time scales, with directional transport over longer time scales. In conclusion, this system enables the study of physiological kinetics of cccDNA at the single-cell level. The differential accessibility of rcccDNA to dCas9 under various physiological conditions may be exploited to elucidate the complex transcriptional and epigenetic regulation of the HBV minichromosome. IMPORTANCE Understanding the formation and maintenance of HBV cccDNA has always been a central issue in the study of HBV pathobiology. However, little progress has been made due to the lack of robust assay systems and its resistance to genetic modification. Here, a live-cell imaging system by grafting CRISPR-Tag into the recombinant cccDNA was established to visualize its molecular behavior in real time. We found that the accessibility of rcccDNA to dCas9-based imaging is related to HBx-regulated mechanisms. We also confirmed the substantial loss of observable rcccDNA in one-round cell division and random distribution of the remaining molecules. Molecular dynamics analysis revealed the confined movement of the rcccDNA episome, suggesting its juxtaposition to chromatin domains. Overall, this novel system offers a unique platform to investigate the intranuclear dynamics of cccDNA within live cells.
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31
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Sano R, Koyama K, Fukuoka N, Ueno H, Yamamura S, Suzuki T. Single-Cell Microarray Chip with Inverse-Tapered Wells to Maintain High Ratio of Cell Trapping. MICROMACHINES 2023; 14:492. [PMID: 36838192 PMCID: PMC9959924 DOI: 10.3390/mi14020492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
A single-cell microarray (SCM) influenced by gravitational force is expected to be one of the simple methods in various fields such as DNA analysis and antibody production. After trapping the cells in the SCM chip, it is necessary to remove the liquid from the SCM to wash away the un-trapped cells on the chip and treat the reagents for analysis. The flow generated during this liquid exchange causes the trapped cells to drop out of conventional vertical wells. In this study, we propose an inverse-tapered well to keep trapped cells from escaping from the SCM. The wells with tapered side walls have a reduced force of flow toward the opening, which prevents trapped cells from escaping. The proposed SCM chip was fabricated using 3D photolithography and polydimethylsiloxane molding techniques. In the trapping experiment using HeLa cells, the cell residual rate increased more than two-fold for the SCM chip with the inverse-tapered well with a taper angle of 30° compared to that for the conventional vertical SCM chip after multiple rounds of liquid exchanges. The proposed well structure increases the number of trapped cells and decreases the cell dropout rate to improve the efficiency of cellular analysis.
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Affiliation(s)
- Ryota Sano
- Division of Mechanical Science and Technology, Gunma University, Kiryu 376-8515, Japan
| | - Kentaro Koyama
- Division of Mechanical Science and Technology, Gunma University, Kiryu 376-8515, Japan
| | - Narumi Fukuoka
- Division of Mechanical Science and Technology, Gunma University, Kiryu 376-8515, Japan
| | - Hidetaka Ueno
- Center for Advanced Medical Engineering Research & Development (CAMED), Kobe University, Kobe 650-0047, Japan
| | - Shohei Yamamura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu 761-0395, Japan
| | - Takaaki Suzuki
- Division of Mechanical Science and Technology, Gunma University, Kiryu 376-8515, Japan
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32
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Cotner M, Meng S, Jost T, Gardner A, De Santiago C, Brock A. Integration of quantitative methods and mathematical approaches for the modeling of cancer cell proliferation dynamics. Am J Physiol Cell Physiol 2023; 324:C247-C262. [PMID: 36503241 PMCID: PMC9886359 DOI: 10.1152/ajpcell.00185.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
Physiological processes rely on the control of cell proliferation, and the dysregulation of these processes underlies various pathological conditions, including cancer. Mathematical modeling can provide new insights into the complex regulation of cell proliferation dynamics. In this review, we first examine quantitative experimental approaches for measuring cell proliferation dynamics in vitro and compare the various types of data that can be obtained in these settings. We then explore the toolbox of common mathematical modeling frameworks that can describe cell behavior, dynamics, and interactions of proliferation. We discuss how these wet-laboratory studies may be integrated with different mathematical modeling approaches to aid the interpretation of the results and to enable the prediction of cell behaviors, specifically in the context of cancer.
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Affiliation(s)
- Michael Cotner
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Sarah Meng
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Tyler Jost
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Andrea Gardner
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Carolina De Santiago
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas
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33
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Chiu W, Schepers J, Francken T, Vangeel L, Abbasi K, Jochmans D, De Jonghe S, Thibaut HJ, Thiel V, Neyts J, Laporte M, Leyssen P. Development of a robust and convenient dual-reporter high-throughput screening assay for SARS-CoV-2 antiviral drug discovery. Antiviral Res 2023; 210:105506. [PMID: 36565756 PMCID: PMC9767876 DOI: 10.1016/j.antiviral.2022.105506] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Massive efforts on both vaccine development and antiviral research were launched to combat the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We contributed, amongst others, by the development of a high-throughput screening (HTS) antiviral assay against SARS-CoV-2 using a fully automated, high-containment robot system. Here, we describe the development of this novel, convenient and phenotypic dual-reporter virus-cell-based high-content imaging assay using the A549+hACE2+TMPRSS2_mCherry reporter lung carcinoma cell line and an ancestral SARS-CoV-2_Wuhan_mNeonGreen reporter virus. Briefly, by means of clonal selection, a host cell subclone was selected that (i) efficiently supports replication of the reporter virus with high expression, upon infection, of the NeonGreen fluorescent reporter protein, (ii) that is not affected by virus-induced cytopathogenic effects and, (iii) that expresses a strong fluorescent mCherry signal in the nucleus. The selected clone matched these criteria with an infection rate on average of 75% with limited cell death. The average (R)Z'-factors of the assay plates were all >0.8, which indicates a robust assay suitable for HTS purposes. A selection of reference compounds that inhibits SARS-CoV-2 replication in vitro were used to validate this novel dual-reporter assay and confirms the data reported in the literature. This assay is a convenient and powerful tool for HTS of large compound libraries against SARS-CoV-2.
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Affiliation(s)
- Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Joost Schepers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Thibault Francken
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Kayvan Abbasi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Gaston Geenslaan 2, 3001, Leuven, Belgium
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Manon Laporte
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium.
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34
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Henke K, Farmer DT, Niu X, Kraus JM, Galloway JL, Youngstrom DW. Genetically engineered zebrafish as models of skeletal development and regeneration. Bone 2023; 167:116611. [PMID: 36395960 PMCID: PMC11080330 DOI: 10.1016/j.bone.2022.116611] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Zebrafish (Danio rerio) are aquatic vertebrates with significant homology to their terrestrial counterparts. While zebrafish have a centuries-long track record in developmental and regenerative biology, their utility has grown exponentially with the onset of modern genetics. This is exemplified in studies focused on skeletal development and repair. Herein, the numerous contributions of zebrafish to our understanding of the basic science of cartilage, bone, tendon/ligament, and other skeletal tissues are described, with a particular focus on applications to development and regeneration. We summarize the genetic strengths that have made the zebrafish a powerful model to understand skeletal biology. We also highlight the large body of existing tools and techniques available to understand skeletal development and repair in the zebrafish and introduce emerging methods that will aid in novel discoveries in skeletal biology. Finally, we review the unique contributions of zebrafish to our understanding of regeneration and highlight diverse routes of repair in different contexts of injury. We conclude that zebrafish will continue to fill a niche of increasing breadth and depth in the study of basic cellular mechanisms of skeletal biology.
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Affiliation(s)
- Katrin Henke
- Department of Orthopaedics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - D'Juan T Farmer
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA.
| | - Xubo Niu
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Jessica M Kraus
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel W Youngstrom
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
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35
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Chiu LY, Sun Q, Zenke FT, Blaukat A, Vassilev LT. Selective ATM inhibition augments radiation-induced inflammatory signaling and cancer cell death. Aging (Albany NY) 2023; 15:492-512. [PMID: 36656721 PMCID: PMC9925676 DOI: 10.18632/aging.204487] [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: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/19/2023]
Abstract
Over half of all cancer patients undergo radiation therapy but there is an unmet need for more efficacious combination strategies with molecular targeted drugs. DNA damage response has emerged as an important intervention point for improving anti-tumor effects of radiation and several inhibitors are currently in development. Ataxia telangiectasia mutated (ATM) kinase is a key regulator of cellular response to DNA double strand breaks and a potential target for radiosensitization. We recently reported two new potent and selective ATM inhibitors, M3541 and M4076, that effectively sensitize cancer cells to radiation and regress human xenografts in clinically relevant animal models. Here, we dive deeper into the cellular events in irradiated cancer cells exposed to ATM inhibitors. Suppression of ATM activity inhibited radiation-induced ATM signaling and abrogated G1 checkpoint activation resulting in enhanced cell death. Our data indicated that entry into mitosis with gross structural abnormalities in multiple chromosomes is the main mechanism behind the increased cell killing. Misalignment and mis-segregation led to formation of multiple micronuclei and robust activation of the interferon response and inflammatory signaling via the cGAS/STING/TBK1 pathway. Cancer cells exposed to radiation in the presence of M3541 were more susceptible to killing in co-culture with NK cells from healthy donors. In addition, strong upregulation of PD-L1 expression was observed in the surviving irradiated cancer cells exposed to M3541. Simultaneous activation of the STING pathway and PD-L1 suggested that combination of radiation, ATM inhibitors and PD-L1 targeted therapy may offer a novel approach to radio-immunotherapy of locally advanced tumors.
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Affiliation(s)
- Li-Ya Chiu
- Translational Innovation Platform Oncology and Immuno-Oncology, EMD Serono, Billerica, MA 01821, USA
| | - Qing Sun
- Translational Innovation Platform Oncology and Immuno-Oncology, EMD Serono, Billerica, MA 01821, USA
| | - Frank T. Zenke
- Translational Innovation Platform Oncology and Immuno-Oncology, The Healthcare Business of Merck KGaA, Darmstadt, Hesse, Germany
| | - Andree Blaukat
- Translational Innovation Platform Oncology and Immuno-Oncology, The Healthcare Business of Merck KGaA, Darmstadt, Hesse, Germany
| | - Lyubomir T. Vassilev
- Translational Innovation Platform Oncology and Immuno-Oncology, EMD Serono, Billerica, MA 01821, USA
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Warecki B, Bast I, Tajima M, Sullivan W. Connections between sister and non-sister telomeres of segregating chromatids maintain euploidy. Curr Biol 2023; 33:58-74.e5. [PMID: 36525974 PMCID: PMC9839490 DOI: 10.1016/j.cub.2022.11.038] [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: 05/04/2022] [Revised: 10/05/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022]
Abstract
The complete separation of sister chromatids during anaphase is a fundamental requirement for successful mitosis. Therefore, divisions with either persistent DNA-based connections or lagging chromosome fragments threaten aneuploidy if unresolved. Here, we demonstrate the existence of an anaphase mechanism in normally dividing cells in which pervasive connections between telomeres of segregating chromosomes aid in rescuing lagging chromosome fragments. We observe that in a large proportion of Drosophila melanogaster neuronal stem cell divisions, early anaphase sister and non-sister chromatids remain connected by thin telomeric DNA threads. Normally, these threads are resolved in mid-to-late anaphase via a spatial mechanism. However, we find that the presence of a nearby unrepaired DNA break recruits histones, BubR1 kinase, Polo kinase, Aurora B kinase, and BAF to the telomeric thread of the broken chromosome, stabilizing it. Stabilized connections then aid lagging chromosome rescue. These results suggest a model in which pervasive anaphase telomere-telomere connections that are normally resolved quickly can instead be stabilized to retain wayward chromosome fragments. Thus, the liability of persistent anaphase inter-chromosomal connections in normal divisions may be offset by their ability to maintain euploidy in the face of chromosome damage and genome loss.
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Affiliation(s)
- Brandt Warecki
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Ian Bast
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Matthew Tajima
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - William Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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37
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Genotoxicity of pyrrolizidine alkaloids in metabolically inactive human cervical cancer HeLa cells co-cultured with human hepatoma HepG2 cells. Arch Toxicol 2023; 97:295-306. [PMID: 36273350 PMCID: PMC9816206 DOI: 10.1007/s00204-022-03394-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/05/2022] [Indexed: 01/19/2023]
Abstract
Pyrrolizidine alkaloids (PAs) are secondary plant metabolites, which can be found as contaminant in various foods and herbal products. Several PAs can cause hepatotoxicity and liver cancer via damaging hepatic sinusoidal endothelial cells (HSECs) after hepatic metabolization. HSECs themselves do not express the required metabolic enzymes for activation of PAs. Here we applied a co-culture model to mimic the in vivo hepatic environment and to study PA-induced effects on not metabolically active neighbour cells. In this co-culture model, bioactivation of PA was enabled by metabolically capable human hepatoma cells HepG2, which excrete the toxic and mutagenic pyrrole metabolites. The human cervical epithelial HeLa cells tagged with H2B-GFP were utilized as non-metabolically active neighbours because they can be identified easily based on their green fluorescence in the co-culture. The PAs europine, riddelliine and lasiocarpine induced micronuclei in HepG2 cells, and in HeLa H2B-GFP cells co-cultured with HepG2 cells, but not in HeLa H2B-GFP cells cultured alone. Metabolic inhibition of cytochrome P450 enzymes with ketoconazole abrogated micronucleus formation. The efflux transporter inhibitors verapamil and benzbromarone reduced micronucleus formation in the co-culture model. Furthermore, mitotic disturbances as an additional genotoxic mechanism of action were observed in HepG2 cells and in HeLa H2B-GFP cells co-cultured with HepG2 cells, but not in HeLa H2B-GFP cells cultured alone. Overall, we were able to show that PAs were activated by HepG2 cells and the metabolites induced genomic damage in co-cultured HeLa cells.
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38
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Yamazaki T, Hatano Y, Kobayashi N, Yamagata K. Targeted DNA Methylation in Mouse Early Embryos. Methods Mol Biol 2023; 2577:243-254. [PMID: 36173578 DOI: 10.1007/978-1-0716-2724-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In germ cell lines, including early preimplantation embryos, centromeres and pericentromeres are known to show a marked hypomethylation pattern compared to somatic cells. Elucidation of the biological function of this region-specific DNA hypomethylation state, region-specific epigenomic manipulation is essential as an analytical method. We have applied genome editing to show that region-specific DNA methylation can be effectively introduced by a fusion protein, TALE, which recognizes pericentromeres, and SssI, a bacterial CpG methyltransferase. This makes it possible to increase the DNA methylation state of the pericentromeres, which is normally about 20%, to about 60-75%, enabling comparative analysis of the developmental processes of normal embryos with hypomethylated pericentromeres and embryos that have been epigenetically edited to be hypermethylated. In this chapter, we describe a method for introducing DNA methylation into pericentromeres of early mouse embryos by expressing TALE-SssI fusion protein and a method for detecting DNA methylation.
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Affiliation(s)
- Taiga Yamazaki
- Division of Biomedical Research, Kitasato University Medical Center, Kitasato University, Kitamoto, Saitama, Japan.
| | - Yu Hatano
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
| | - Noritada Kobayashi
- Division of Biomedical Research, Kitasato University Medical Center, Kitasato University, Kitamoto, Saitama, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan.
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Reimann H, Stopper H, Hintzsche H. Fate of micronuclei and micronucleated cells after treatment of HeLa cells with different genotoxic agents. Arch Toxicol 2023; 97:875-889. [PMID: 36564592 PMCID: PMC9968706 DOI: 10.1007/s00204-022-03433-9] [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: 10/13/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Although micronuclei are well-known biomarkers of genotoxic damage, the biological consequences of micronucleus induction are only poorly understood. To further elucidate these consequences, HeLa cells stably expressing histone 2B coupled with green fluorescent protein were used for long-term live cell imaging to investigate the fate of micronuclei and micronucleated cells after treatment of cells with various genotoxic agents (doxorubicin (20, 30 and nM), tert-butyl hydroperoxide (tBHP, 50, 100 and 150 µM), radiation (0.5, 1 and 2 Gy), methyl methanesulfonate (MMS, 20, 25 and 30 µg/ml) and vinblastine (1, 2 and 3 nM)). Most micronuclei persist for multiple cell cycles or reincorporate while micronucleated cells were more prone to cell death, senescence and fatal mitotic errors compared to non-micronucleated cells, which is consistent with previous studies using etoposide. No clear substance-related effects on the fate of micronuclei and micronucleated cells were observed. To further investigate the fate of micronuclei, extrusion of micronuclei was studied with treatments reported as inducing the extrusion of micronuclei. Since extrusion was not observed in HeLa cells, the relevance of extrusion of micronuclei remains unclear. In addition, degradation of micronuclei was analysed via immunostaining of γH2AX, which demonstrated a high level of DNA damage in micronuclei compared to the main nuclei. Furthermore, transduction with two reporter genes (LC3B-dsRed and LaminB1-dsRed) was conducted followed by long-term live cell imaging. While autophagy marker LC3B was not associated with micronuclei, Lamin B1 was found in approximately 50% of all micronuclei. While degradation of micronuclei was not observed to be a frequent fate of micronuclei, the results show impaired stability of DNA and micronuclear envelope indicating rupture of micronuclei as a pre-step to chromothripsis.
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Affiliation(s)
- Hauke Reimann
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
- Bavarian Health and Food Safety Authority, Erlangen, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
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Mazzarini M, Arciprete F, Picconi O, Valeri M, Verachi P, Martelli F, Migliaccio AR, Falchi M, Zingariello M. Single cell analysis of the localization of the hematopoietic stem cells within the bone marrow architecture identifies niche-specific proliferation dynamics. Front Med (Lausanne) 2023; 10:1166758. [PMID: 37188088 PMCID: PMC10175646 DOI: 10.3389/fmed.2023.1166758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Introduction Hematopoietic stem cells (HSC) reside in the bone marrow (BM) in specialized niches which provide support for their self-replication and differentiation into the blood cells. Recently, numerous studies using sophisticated molecular and microscopic technology have provided snap-shots information on the identity of the BM niches in mice. In adults, HSC are localized around arterioles and sinusoids/venules whereas in juvenile mice they are in close to the osteoblasts. However, although it is well recognized that in mice the nature of the hematopoietic niche change with age or after exposure to inflammatory insults, much work remains to be done to identify changes occurring under these conditions. The dynamic changes occurring in niche/HSC interactions as HSC enter into cycle are also poorly defined. Methods We exploit mice harboring the hCD34tTA/Tet-O-H2BGFP transgene to establish the feasibility to assess interactions of the HSC with their niche as they cycle. In this model, H2BGFP expression is driven by the TET trans-activator under the control of the human CD34 promoter which in mice is active only in the HSC. Since Doxycycline inhibits TET, HSC exposed to this drug no longer express H2BGFP and loose half of their label every division allowing establishing the dynamics of their first 1-3 divisions. To this aim, we first validated user-friendly confocal microscopy methods to determine HSC divisions by hemi-decrement changes in levels of GFP expression. We then tracked the interaction occurring in old mice between the HSC and their niche during the first HSC divisions. Results We determined that in old mice, most of the HSC are located around vessels, both arterioles which sustain quiescence and self-replication, and venules/sinusoids, which sustain differentiation. After just 1 week of exposure to Doxycycline, great numbers of the HSC around the venules lost most of their GFP label, indicating that they had cycled. By contrast, the few HSC surrounding the arterioles retained maximal levels of GFP expression, indicating that they are either dormant or cycle at very low rates. Conclusion These results reveal that in old mice, HSC cycle very dynamically and are biased toward interactions with the niche that instructs them to differentiate.
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Affiliation(s)
- Maria Mazzarini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- Altius Institute for Biomedical Sciences, Seattle, WA, United States
| | - Francesca Arciprete
- Unit of Microscopic and Ultrastructural Anatomy, University Campus Bio-Medico, Rome, Italy
| | - Orietta Picconi
- National Center for HIV/AIDS Research, Istituto Superiore di Sanità, Rome, Italy
| | - Mauro Valeri
- Center for Animal Experimentation and Well-Being, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Verachi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Martelli
- National Center for Preclinical and Clinical Research and Evaluation of Pharmaceutical Drugs, Istituto Superiore di Sanità, Rome, Italy
| | - Anna Rita Migliaccio
- Altius Institute for Biomedical Sciences, Seattle, WA, United States
- Unit of Microscopic and Ultrastructural Anatomy, University Campus Bio-Medico, Rome, Italy
- *Correspondence: Anna Rita Migliaccio ;
| | - Mario Falchi
- National Center for HIV/AIDS Research, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Zingariello
- Altius Institute for Biomedical Sciences, Seattle, WA, United States
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Malaquin N, Rodier F. Dynamic and scalable assessment of the senescence-associated secretory phenotype (SASP). Methods Cell Biol 2022; 181:181-195. [PMID: 38302239 DOI: 10.1016/bs.mcb.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dual-faced cellular senescence is responsible for beneficial biological processes and for age-related pathologies. Senescent cells under stable proliferation arrest develop numerous senescence-associated phenotypes such as the potent pro-inflammatory secretome called the senescence-associated secretory phenotype (SASP). The SASP shapes the senescent microenvironment and influences the biology of adjacent cells, including the modulation of proliferation and migration/invasion, reinforcement/induction of peripheral senescence, and immune cell activity or recruitment. The SASP is a dynamic process with multiple waves of secreted factors described to interlace over a period of many days. Whether the senescence phenotype reaches a mature stable state remains controversial. Overall, the complexity of the context-dependent and timely SASP compositions and its varied microenvironmental impact demonstrate the importance of properly assessing SASP over time. In this chapter, we focus on scalable and dynamic experimental procedures to prepare SASP conditioned medium over time from cells receiving senescence-inducing stimuli. This SASP-containing conditioned medium can be used to assess the composition of the SASP, study SASP-related signaling pathways or evaluate the paracrine microenvironmental impact of senescent cells.
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Affiliation(s)
- Nicolas Malaquin
- Centre de recherche du CHUM (CRCHUM) and Institut du cancer de Montréal, Montréal, QC, Canada
| | - Francis Rodier
- Centre de recherche du CHUM (CRCHUM) and Institut du cancer de Montréal, Montréal, QC, Canada; Département de radiologie, radio-oncologie et médecine nucléaire, Université de Montréal, Montreal, QC, Canada.
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42
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Yi E, Chamorro González R, Henssen AG, Verhaak RGW. Extrachromosomal DNA amplifications in cancer. Nat Rev Genet 2022; 23:760-771. [PMID: 35953594 PMCID: PMC9671848 DOI: 10.1038/s41576-022-00521-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 12/19/2022]
Abstract
Extrachromosomal DNA (ecDNA) amplification is an important driver alteration in cancer. It has been observed in most cancer types and is associated with worse patient outcome. The functional impact of ecDNA has been linked to its unique properties, such as its circular structure that is associated with altered chromatinization and epigenetic regulatory landscape, as well as its ability to randomly segregate during cell division, which fuels intercellular copy number heterogeneity. Recent investigations suggest that ecDNA is structurally more complex than previously anticipated and that it localizes to specialized nuclear bodies (hubs) and can act in trans as an enhancer for genes on other ecDNAs or chromosomes. In this Review, we synthesize what is currently known about how ecDNA is generated and how its genetic and epigenetic architecture affects proto-oncogene deregulation in cancer. We discuss how recently identified ecDNA functions may impact oncogenesis but also serve as new therapeutic vulnerabilities in cancer.
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Affiliation(s)
- Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rocío Chamorro González
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
| | - Anton G Henssen
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Neurosurgery, Amsterdam UMC, Amsterdam, the Netherlands.
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43
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Bueno C, Blanquer M, García-Bernal D, Martínez S, Moraleda JM. Binucleated human bone marrow-derived mesenchymal cells can be formed during neural-like differentiation with independence of any cell fusion events. Sci Rep 2022; 12:20615. [PMID: 36450873 PMCID: PMC9712539 DOI: 10.1038/s41598-022-24996-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/23/2022] [Indexed: 12/09/2022] Open
Abstract
Although it has been reported that bone marrow-derived cells (BMDCs) can transdifferentiate into neural cells, the findings are considered unlikely. It has been argued that the rapid neural transdifferentiation of BMDCs reported in culture studies is actually due to cytotoxic changes induced by the media. While transplantation studies indicated that BMDCs can form new neurons, it remains unclear whether the underlying mechanism is transdifferentiation or BMDCs-derived cell fusion with the existing neuronal cells. Cell fusion has been put forward to explain the presence of gene-marked binucleated neurons after gene-marked BMDCs transplantation. In the present study, we demostrated that human BMDCs can rapidly adopt a neural-like morphology through active neurite extension and binucleated human BMDCs can form with independence of any cell fusion events. We also showed that BMDCs neural-like differentiation involves the formation of intermediate cells which can then redifferentiate into neural-like cells, redifferentiate back to the mesenchymal fate or even repeatedly switch lineages without cell division. Furthermore, we have discovered that nuclei from intermediate cells rapidly move within the cell, adopting different morphologies and even forming binucleated cells. Therefore, our results provide a stronger basis for rejecting the idea that BMDCs neural transdifferentiation is merely an artefact.
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Affiliation(s)
- Carlos Bueno
- grid.10586.3a0000 0001 2287 8496Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Institute of Biomedical Research (IMIB), Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
| | - Miguel Blanquer
- grid.10586.3a0000 0001 2287 8496Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Institute of Biomedical Research (IMIB), Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
| | - David García-Bernal
- grid.10586.3a0000 0001 2287 8496Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Institute of Biomedical Research (IMIB), Faculty of Medicine, University of Murcia, 30120 Murcia, Spain ,grid.10586.3a0000 0001 2287 8496Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Murcia, 30100 Murcia, Spain
| | - Salvador Martínez
- grid.26811.3c0000 0001 0586 4893Instituto de Neurociencias de Alicante (UMH-CSIC), Universidad Miguel Hernandez, 03550 San Juan, Alicante, Spain
| | - José M. Moraleda
- grid.10586.3a0000 0001 2287 8496Medicine Department and Hematopoietic Transplant and Cellular Therapy Unit, Institute of Biomedical Research (IMIB), Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
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Aguilera RJ. A virus changed my life. Mol Biol Cell 2022; 33:ae2. [PMID: 36441842 PMCID: PMC9727801 DOI: 10.1091/mbc.e22-08-0357] [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] [Indexed: 11/29/2022] Open
Abstract
The E. E. Just Award commemorates the great African-American cell biologist Dr. Ernest Everett Just, who was a successful pioneer in an era of systemic exclusion of minorities in science and academia. Receiving this award is not only an honor but a recognition of my long-standing commitment to helping Persons Excluded due to Ethnicity or Race (PEERS) to achieve success in biomedical careers. As a proud member of this group, I have devoted most of my career to training underrepresented undergraduate and graduate students to pursue scientific careers. My early work as a molecular immunologist focused on the search for enzymes involved in antigen-receptor gene recombination, as well as the characterization of nuclear factors involved in recombination and the transcriptional regulation of the murine recombination-activating genes. Over the past two decades, my research has focused on discovering and evaluating novel anticancer agents that can be used to treat various cancer types.
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Affiliation(s)
- Renato J. Aguilera
- Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968-0519,*Address correspondence to: Renato J. Aguilera ()
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45
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Mota A, Berezicki S, Wernersson E, Harbers L, Li-Wang X, Gradin K, Peuckert C, Crosetto N, Bienko M. FRET-FISH probes chromatin compaction at individual genomic loci in single cells. Nat Commun 2022; 13:6680. [PMID: 36335096 PMCID: PMC9637210 DOI: 10.1038/s41467-022-34183-y] [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: 12/01/2021] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.
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Affiliation(s)
- Ana Mota
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Szymon Berezicki
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Erik Wernersson
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Luuk Harbers
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Xiaoze Li-Wang
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Katarina Gradin
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Christiane Peuckert
- grid.10548.380000 0004 1936 9377Stockholm University, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm, Sweden
| | - Nicola Crosetto
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden ,grid.510779.d0000 0004 9414 6915Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Magda Bienko
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden ,grid.510779.d0000 0004 9414 6915Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
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Degrelle SA, Ferecatu I, Fournier T. Novel fluorescent and secreted transcriptional reporters for quantifying activity of the xenobiotic sensor aryl hydrocarbon receptor (AHR). ENVIRONMENT INTERNATIONAL 2022; 169:107545. [PMID: 36179647 DOI: 10.1016/j.envint.2022.107545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that plays a critical role in diverse biological processes, including xenobiotic metabolism, carcinogenesis, and physiological functions such as regulation of the immune system and cell differentiation. To improve studies of AHR activity, we constructed two new reporter genes: a fluorescent GFP-tagged histone 2B (XRE-H2B-eGFP) and a secreted nanoluciferase (XRE-pNL1.3[secNluc]). Here, we demonstrate how these reporters can be used to monitor AHR activity in different types of cells, including human primary trophoblasts and cell lines, following incubation with a strong AHR ligand, benzo[a]pyrene (B[a]P), or an AHR inhibitor (CH223191). Compared to vehicle control cells, a significant increase in AHR activity was observed in cells treated with 0.5 and/or 2 µM B[a]P and a significant decrease was detected in response to treatment with 3 µM CH223191. These new plasmids have great potential for use in a variety of applications, such as screening for endogenous or exogenous ligands of AHR.
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Affiliation(s)
- Séverine A Degrelle
- Université Paris Cité, INSERM, UMR-S1139 Physiopathologie et Pharmacotoxicologie Placentaire Humaine, Microbiote pré et post-natal (3PHM), Paris F-75006, France; Inovarion, Paris F-75005, France.
| | - Ioana Ferecatu
- Université Paris Cité, INSERM, UMR-S1139 Physiopathologie et Pharmacotoxicologie Placentaire Humaine, Microbiote pré et post-natal (3PHM), Paris F-75006, France
| | - Thierry Fournier
- Université Paris Cité, INSERM, UMR-S1139 Physiopathologie et Pharmacotoxicologie Placentaire Humaine, Microbiote pré et post-natal (3PHM), Paris F-75006, France
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47
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Abstract
In cancer, complex genome rearrangements and other structural alterations, including the amplification of oncogenes on circular extrachromosomal DNA (ecDNA) elements, drive the formation and progression of tumors. ecDNA is a particularly challenging structural alteration. By untethering oncogenes from chromosomal constraints, it elevates oncogene copy number, drives intratumoral genetic heterogeneity, promotes rapid tumor evolution, and results in treatment resistance. The profound changes in DNA shape and nuclear architecture generated by ecDNA alter the transcriptional landscape of tumors by catalyzing new types of regulatory interactions that do not occur on chromosomes. The current suite of tools for interrogating cancer genomes is well suited for deciphering sequence but has limited ability to resolve the complex changes in DNA structure and dynamics that ecDNA generates. Here, we review the challenges of resolving ecDNA form and function and discuss the emerging tool kit for deciphering ecDNA architecture and spatial organization, including what has been learned to date about how this dramatic change in shape alters tumor development, progression, and drug resistance.
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Affiliation(s)
- Vineet Bafna
- Department of Computer Science and Engineering and Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA;
| | - Paul S Mischel
- Department of Pathology and ChEM-H, Stanford University School of Medicine, Stanford, California, USA;
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48
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Horsnell HL, Tetley RJ, De Belly H, Makris S, Millward LJ, Benjamin AC, Heeringa LA, de Winde CM, Paluch EK, Mao Y, Acton SE. Lymph node homeostasis and adaptation to immune challenge resolved by fibroblast network mechanics. Nat Immunol 2022; 23:1169-1182. [PMID: 35882934 PMCID: PMC9355877 DOI: 10.1038/s41590-022-01272-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 06/15/2022] [Indexed: 11/23/2022]
Abstract
Emergent physical properties of tissues are not readily understood by reductionist studies of their constituent cells. Here, we show molecular signals controlling cellular, physical, and structural properties and collectively determine tissue mechanics of lymph nodes, an immunologically relevant adult tissue. Lymph nodes paradoxically maintain robust tissue architecture in homeostasis yet are continually poised for extensive expansion upon immune challenge. We find that in murine models of immune challenge, cytoskeletal mechanics of a cellular meshwork of fibroblasts determine tissue tension independently of extracellular matrix scaffolds. We determine that C-type lectin-like receptor 2 (CLEC-2)-podoplanin signaling regulates the cell surface mechanics of fibroblasts, providing a mechanically sensitive pathway to regulate lymph node remodeling. Perturbation of fibroblast mechanics through genetic deletion of podoplanin attenuates T cell activation. We find that increased tissue tension through the fibroblastic stromal meshwork is required to trigger the initiation of fibroblast proliferation and restore homeostatic cellular ratios and tissue structure through lymph node expansion.
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Affiliation(s)
- Harry L Horsnell
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Robert J Tetley
- Tissue Mechanics Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Henry De Belly
- Physiological Laboratory, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Spyridon Makris
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Lindsey J Millward
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Agnesska C Benjamin
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Lucas A Heeringa
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Charlotte M de Winde
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Ewa K Paluch
- Physiological Laboratory, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Yanlan Mao
- Tissue Mechanics Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Sophie E Acton
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
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49
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Arrey G, Keating ST, Regenberg B. A unifying model for extrachromosomal circular DNA load in eukaryotic cells. Semin Cell Dev Biol 2022; 128:40-50. [PMID: 35292190 DOI: 10.1016/j.semcdb.2022.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023]
Abstract
Extrachromosomal circular DNA (eccDNA) with exons and whole genes are common features of eukaryotic cells. Work from especially tumours and the yeast Saccharomyces cerevisiae has revealed that eccDNA can provide large selective advantages and disadvantages. Besides the phenotypic effect due to expression of an eccDNA fragment, eccDNA is different from other mutations in that it is released from 1:1 segregation during cell division. This means that eccDNA can quickly change copy number, pickup secondary mutations and reintegrate into a chromosome to establish substantial genetic variation that could not have evolved via canonical mechanisms. We propose a unifying 5-factor model for conceptualizing the eccDNA load of a eukaryotic cell, emphasizing formation, replication, segregation, selection and elimination. We suggest that the magnitude of these sequential events and their interactions determine the copy number of eccDNA in mitotically dividing cells. We believe that our model will provide a coherent framework for eccDNA research, to understand its biology and the factors that can be manipulated to modulate eccDNA load in eukaryotic cells.
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Affiliation(s)
- Gerard Arrey
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Samuel T Keating
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Regenberg
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark.
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50
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Hung KL, Mischel PS, Chang HY. Gene regulation on extrachromosomal DNA. Nat Struct Mol Biol 2022; 29:736-744. [PMID: 35948767 PMCID: PMC10246724 DOI: 10.1038/s41594-022-00806-7] [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: 01/28/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) is prevalent in human cancer and is associated with poor outcomes. Clonal, megabase-sized circular ecDNAs in cancer are distinct from nonclonal, small sub-kilobase-sized DNAs that may arise during normal tissue homeostasis. ecDNAs enable profound changes in gene regulation beyond copy-number gains. An emerging principle of ecDNA regulation is the formation of ecDNA hubs: micrometer-sized nuclear structures of numerous copies of ecDNAs tethered by proteins in spatial proximity. ecDNA hubs enable cooperative and intermolecular sharing of DNA regulatory elements for potent and combinatorial gene activation. The 3D context of ecDNA shapes its gene expression potential, selection for clonal heterogeneity among ecDNAs, distribution through cell division, and reintegration into chromosomes. Technologies for studying gene regulation and structure of ecDNA are starting to answer long-held questions on the distinct rules that govern cancer genes beyond chromosomes.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine and ChEM-H, Stanford University, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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