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Abstract
Multiplexed imaging uncovers precise three-dimensional maps of single nuclei.
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Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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2
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Bogolyubov DS, Chistyakova LV, Goodkov AV. Glomerulosomes: morphologically distinct nuclear organelles of unknown nature. Protoplasma 2022; 259:1409-1415. [PMID: 35103866 DOI: 10.1007/s00709-022-01742-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
The nucleus of some representatives of the genus Pelomyxa (Amoebozoa, Archamoebae, Pelobiontida) contains specific bodies (membrane-less organelles). They may be either embedded in the nucleolar mass or detached from the nucleolus. We termed these nuclear bodies the glomerulosomes for their characteristic ultrastructural appearance. The glomerulosomes are distinct nuclear bodies, about 1 μm in diameter. The morphological and diagnostic unit of a glomerulosome is an electron-dense thread/string, about 30-40 nm in thickness. These threads are not direct continuation of the nucleolar material. The threads create the unique geometric appearance of the glomerulosome by being organized into precisely parallel rows/cords. Each cord of the threads can curve at different angles within the glomerulosome body, but the threads themselves are not coiled. Nowadays, the glomerulosomes have been discovered in P. palustris, P. stagnalis, P. paradoxa, and Pelomyxa sp. Despite the unique appearance of glomerulosomes, their existence may be a more common phenomenon in eukaryotic cells than just a specific feature of the nucleus of elected pelomyxes.
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Affiliation(s)
- Dmitry S Bogolyubov
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | | | - Andrew V Goodkov
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, 194064, Russia
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3
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McCord RP, Xu Y, Li H, Das P, San Martin R. SnapShot: Chromosome organization. Mol Cell 2022; 82:2350-2350.e1. [PMID: 35714589 DOI: 10.1016/j.molcel.2022.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chromosomes in higher eukaryotes are folded at different length scales into loop extrusion domains, spatial compartments, and chromosome territories and exhibit interactions with nuclear structures such as the lamina. Microscopic methods can probe this structure by measuring positions of chromosomes in the nuclear space in individual cells, while sequencing-based contact capture approaches can report the frequency of contacts of different regions within these structural layers. To view this SnapShot, open or download the PDF.
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Affiliation(s)
- Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Yang Xu
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Heng Li
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Priyojit Das
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Rebeca San Martin
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN 37996, USA
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4
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Freyter BM, Abd Al-razaq MA, Isermann A, Dietz A, Azimzadeh O, Hekking L, Gomolka M, Rübe CE. Nuclear Fragility in Radiation-Induced Senescence: Blebs and Tubes Visualized by 3D Electron Microscopy. Cells 2022; 11:cells11020273. [PMID: 35053389 PMCID: PMC8774169 DOI: 10.3390/cells11020273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/19/2021] [Accepted: 01/12/2022] [Indexed: 12/10/2022] Open
Abstract
Irreparable DNA damage following ionizing radiation (IR) triggers prolonged DNA damage response and induces premature senescence. Cellular senescence is a permanent state of cell-cycle arrest characterized by chromatin restructuring, altered nuclear morphology and acquisition of secretory phenotype, which contributes to senescence-related inflammation. However, the mechanistic connections for radiation-induced DNA damage that trigger these senescence-associated hallmarks are poorly understood. In our in vitro model of radiation-induced senescence, mass spectrometry-based proteomics was combined with high-resolution imaging techniques to investigate the interrelations between altered chromatin compaction, nuclear envelope destabilization and nucleo-cytoplasmic chromatin blebbing. Our findings confirm the general pathophysiology of the senescence-response, with disruption of nuclear lamin organization leading to extensive chromatin restructuring and destabilization of the nuclear membrane with release of chromatin fragments into the cytosol, thereby activating cGAS-STING-dependent interferon signaling. By serial block-face scanning electron microscopy (SBF-SEM) whole-cell datasets were acquired to investigate the morphological organization of senescent fibroblasts. High-resolution 3-dimensional (3D) reconstruction of the complex nuclear shape allows us to precisely visualize the segregation of nuclear blebs from the main nucleus and their fusion with lysosomes. By multi-view 3D electron microscopy, we identified nanotubular channels formed in lamin-perturbed nuclei of senescent fibroblasts; the potential role of these nucleo-cytoplasmic nanotubes for expulsion of damaged chromatin has to be examined.
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Affiliation(s)
- Benjamin M. Freyter
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Mutaz A. Abd Al-razaq
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Anna Isermann
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Anne Dietz
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | - Omid Azimzadeh
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | | | - Maria Gomolka
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | - Claudia E. Rübe
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
- Correspondence: ; Tel.: +49-6841-1634614; Fax: +49-6841-1624699
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5
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Abstract
Nuage are RNA-rich condensates that assemble around the nuclei of developing germ cells. Many proteins required for the biogenesis and function of silencing small RNAs (sRNAs) enrich in nuage, and it is often assumed that nuage is the cellular site where sRNAs are synthesized and encounter target transcripts for silencing. Using C. elegans as a model, we examine the complex multicondensate architecture of nuage and review evidence for compartmentalization of silencing pathways. We consider the possibility that nuage condensates balance the activity of competing sRNA pathways and serve to limit, rather than enhance, sRNA amplification to protect transcripts from dangerous runaway silencing.
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Affiliation(s)
- John Paul Tsu Ouyang
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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6
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Fichtman B, Regmi SG, Dasso M, Harel A. High-Resolution Imaging and Analysis of Individual Nuclear Pore Complexes. Methods Mol Biol 2022; 2502:461-471. [PMID: 35412256 DOI: 10.1007/978-1-0716-2337-4_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Field emission scanning electron microscopy (FESEM) is a well-established technique for acquiring three-dimensional surface images of nuclear pore complexes (NPCs). We present an optimized protocol for the exposure of mammalian cell nuclei and direct surface imaging of nuclear envelopes by FESEM, allowing for a detailed morphological comparison of individual NPCs, without the need for averaging techniques. This provides a unique high resolution tool for studying the effects of cellular stress, specific genetic manipulations and inherited diseases on the ultrastructure of human NPCs.
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Affiliation(s)
- Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Saroj G Regmi
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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Sanchez V, Britt W. Human Cytomegalovirus Egress: Overcoming Barriers and Co-Opting Cellular Functions. Viruses 2021; 14:v14010015. [PMID: 35062219 PMCID: PMC8778548 DOI: 10.3390/v14010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
The assembly of human cytomegalovirus (HCMV) and other herpesviruses includes both nuclear and cytoplasmic phases. During the prolonged replication cycle of HCMV, the cell undergoes remarkable changes in cellular architecture that include marked increases in nuclear size and structure as well as the reorganization of membranes in cytoplasm. Similarly, significant changes occur in cellular metabolism, protein trafficking, and cellular homeostatic functions. These cellular modifications are considered integral in the efficient assembly of infectious progeny in productively infected cells. Nuclear egress of HCMV nucleocapsids is thought to follow a pathway similar to that proposed for other members of the herpesvirus family. During this process, viral nucleocapsids must overcome structural barriers in the nucleus that limit transit and, ultimately, their delivery to the cytoplasm for final assembly of progeny virions. HCMV, similar to other herpesviruses, encodes viral functions that co-opt cellular functions to overcome these barriers and to bridge the bilaminar nuclear membrane. In this brief review, we will highlight some of the mechanisms that define our current understanding of HCMV egress, relying heavily on the current understanding of egress of the more well-studied α-herpesviruses, HSV-1 and PRV.
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Affiliation(s)
- Veronica Sanchez
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL 35294, USA;
- Correspondence:
| | - William Britt
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL 35294, USA;
- Department of Microbiology, University of Alabama School of Medicine, Birmingham, AL 35294, USA
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Skalický V, Vojtková T, Pěnčík A, Vrána J, Juzoń K, Koláčková V, Sedlářová M, Kubeš MF, Novák O. Auxin Metabolite Profiling in Isolated and Intact Plant Nuclei. Int J Mol Sci 2021; 22:12369. [PMID: 34830250 PMCID: PMC8620152 DOI: 10.3390/ijms222212369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
The plant nucleus plays an irreplaceable role in cellular control and regulation by auxin (indole-3-acetic acid, IAA) mainly because canonical auxin signaling takes place here. Auxin can enter the nucleus from either the endoplasmic reticulum or cytosol. Therefore, new information about the auxin metabolome (auxinome) in the nucleus can illuminate our understanding of subcellular auxin homeostasis. Different methods of nuclear isolation from various plant tissues have been described previously, but information about auxin metabolite levels in nuclei is still fragmented and insufficient. Herein, we tested several published nucleus isolation protocols based on differential centrifugation or flow cytometry. The optimized sorting protocol leading to promising yield, intactness, and purity was then combined with an ultra-sensitive mass spectrometry analysis. Using this approach, we can present the first complex report on the auxinome of isolated nuclei from cell cultures of Arabidopsis and tobacco. Moreover, our results show dynamic changes in auxin homeostasis at the intranuclear level after treatment of protoplasts with free IAA, or indole as a precursor of auxin biosynthesis. Finally, we can conclude that the methodological procedure combining flow cytometry and mass spectrometry offers new horizons for the study of auxin homeostasis at the subcellular level.
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Affiliation(s)
- Vladimír Skalický
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
| | - Tereza Vojtková
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (J.V.); (V.K.)
| | - Katarzyna Juzoń
- Department of Biotechnology, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Krakow, Poland;
| | - Veronika Koláčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic; (J.V.); (V.K.)
| | - Michaela Sedlářová
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic;
| | - Martin F. Kubeš
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic; (V.S.); (T.V.); (A.P.)
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Govind D, Becker JU, Miecznikowski J, Rosenberg AZ, Dang J, Tharaux PL, Yacoub R, Thaiss F, Hoyer PF, Manthey D, Lutnick B, Worral AM, Mohammad I, Walavalkar V, Tomaszewski JE, Jen KY, Sarder P. PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole-Slide Images. J Am Soc Nephrol 2021; 32:2795-2813. [PMID: 34479966 PMCID: PMC8806084 DOI: 10.1681/asn.2021050630] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/08/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Podocyte depletion precedes progressive glomerular damage in several kidney diseases. However, the current standard of visual detection and quantification of podocyte nuclei from brightfield microscopy images is laborious and imprecise. METHODS We have developed PodoSighter, an online cloud-based tool, to automatically identify and quantify podocyte nuclei from giga-pixel brightfield whole-slide images (WSIs) using deep learning. Ground-truth to train the tool used immunohistochemically or immunofluorescence-labeled images from a multi-institutional cohort of 122 histologic sections from mouse, rat, and human kidneys. To demonstrate the generalizability of our tool in investigating podocyte loss in clinically relevant samples, we tested it in rodent models of glomerular diseases, including diabetic kidney disease, crescentic GN, and dose-dependent direct podocyte toxicity and depletion, and in human biopsies from steroid-resistant nephrotic syndrome and from human autopsy tissues. RESULTS The optimal model yielded high sensitivity/specificity of 0.80/0.80, 0.81/0.86, and 0.80/0.91, in mouse, rat, and human images, respectively, from periodic acid-Schiff-stained WSIs. Furthermore, the podocyte nuclear morphometrics extracted using PodoSighter were informative in identifying diseased glomeruli. We have made PodoSighter freely available to the general public as turnkey plugins in a cloud-based web application for end users. CONCLUSIONS Our study demonstrates an automated computational approach to detect and quantify podocyte nuclei in standard histologically stained WSIs, facilitating podocyte research, and enabling possible future clinical applications.
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Affiliation(s)
- Darshana Govind
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
| | - Jan U. Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | | | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Rabi Yacoub
- Department of Internal Medicine, University at Buffalo, Buffalo, New York
| | - Friedrich Thaiss
- Third Medical Department of Clinical Medicine, University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Peter F. Hoyer
- Pediatric Nephrology, University Hospital Essen, Essen, Germany
| | | | - Brendon Lutnick
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
| | - Amber M. Worral
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
| | - Imtiaz Mohammad
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
| | - Vighnesh Walavalkar
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - John E. Tomaszewski
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
| | - Kuang-Yu Jen
- Department of Pathology and Laboratory Medicine, University of California, Sacramento, California
| | - Pinaki Sarder
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York
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Cha HJ, Uyan Ö, Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan GC, Dekker J, Orkin SH. Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nat Commun 2021; 12:6241. [PMID: 34716321 PMCID: PMC8556400 DOI: 10.1038/s41467-021-26574-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Precise control of gene expression during differentiation relies on the interplay of chromatin and nuclear structure. Despite an established contribution of nuclear membrane proteins to developmental gene regulation, little is known regarding the role of inner nuclear proteins. Here we demonstrate that loss of the nuclear scaffolding protein Matrin-3 (Matr3) in erythroid cells leads to morphological and gene expression changes characteristic of accelerated maturation, as well as broad alterations in chromatin organization similar to those accompanying differentiation. Matr3 protein interacts with CTCF and the cohesin complex, and its loss perturbs their occupancy at a subset of sites. Destabilization of CTCF and cohesin binding correlates with altered transcription and accelerated differentiation. This association is conserved in embryonic stem cells. Our findings indicate Matr3 negatively affects cell fate transitions and demonstrate that a critical inner nuclear protein impacts occupancy of architectural factors, culminating in broad effects on chromatin organization and cell differentiation.
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Affiliation(s)
- Hye Ji Cha
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Özgün Uyan
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yan Kai
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Tianxin Liu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Qian Zhu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Giovanni A Botten
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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11
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Simsone Z, Freivalds T, Bēma D, Miķelsone I, Patetko L, Bērziņš J, Harju L, Buiķis I. Cancer microcell initiation and determination. BMC Cancer 2021; 21:1087. [PMID: 34625031 PMCID: PMC8501611 DOI: 10.1186/s12885-021-08813-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Cancer remains one of the leading causes of death worldwide, despite the possibilities to detect early onset of the most common cancer types. The search for the optimal therapy is complicated by the cancer diversity within tumors and the unsynchronized development of cancerous cells. Therefore, it is necessary to characterize cancer cell populations after treatment has been applied, because cancer recurrence is not rare. In our research, we concentrated on small cancer cell subpopulation (microcells) that has a potential to be cancer resistance source. Previously made experiments has shown that these cells in small numbers form in specific circumstances after anticancer treatment. METHODS In experiments described in this research, the anticancer agents' paclitaxel and doxorubicin were used to stimulate the induction of microcells in fibroblast, cervix adenocarcinoma, and melanoma cell lines. Mainly for the formation of microcells in melanoma cells. The drug-stimulated cells were then characterized in terms of their formation efficiency, morphology, and metabolic activity. RESULTS We observed the development of cancer microcells and green fluorescent protein (GFP) transfection efficiency after stress. In the time-lapse experiment, we observed microcell formation through a renewal process and GFP expression in the microcells. Additionally, the microcells were viable after anticancer treatment, as indicated by the nicotinamide adenine dinucleotide hydrogen phosphate (NADPH) enzyme activity assay results. Taken together, these findings indicate that cancer microcells are viable and capable of resisting the stress induced by anticancer drugs, and these cells are prone to chemical substance uptake from the environment. CONCLUSION Microcells are not only common to a specific cancer type, but can be found in any tumor type. This study could help to understand cancer emergence and recurrence. The appearance of microcells in the studied cancer cell population could be an indicator of the individual anticancer therapy effectiveness and patient survival.
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Affiliation(s)
- Zane Simsone
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Jelgavas Street 3, Riga, LV-1004 Latvia
| | - Tālivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Jelgavas Street 3, Riga, LV-1004 Latvia
| | - Dina Bēma
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Jelgavas Street 3, Riga, LV-1004 Latvia
- Institute of Clinical and Preventive Medicine, University of Latvia, Gailezera Street 1, Riga, LV 1079 Latvia
| | - Indra Miķelsone
- Department of Human Physiology and Biochemistry, Rīga Stradiņš University, Dzirciema Street 16, Riga, LV-1007 Latvia
| | - Liene Patetko
- Laboratory of Bioanalytical and Biodosimetry Methods, Faculty of Biology, University of Latvia, Jelgavas Street 3, Riga, LV-1004 Latvia
| | - Juris Bērziņš
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Jelgavas Street 3, Riga, LV-1004 Latvia
| | - Līga Harju
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Jelgavas Street 3, Riga, LV-1004 Latvia
| | - Indulis Buiķis
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Jelgavas Street 3, Riga, LV-1004 Latvia
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Feleke R, Reynolds RH, Smith AM, Tilley B, Taliun SAG, Hardy J, Matthews PM, Gentleman S, Owen DR, Johnson MR, Srivastava PK, Ryten M. Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseases. Acta Neuropathol 2021; 142:449-474. [PMID: 34309761 PMCID: PMC8357687 DOI: 10.1007/s00401-021-02343-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
Parkinson's disease (PD), Parkinson's disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of disease-modifying therapies. Transcriptomic profiling can contribute to addressing this gap, but remains limited in the LBDs. Here, we applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group), to transcriptomically profile the LBDs. Using this approach, we (i) found transcriptional alterations in multiple cell types across the LBDs; (ii) discovered evidence for widespread dysregulation of RNA splicing, particularly in PDD and DLB; (iii) identified potential splicing factors, with links to other dementia-related neurodegenerative diseases, coordinating this dysregulation; and (iv) identified transcriptomic commonalities and distinctions between the LBDs that inform understanding of the relationships between these three clinical disorders. Together, these findings have important implications for the design of RNA-targeted therapies for these diseases and highlight a potential molecular "window" of therapeutic opportunity between the initial onset of PD and subsequent development of Lewy body dementia.
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Affiliation(s)
- Rahel Feleke
- Department of Brain Sciences, Imperial College London, London, UK
| | - Regina H Reynolds
- Department of Neurodegenerative Disease, University College London, London, UK
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK
| | - Amy M Smith
- Dementia Research Institute at Imperial College London, London, UK
| | - Bension Tilley
- Department of Brain Sciences, Imperial College London, London, UK
| | - Sarah A Gagliano Taliun
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
- Montréal Heart Institute, Montréal, QC, Canada
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - John Hardy
- Department of Neurodegenerative Disease, University College London, London, UK
- UK Dementia Research Institute at University College London, London, UK
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, London, UK
- Dementia Research Institute at Imperial College London, London, UK
| | - Steve Gentleman
- Department of Brain Sciences, Imperial College London, London, UK
- Dementia Research Institute at Imperial College London, London, UK
| | - David R Owen
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - Prashant K Srivastava
- Dementia Research Institute at Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Mina Ryten
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK.
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13
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Christman DA, Curry HN, Rouhana L. Heterotrimeric Kinesin II is required for flagellar assembly and elongation of nuclear morphology during spermiogenesis in Schmidtea mediterranea. Dev Biol 2021; 477:191-204. [PMID: 34090925 PMCID: PMC8277772 DOI: 10.1016/j.ydbio.2021.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 05/08/2021] [Accepted: 05/22/2021] [Indexed: 11/19/2022]
Abstract
Development of sperm requires microtubule-based movements that drive assembly of a compact head and flagellated tails. Much is known about how flagella are built given their shared molecular core with motile cilia, but less is known about the mechanisms that shape the sperm head. The Kinesin Superfamily Protein 3A (KIF3A) pairs off with a second motor protein (KIF3B) and the Kinesin Associated Protein 3 (KAP3) to form Heterotrimeric Kinesin II. This complex drives intraflagellar transport (IFT) along microtubules during ciliary assembly. We show that KIF3A and KAP3 orthologs in Schmidtea mediterranea are required for axonemal assembly and nuclear elongation during spermiogenesis. Expression of Smed-KAP3 is enriched during planarian spermatogenesis with transcript abundance peaking in spermatocyte and spermatid cells. Disruption of Smed-kif3A or Smed-KAP3 expression by RNA-interference results in loss of spermatozoa and accumulation of unelongated spermatids. Confocal microscopy of planarian testis lobes stained with alpha-tubulin antibodies revealed that spermatids with disrupted Kinesin II function fail to assemble flagella, and visualization with 4',6-diamidino-2-phenylindole (DAPI) revealed reduced nuclear elongation. Disruption of Smed-kif3A or Smed-KAP3 expression also resulted in edema, reduced locomotion, and loss of epidermal cilia, which corroborates with somatic phenotypes previously reported for Smed-kif3B. These findings demonstrate that heterotrimeric Kinesin II drives assembly of cilia and flagella, as well as rearrangements of nuclear morphology in developing sperm. Prolonged activity of heterotrimeric Kinesin II in manchette-like structures with extended presence during spermiogenesis is hypothesized to result in the exaggerated nuclear elongation observed in sperm of turbellarians and other lophotrochozoans.
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Affiliation(s)
- Donovan A Christman
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435-0001, USA
| | - Haley N Curry
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435-0001, USA
| | - Labib Rouhana
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435-0001, USA.
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14
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Barrera J, Song L, Gamache JE, Garrett ME, Safi A, Yun Y, Premasinghe I, Sprague D, Chipman D, Li J, Fradin H, Soldano K, Gordân R, Ashley-Koch AE, Crawford GE, Chiba-Falek O. Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains. Mol Neurodegener 2021; 16:58. [PMID: 34429139 PMCID: PMC8383438 DOI: 10.1186/s13024-021-00481-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the post-GWAS era, there is an unmet need to decode the underpinning genetic etiologies of late-onset Alzheimer's disease (LOAD) and translate the associations to causation. METHODS We conducted ATAC-seq profiling using NeuN sorted-nuclei from 40 frozen brain tissues to determine LOAD-specific changes in chromatin accessibility landscape in a cell-type specific manner. RESULTS We identified 211 LOAD-specific differential chromatin accessibility sites in neuronal-nuclei, four of which overlapped with LOAD-GWAS regions (±100 kb of SNP). While the non-neuronal nuclei did not show LOAD-specific differences, stratification by sex identified 842 LOAD-specific chromatin accessibility sites in females. Seven of these sex-dependent sites in the non-neuronal samples overlapped LOAD-GWAS regions including APOE. LOAD loci were functionally validated using single-nuclei RNA-seq datasets. CONCLUSIONS Using brain sorted-nuclei enabled the identification of sex-dependent cell type-specific LOAD alterations in chromatin structure. These findings enhance the interpretation of LOAD-GWAS discoveries, provide potential pathomechanisms, and suggest novel LOAD-loci.
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Affiliation(s)
- Julio Barrera
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Julia E. Gamache
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Melanie E. Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Young Yun
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Ivana Premasinghe
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Daniel Sprague
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Danielle Chipman
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Jeffrey Li
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Hélène Fradin
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Karen Soldano
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27705 USA
- Department of Computer Science, Duke University, Durham, NC 27705 USA
| | - Allison E. Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
- Department of Medicine, Duke University Medical Center, DUMC, Box 104775, Durham, NC 27708 USA
| | - Gregory E. Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, DUMC, Box 3382, Durham, NC 27708 USA
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC 27708 USA
| | - Ornit Chiba-Falek
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
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15
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Schwenke J, Yusuf M, Shemilt LA, Wagner U, Sajid A, Morrison GR, Zhang F, Parsons A, Rau C, Robinson IK. Quantitative phase measurements of human cell nuclei using X-ray ptychography. J Synchrotron Radiat 2021; 28:1166-1173. [PMID: 34212880 DOI: 10.1107/s1600577521004586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 06/13/2023]
Abstract
The human cell nucleus serves as an important organelle holding the genetic blueprint for life. In this work, X-ray ptychography was applied to assess the masses of human cell nuclei using its unique phase shift information. Measurements were carried out at the I13-1 beamline at the Diamond Light Source that has extremely large transverse coherence properties. The ptychographic diffractive imaging approach allowed imaging of large structures that gave quantitative measurements of the phase shift in 2D projections. In this paper a modified ptychography algorithm that improves the quality of the reconstruction for weak scattering samples is presented. The application of this approach to calculate the mass of several human nuclei is also demonstrated.
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Affiliation(s)
- Jorg Schwenke
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Mohammed Yusuf
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Laura A Shemilt
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Ulrich Wagner
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Atiqa Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi, Pakistan
| | - Graeme R Morrison
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Fucai Zhang
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Aaron Parsons
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Christoph Rau
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Ian K Robinson
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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16
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Abstract
Fat stored in the form of lipid droplets has long been considered a defining characteristic of cytoplasm. However, recent studies have shown that nuclear lipid droplets occur in multiple cells and tissues, including in human patients with fatty liver disease. The function(s) of stored fat in the nucleus has not been determined, and it is possible that nuclear fat is beneficial in some situations. Conversely, nuclear lipid droplets might instead be deleterious by disrupting nuclear organization or triggering aggregation of hydrophobic proteins. We show here that nuclear lipid droplets occur normally in C. elegans intestinal cells and germ cells, but appear to be associated with damage only in the intestine. Lipid droplets in intestinal nuclei can be associated with novel bundles of microfilaments (nuclear actin) and membrane tubules that might have roles in damage repair. To increase the normal, low frequency of nuclear lipid droplets in wild-type animals, we used a forward genetic screen to isolate mutants with abnormally large or abundant nuclear lipid droplets. Genetic analysis and cloning of three such mutants showed that the genes encode the lipid regulator SEIP-1/seipin, the inner nuclear membrane protein NEMP-1/Nemp1/TMEM194A, and a component of COPI vesicles called COPA-1/α-COP. We present several lines of evidence that the nuclear lipid droplet phenotype of copa-1 mutants results from a defect in retrieving mislocalized membrane proteins that normally reside in the endoplasmic reticulum. The seip-1 mutant causes most germ cells to have nuclear lipid droplets, the largest of which occupy more than a third of the nuclear volume. Nevertheless, the nuclear lipid droplets do not trigger apoptosis, and the germ cells differentiate into gametes that produce viable, healthy progeny. Thus, our results suggest that nuclear lipid droplets are detrimental to intestinal nuclei, but have no obvious deleterious effect on germ nuclei. Several human disorders such as obesity are associated with abnormal fat storage. Cells normally store fat in cytoplasmic organelles called lipid droplets. However, recent studies have shown that fat can also form inside of the cell nucleus, and the effects of nuclear fat are not known. Here we use the cell biology and genetics of the model organism C. elegans to study the causes and consequences of nuclear fat. We show that intestinal cells can contain nuclear fat, particularly during high-low-high changes in cytoplasmic fat that involve de novo fat synthesis. Nuclear fat is associated with multiple changes in intestinal nuclei that appear to represent damage and repair. Germ nuclei that normally differentiate into oocytes can also contain nuclear fat. In germ cells, however, even high levels of nuclear fat appear to cause little or no damage. Our results suggest that intestinal nuclei and germ cell nuclei might have different responses to nuclear fat in part because they differ in chromosomal organization at the nuclear envelope.
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Affiliation(s)
| | - Meghan C. Bacher
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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17
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Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science 2021; 372:984-989. [PMID: 34045355 PMCID: PMC8172041 DOI: 10.1126/science.abe2218] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
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Affiliation(s)
- Claire Hoencamp
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Ahmed M O Elbatsh
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | | | - Jonne A Raaijmakers
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Tom van Schaik
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | | | - Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - SP, 15054-000, Brazil
| | - Roy G H P van Heesbeen
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Bram van den Broek
- BioImaging Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Aditya N Mhaskar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Brian Glenn St Hilaire
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie Pham
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zane Colaric
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhenzhen Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Namita Mitra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Lui
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weijie Yao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leonid L Moroz
- Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
| | - Andrea Kohn
- Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
| | - Judy St Leger
- Department of Biosciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | | | | | | | - Fabian Lim
- Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emma Farley
- Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), 06466 Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University Göttingen, 37075 Göttingen, Germany
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Alexander Haddad
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Chauss
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ayse Sena Mutlu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evin Hildebrandt
- Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA
| | - Hans H Cheng
- Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA
| | | | - Theresa L U Burnham
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA
- Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
| | - Kevin A Hovel
- Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
| | - Andrew J Beel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pierre-Jean Mattei
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Gregory Cary
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Federica Di Palma
- Department of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Asha S Multani
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sen Pathak
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liesl Nel-Themaat
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - René H Medema
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, TX 77005, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin D Rowland
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
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18
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Lester E, Ooi FK, Bakkar N, Ayers J, Woerman AL, Wheeler J, Bowser R, Carlson GA, Prusiner SB, Parker R. Tau aggregates are RNA-protein assemblies that mislocalize multiple nuclear speckle components. Neuron 2021; 109:1675-1691.e9. [PMID: 33848474 PMCID: PMC8141031 DOI: 10.1016/j.neuron.2021.03.026] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/05/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Tau aggregates contribute to neurodegenerative diseases, including frontotemporal dementia and Alzheimer's disease (AD). Although RNA promotes tau aggregation in vitro, whether tau aggregates in cells contain RNA is unknown. We demonstrate, in cell culture and mouse brains, that cytosolic and nuclear tau aggregates contain RNA with enrichment for small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). Nuclear tau aggregates colocalize with and alter the composition, dynamics, and organization of nuclear speckles, membraneless organelles involved in pre-mRNA splicing. Moreover, several nuclear speckle components, including SRRM2, mislocalize to cytosolic tau aggregates in cells, mouse brains, and brains of individuals with AD, frontotemporal dementia (FTD), and corticobasal degeneration (CBD). Consistent with these alterations, we observe that the presence of tau aggregates is sufficient to alter pre-mRNA splicing. This work identifies tau alteration of nuclear speckles as a feature of tau aggregation that may contribute to the pathology of tau aggregates.
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Affiliation(s)
- Evan Lester
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Felicia K Ooi
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Nadine Bakkar
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Jacob Ayers
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Amanda L Woerman
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Joshua Wheeler
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Robert Bowser
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - George A Carlson
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA.
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19
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Peng GE, Pessino V, Huang B, von Zastrow M. Spatial decoding of endosomal cAMP signals by a metastable cytoplasmic PKA network. Nat Chem Biol 2021; 17:558-566. [PMID: 33649598 PMCID: PMC8084946 DOI: 10.1038/s41589-021-00747-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
G-protein-coupled receptor-regulated cAMP production from endosomes can specify signaling to the nucleus by moving the source of cAMP without changing its overall amount. How this is possible remains unknown because cAMP gradients dissipate over the nanoscale, whereas endosomes typically localize micrometers from the nucleus. We show that the key location-dependent step for endosome-encoded transcriptional control is nuclear entry of cAMP-dependent protein kinase (PKA) catalytic subunits. These are sourced from punctate accumulations of PKA holoenzyme that are densely distributed in the cytoplasm and titrated by global cAMP into a discrete metastable state, in which catalytic subunits are bound but dynamically exchange. Mobile endosomes containing activated receptors collide with the metastable PKA puncta and pause in close contact. We propose that these properties enable cytoplasmic PKA to act collectively like a semiconductor, converting nanoscale cAMP gradients generated from endosomes into microscale elevations of free catalytic subunits to direct downstream signaling.
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Affiliation(s)
- Grace E Peng
- Program in Cell Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Veronica Pessino
- Graduate Program of Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Swab56 Corp. and Neurophotometrics Ltd, San Diego, CA, USA
| | - Bo Huang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark von Zastrow
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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20
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Roszkowiak L, Korzynska A, Siemion K, Zak J, Pijanowska D, Bosch R, Lejeune M, Lopez C. System for quantitative evaluation of DAB&H-stained breast cancer biopsy digital images (CHISEL). Sci Rep 2021; 11:9291. [PMID: 33927266 PMCID: PMC8085130 DOI: 10.1038/s41598-021-88611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/14/2021] [Indexed: 02/02/2023] Open
Abstract
This study presents CHISEL (Computer-assisted Histopathological Image Segmentation and EvaLuation), an end-to-end system capable of quantitative evaluation of benign and malignant (breast cancer) digitized tissue samples with immunohistochemical nuclear staining of various intensity and diverse compactness. It stands out with the proposed seamless segmentation based on regions of interest cropping as well as the explicit step of nuclei cluster splitting followed by a boundary refinement. The system utilizes machine learning and recursive local processing to eliminate distorted (inaccurate) outlines. The method was validated using two labeled datasets which proved the relevance of the achieved results. The evaluation was based on the IISPV dataset of tissue from biopsy of breast cancer patients, with markers of T cells, along with Warwick Beta Cell Dataset of DAB&H-stained tissue from postmortem diabetes patients. Based on the comparison of the ground truth with the results of the detected and classified objects, we conclude that the proposed method can achieve better or similar results as the state-of-the-art methods. This system deals with the complex problem of nuclei quantification in digitalized images of immunohistochemically stained tissue sections, achieving best results for DAB&H-stained breast cancer tissue samples. Our method has been prepared with user-friendly graphical interface and was optimized to fully utilize the available computing power, while being accessible to users with fewer resources than needed by deep learning techniques.
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Affiliation(s)
- Lukasz Roszkowiak
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Ks. Trojdena 4 st., 02-109, Warsaw, Poland.
| | - Anna Korzynska
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Ks. Trojdena 4 st., 02-109, Warsaw, Poland
| | - Krzysztof Siemion
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Ks. Trojdena 4 st., 02-109, Warsaw, Poland
- Medical Pathomorphology Department, Medical University of Bialystok, Białystok, Poland
| | - Jakub Zak
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Ks. Trojdena 4 st., 02-109, Warsaw, Poland
| | - Dorota Pijanowska
- Nalecz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Ks. Trojdena 4 st., 02-109, Warsaw, Poland
| | - Ramon Bosch
- Pathology Department, Hospital de Tortosa Verge de la Cinta, Institut d'Investigacio Sanitaria Pere Virgili (IISPV), URV, Tortosa, Spain
| | - Marylene Lejeune
- Molecular Biology and Research Section, Hospital de Tortosa Verge de la Cinta, Institut d'Investigacio Sanitaria Pere Virgili (IISPV), URV, Tortosa, Spain
| | - Carlos Lopez
- Molecular Biology and Research Section, Hospital de Tortosa Verge de la Cinta, Institut d'Investigacio Sanitaria Pere Virgili (IISPV), URV, Tortosa, Spain
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21
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Holloway SB, Colon GR, Zheng W, Lea JS. Tumor Necrotic Debris and High Nuclear Grade: Newly Identified High-risk Factors for Early-stage Endocervical Adenocarcinoma. Am J Clin Oncol 2021; 44:162-168. [PMID: 33606367 DOI: 10.1097/coc.0000000000000798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Invasive pattern of endocervical adenocarcinomas (EACs) is known to influence lymph node metastasis and cancer recurrence. In this study we describe the prognostic significance of necrotic tumor debris (NTD) and tumor nuclear grade on recurrence risk stratification of early-stage cervical adenocarcinoma. METHODS Patients who underwent surgery from 2007 to 2018 for International Federation of Gynecology and Obstetrics (FIGO) stage IA1-IB2 EAC, for whom pathology was available for review were included in this study. Clinico-pathologic variables and clinical recurrence risk stratification (low, intermediate, or high risk) were correlated to intraluminal NTD and tumor nuclear grade (N3). RESULTS Among 50 patients meeting inclusion criteria, all were managed surgically and clinically risk stratified as low (n=33), intermediate (n=13), and high risk (n=4). Twenty-three patients (46%) were NTD-N3 negative and 27 (54%) were NTD-N3 positive. NTD-N3 was significantly associated with higher stage, tumor grade, larger tumor size, positive lymphovascular space invasion, and recurrence of disease (P=0.025). Patients with stage IB1 EAC who were stratified as intermediate or high-risk for recurrence were positive for NTD-N3. Lack of NTD-N3 had 100% negative predictive value for disease recurrence. CONCLUSIONS NTD-N3, a novel pathologic finding, may be used to further stratify overall recurrence risk, and may play a role in individualization of patient care in early-stage EAC.
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Affiliation(s)
| | | | - Wenxin Zheng
- Departments of Obstetrics & Gynecology
- Pathology
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jayanthi S Lea
- Departments of Obstetrics & Gynecology
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
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22
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Jung YL, Kirli K, Alver BH, Park PJ. Resources and challenges for integrative analysis of nuclear architecture data. Curr Opin Genet Dev 2021; 67:103-110. [PMID: 33450522 PMCID: PMC8084903 DOI: 10.1016/j.gde.2020.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 11/22/2022]
Abstract
A large amount of genomic data for profiling three-dimensional genome architecture have accumulated from large-scale consortium projects as well as from individual laboratories. In this review, we summarize recent landmark datasets and collections in the field. We describe the challenges in collection, annotation, and analysis of these data, particularly for integration of sequencing and microscopy data. We introduce efforts from consortia and independent groups to harmonize diverse datasets. As the resolution and throughput of sequencing and imaging technologies continue to increase, more efficient utilization and integration of collected data will be critical for a better understanding of nuclear architecture.
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Affiliation(s)
- Youngsook L Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Koray Kirli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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23
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Abstract
Studies of nuclear architecture using chromosome conformation capture methods have provided a detailed view of how chromatin folds in the 3D nuclear space. New variants of this technology now afford unprecedented resolution and allow the identification of ever smaller folding domains that offer new insights into the mechanisms by which this organization is established and maintained. Here we review recent results in this rapidly evolving field with an emphasis on CTCF function, with the goal of gaining a mechanistic understanding of the principles by which chromatin is folded in the eukaryotic nucleus.
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Affiliation(s)
- Jian-Feng Xiang
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA
| | - Victor G Corces
- Emory University School of Medicine, Department of Human Genetics, 615 Michael Street, Atlanta, GA 30322, USA.
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24
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Abstract
Quantification of nuclear stiffness is challenging for cells encapsulated within a 3D extracellular matrix (ECM). Here, we describe an experimental setup for measuring microenvironment-dependent tuning of nuclear stiffness using an atomic force microscope (AFM). In our setup, ECM-coated polyacrylamide hydrogels mimic the stiffness of the microenvironment, enabling the measurement of nuclear stiffness using an AFM probe in live cancer cells. For complete details on the use and execution of this protocol, please refer to Das et al. (2019) (https://doi.org/10.1016/j.matbio.2019.01.001).
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Affiliation(s)
- Amlan Barai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Alakesh Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shamik Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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25
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Ratti S, Rusciano I, Mongiorgi S, Owusu Obeng E, Cappellini A, Teti G, Falconi M, Talozzi L, Capellari S, Bartoletti-Stella A, Guaraldi P, Cortelli P, Suh PG, Cocco L, Manzoli L, Ramazzotti G. Cell signaling pathways in autosomal-dominant leukodystrophy (ADLD): the intriguing role of the astrocytes. Cell Mol Life Sci 2021; 78:2781-2795. [PMID: 33034697 PMCID: PMC8004488 DOI: 10.1007/s00018-020-03661-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/02/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
Autosomal-dominant leukodystrophy (ADLD) is a rare fatal neurodegenerative disorder with overexpression of the nuclear lamina component, Lamin B1 due to LMNB1 gene duplication or deletions upstream of the gene. The molecular mechanisms responsible for driving the onset and development of this pathology are not clear yet. Vacuolar demyelination seems to be one of the most significant histopathological observations of ADLD. Considering the role of oligodendrocytes, astrocytes, and leukemia inhibitory factor (LIF)-activated signaling pathways in the myelination processes, this work aims to analyze the specific alterations in different cell populations from patients with LMNB1 duplications and engineered cellular models overexpressing Lamin B1 protein. Our results point out, for the first time, that astrocytes may be pivotal in the evolution of the disease. Indeed, cells from ADLD patients and astrocytes overexpressing LMNB1 show severe ultrastructural nuclear alterations, not present in oligodendrocytes overexpressing LMNB1. Moreover, the accumulation of Lamin B1 in astrocytes induces a reduction in LIF and in LIF-Receptor (LIF-R) levels with a consequential decrease in LIF secretion. Therefore, in both our cellular models, Jak/Stat3 and PI3K/Akt axes, downstream of LIF/LIF-R, are downregulated. Significantly, the administration of exogenous LIF can partially reverse the toxic effects induced by Lamin B1 accumulation with differences between astrocytes and oligodendrocytes, highlighting that LMNB1 overexpression drastically affects astrocytic function reducing their fundamental support to oligodendrocytes in the myelination process. In addition, inflammation has also been investigated, showing an increased activation in ADLD patients' cells.
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Affiliation(s)
- Stefano Ratti
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Isabella Rusciano
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Sara Mongiorgi
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Eric Owusu Obeng
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Alessandra Cappellini
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Gabriella Teti
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Via Irnerio 48, Bologna, Italy
| | - Mirella Falconi
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Via Irnerio 48, Bologna, Italy
| | - Lia Talozzi
- Functional MR Unit, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Sabina Capellari
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC NeuroMet, Bologna, Italy
| | | | - Pietro Guaraldi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC NeuroMet, Bologna, Italy
| | - Pietro Cortelli
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC NeuroMet, Bologna, Italy
| | - Pann-Ghill Suh
- Korea Brain Research Institute, Daegu, Republic of Korea
- School of Life Sciences, UNIST, Ulsan, Republic of Korea
| | - Lucio Cocco
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.
| | - Lucia Manzoli
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.
| | - Giulia Ramazzotti
- Cellular Signalling Laboratory, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
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26
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El-Naggar MM, Tinsley RC, Cable J. Ultrastructural observations on the oncomiracidium epidermis and adult tegument of Discocotyle sagittata, a monogenean gill parasite of salmonids. Parasitol Res 2021; 120:899-910. [PMID: 33432440 PMCID: PMC7889578 DOI: 10.1007/s00436-020-07045-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/28/2020] [Indexed: 11/30/2022]
Abstract
During their different life stages, parasites undergo remarkable morphological, physiological, and behavioral "metamorphoses" to meet the needs of their changing habitats. This is even true for ectoparasites, such as the monogeneans, which typically have a free-swimming larval stage (oncomiracidium) that seeks out and attaches to the external surfaces of fish where they mature. Before any obvious changes occur, there are ultrastructural differences in the oncomiracidium's outer surface that prepare it for a parasitic existence. The present findings suggest a distinct variation in timing of the switch from oncomiracidia epidermis to the syncytial structure of the adult tegument and so, to date, there are three such categories within the Monogenea: (1) Nuclei of both ciliated cells and interciliary cytoplasm are shed from the surface layer and the epidermis becomes a syncytial layer during the later stages of embryogenesis; (2) nuclei of both ciliated cells and interciliary syncytium remain distinct and the switch occurs later after the oncomiracidia hatch (as in the present study); and (3) the nuclei remain distinct in the ciliated epidermis but those of the interciliary epidermis are lost during embryonic development. Here we describe how the epidermis of the oncomiracidium of Discocotyle sagittata is differentiated into two regions, a ciliated cell layer and an interciliary, syncytial cytoplasm, both of which are nucleated. The interciliary syncytium extends in-between and underneath the ciliated cells and sometimes covers part of their apical surfaces, possibly the start of their shedding process. The presence of membranous whorls and pyknotic nuclei over the surface are indicative of membrane turnover suggesting that the switch in epidermis morphology is already initiated at this stage. The body tegument and associated putative sensory receptors of subadult and adult D. sagittata are similar to those in other monogeneans.
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Affiliation(s)
- Mohamed Mohamed El-Naggar
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Richard C Tinsley
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK.
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27
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Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F. In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science 2021; 371:eaay3446. [PMID: 33384301 PMCID: PMC7962746 DOI: 10.1126/science.aay3446] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/17/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
Abstract
Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.
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Affiliation(s)
- Andrew C Payne
- Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Zachary D Chiang
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paul L Reginato
- Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | | | - Evan M Murray
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Chun-Chen Yao
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | | | - Andrew S Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ajay S Labade
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
- Department of Biology, MIT, Cambridge, MA 02139, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Edward S Boyden
- Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- McGovern Institute, MIT, Cambridge, MA 02139, USA
- Koch Institute, MIT, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Centers for Neurobiological Engineering and Extreme Bionics, MIT, Cambridge, MA 02139, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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28
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Büttner M, Lagerholm CB, Waithe D, Galiani S, Schliebs W, Erdmann R, Eggeling C, Reglinski K. Challenges of Using Expansion Microscopy for Super-resolved Imaging of Cellular Organelles. Chembiochem 2021; 22:686-693. [PMID: 33049107 PMCID: PMC7894168 DOI: 10.1002/cbic.202000571] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/07/2020] [Indexed: 12/26/2022]
Abstract
Expansion microscopy (ExM) has been successfully used to improve the spatial resolution when imaging tissues by optical microscopy. In ExM, proteins of a fixed sample are crosslinked to a swellable acrylamide gel, which expands when incubated in water. Therefore, ExM allows enlarged subcellular structures to be resolved that would otherwise be hidden to standard confocal microscopy. Herein, we aim to validate ExM for the study of peroxisomes, mitochondria, nuclei and the plasma membrane. Upon comparison of the expansion factors of these cellular compartments in HEK293 cells within the same gel, we found significant differences, of a factor of above 2, in expansion factors. For peroxisomes, the expansion factor differed even between peroxisomal membrane and matrix marker; this underlines the need for a thorough validation of expansion factors of this powerful technique. We further give an overview of possible quantification methods for the determination of expansion factors of intracellular organelles, and we highlight some potentials and challenges.
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Affiliation(s)
- Maximilian Büttner
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular MedicineUniversity of Oxford Headley WayOxfordOX3 9DSUK
- Institute for Anatomy and Cell BiologyMartin-Luther-University Halle-WittenbergGroße Steinstraße 5206108HalleGermany
| | - Christoffer B. Lagerholm
- Wolfson Imaging Centre MRC Weatherall Institute of Molecular MedicineUniversity of Oxford Headley WayOxfordOX3 9DSUK
| | - Dominic Waithe
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular MedicineUniversity of Oxford Headley WayOxfordOX3 9DSUK
- Wolfson Imaging Centre MRC Weatherall Institute of Molecular MedicineUniversity of Oxford Headley WayOxfordOX3 9DSUK
| | - Silvia Galiani
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular MedicineUniversity of Oxford Headley WayOxfordOX3 9DSUK
- Wolfson Imaging Centre MRC Weatherall Institute of Molecular MedicineUniversity of Oxford Headley WayOxfordOX3 9DSUK
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry Systemic BiochemistryRuhr-University BochumUniversitätsstraße 15044801BochumGermany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry Systemic BiochemistryRuhr-University BochumUniversitätsstraße 15044801BochumGermany
| | - Christian Eggeling
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular MedicineUniversity of Oxford Headley WayOxfordOX3 9DSUK
- Leibniz-Institute of Photonic Technologies & Institute of Applied Optic and BiophysicsFriedrich-Schiller University JenaMax-Wien-Platz 107743JenaGermany
| | - Katharina Reglinski
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular MedicineUniversity of Oxford Headley WayOxfordOX3 9DSUK
- Leibniz-Institute of Photonic Technologies & Institute of Applied Optic and BiophysicsFriedrich-Schiller University JenaMax-Wien-Platz 107743JenaGermany
- University Hospital JenaBachstraße 1807743JenaGermany
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29
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Abdollahzadeh A, Belevich I, Jokitalo E, Sierra A, Tohka J. DeepACSON automated segmentation of white matter in 3D electron microscopy. Commun Biol 2021; 4:179. [PMID: 33568775 PMCID: PMC7876004 DOI: 10.1038/s42003-021-01699-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Tracing the entirety of ultrastructures in large three-dimensional electron microscopy (3D-EM) images of the brain tissue requires automated segmentation techniques. Current segmentation techniques use deep convolutional neural networks (DCNNs) and rely on high-contrast cellular membranes and high-resolution EM volumes. On the other hand, segmenting low-resolution, large EM volumes requires methods to account for severe membrane discontinuities inescapable. Therefore, we developed DeepACSON, which performs DCNN-based semantic segmentation and shape-decomposition-based instance segmentation. DeepACSON instance segmentation uses the tubularity of myelinated axons and decomposes under-segmented myelinated axons into their constituent axons. We applied DeepACSON to ten EM volumes of rats after sham-operation or traumatic brain injury, segmenting hundreds of thousands of long-span myelinated axons, thousands of cell nuclei, and millions of mitochondria with excellent evaluation scores. DeepACSON quantified the morphology and spatial aspects of white matter ultrastructures, capturing nanoscopic morphological alterations five months after the injury.
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Affiliation(s)
- Ali Abdollahzadeh
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Alejandra Sierra
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Jussi Tohka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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30
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Scheffler K, Uraji J, Jentoft I, Cavazza T, Mönnich E, Mogessie B, Schuh M. Two mechanisms drive pronuclear migration in mouse zygotes. Nat Commun 2021; 12:841. [PMID: 33547291 PMCID: PMC7864974 DOI: 10.1038/s41467-021-21020-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
A new life begins with the unification of the maternal and paternal chromosomes upon fertilization. The parental chromosomes first become enclosed in two separate pronuclei near the surface of the fertilized egg. The mechanisms that then move the pronuclei inwards for their unification are only poorly understood in mammals. Here, we report two mechanisms that act in concert to unite the parental genomes in fertilized mouse eggs. The male pronucleus assembles within the fertilization cone and is rapidly moved inwards by the flattening cone. Rab11a recruits the actin nucleation factors Spire and Formin-2 into the fertilization cone, where they locally nucleate actin and further accelerate the pronucleus inwards. In parallel, a dynamic network of microtubules assembles that slowly moves the male and female pronuclei towards the cell centre in a dynein-dependent manner. Both mechanisms are partially redundant and act in concert to unite the parental pronuclei in the zygote's centre.
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Affiliation(s)
- Kathleen Scheffler
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Julia Uraji
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ida Jentoft
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tommaso Cavazza
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Eike Mönnich
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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Liu JL, Gall JG. Cold shock induces novel nuclear bodies in Xenopus oocytes. Exp Cell Res 2021; 398:112386. [PMID: 33220259 PMCID: PMC7771896 DOI: 10.1016/j.yexcr.2020.112386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/22/2022]
Abstract
Here we describe novel spherical structures that are induced by cold shock on the lampbrush chromosomes (LBCs) of Xenopus laevis oocytes. We call these structures cold bodies or C-bodies. C-bodies are distributed symmetrically on homologous LBCs, with a pattern similar to that of 5S rDNA. Neither active transcription nor translation is necessary for their formation. Similar protrusions occur on the edges of some nucleoli. Endogenous LBCs as well as those derived from injected sperm form C-bodies under cold shock conditions. The function of C-bodies is unknown.
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Affiliation(s)
- Ji-Long Liu
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
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32
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Kubalová I, Schmidt Černohorská M, Huranová M, Weisshart K, Houben A, Schubert V. Prospects and limitations of expansion microscopy in chromatin ultrastructure determination. Chromosome Res 2020; 28:355-368. [PMID: 32939606 PMCID: PMC7691311 DOI: 10.1007/s10577-020-09637-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 02/04/2023]
Abstract
Expansion microscopy (ExM) is a method to magnify physically a specimen with preserved ultrastructure. It has the potential to explore structural features beyond the diffraction limit of light. The procedure has been successfully used for different animal species, from isolated macromolecular complexes through cells to tissue slices. Expansion of plant-derived samples is still at the beginning, and little is known, whether the chromatin ultrastructure becomes altered by physical expansion. In this study, we expanded isolated barley nuclei and compared whether ExM can provide a structural view of chromatin comparable with super-resolution microscopy. Different fixation and denaturation/digestion conditions were tested to maintain the chromatin ultrastructure. We achieved up to ~4.2-times physically expanded nuclei corresponding to a maximal resolution of ~50-60 nm when imaged by wild-field (WF) microscopy. By applying structured illumination microscopy (SIM, super-resolution) doubling the WF resolution, the chromatin structures were observed at a resolution of ~25-35 nm. WF microscopy showed a preserved nucleus shape and nucleoli. Moreover, we were able to detect chromatin domains, invisible in unexpanded nuclei. However, by applying SIM, we observed that the preservation of the chromatin ultrastructure after the expansion was not complete and that the majority of the tested conditions failed to keep the ultrastructure. Nevertheless, using expanded nuclei, we localized successfully centromere repeats by fluorescence in situ hybridization (FISH) and the centromere-specific histone H3 variant CENH3 by indirect immunolabelling. However, although these repeats and proteins were localized at the correct position within the nuclei (indicating a Rabl orientation), their ultrastructural arrangement was impaired.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Markéta Schmidt Černohorská
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics,, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martina Huranová
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics,, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
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33
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Ma J, Do M, Le Gros MA, Peskin CS, Larabell CA, Mori Y, Isaacson SA. Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus. PLoS Comput Biol 2020; 16:e1008356. [PMID: 33196636 PMCID: PMC7704053 DOI: 10.1371/journal.pcbi.1008356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 11/30/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
For a chemical signal to propagate across a cell, it must navigate a tortuous environment involving a variety of organelle barriers. In this work we study mathematical models for a basic chemical signal, the arrival times at the nuclear membrane of proteins that are activated at the cell membrane and diffuse throughout the cytosol. Organelle surfaces within human B cells are reconstructed from soft X-ray tomographic images, and modeled as reflecting barriers to the molecules’ diffusion. We show that signal inactivation sharpens signals, reducing variability in the arrival time at the nuclear membrane. Inactivation can also compensate for an observed slowdown in signal propagation induced by the presence of organelle barriers, leading to arrival times at the nuclear membrane that are comparable to models in which the cytosol is treated as an open, empty region. In the limit of strong signal inactivation this is achieved by filtering out molecules that traverse non-geodesic paths. The inside of cells is a complex spatial environment, filled with organelles, filaments and proteins. It is an open question how cell signaling pathways function robustly in the presence of such spatial heterogeneity. In this work we study how organelle barriers influence the most basic of chemical signals; the diffusive propagation of an activated protein from the cell membrane to nucleus. Three-dimensional B cell organelle and membrane geometries reconstructed from soft X-ray tomographic images are used in building mathematical models of the signal propagation process. Our models demonstrate that organelle barriers significantly increase the time required for a diffusing protein to traverse from the cell membrane to nucleus when compared to a cell with an empty cytosolic space. We also show that signal inactivation, a fundamental component of all signaling pathways, can provide robustness in the signal arrival time in two ways. Increasing rates of signal inactivation reduce variability in the arrival time, while also dramatically reducing the degree to which organelle barriers increase the arrival time (in comparison to a cell with an empty cytosol).
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Affiliation(s)
- Jingwei Ma
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America
| | - Myan Do
- Department of Cellular and Molecular Medicine, University of California, San Diego Medical School, San Diego, California, United States of America
| | - Mark A. Le Gros
- Department of Anatomy, University of California, San Francisco, San Francisco, California, United States of America
- National Center for X-ray Tomography, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Charles S. Peskin
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
| | - Carolyn A. Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, California, United States of America
- National Center for X-ray Tomography, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Yoichiro Mori
- Department of Mathematics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Samuel A. Isaacson
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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Gwo JC, Hsu TH. Ultrastructure of sperm and complete mitochondrial genome in Meretrix sp. (Bivalvia: Veneridae) from Taiwan. Tissue Cell 2020; 67:101454. [PMID: 33160271 DOI: 10.1016/j.tice.2020.101454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022]
Abstract
Spermatozoan ultrastructure and complete mitochondrial genome in the marine bivalve mollusk Meretrix sp. (Taiwan) from Taiwan are described and contrasted with other bivalves, especially within Meretrix. We have examined the features of the mature gonadal spermatozoa of Meretrix sp. (Taiwan) and provided comparisons with the other four Meretrix species (M. petechialis, M. meretrix, M. lyrata, and M. lamarckii). The morphological characteristics of these spermatozoa are diagnostic for each of the species studied here. The most marked interspecific difference was found in the acrosome. Meretrix sp. (Taiwan) is genetically distinct and is a different species from M. petechialis and M. lusoria (Japan) based on complete mitochondrial genome data. Sperm data for Meretrix are limited but show remarkable congruence with the molecular results. We suggest use Meretrix formosa Gwo and Hsu as the scientific name for Taiwanese hard clams, Meretrix sp. (Taiwan). Additional species, particularly the Japanese hard clam (M. lusoria) require examination before this tentative conclusion can be verified.
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Affiliation(s)
- Jin-Chywan Gwo
- Department of Aquaculture, Taiwan National Ocean University, Keelung 20224, Taiwan.
| | - Te-Hua Hsu
- Department of Aquaculture, Taiwan National Ocean University, Keelung 20224, Taiwan
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35
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Zhang J, Li Y, Zhao S, Wu X. Identification of A functional region in Bombyx mori nucleopolyhedrovirus VP39 that is essential for nuclear actin polymerization. Virology 2020; 550:37-50. [PMID: 32877775 DOI: 10.1016/j.virol.2020.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 02/03/2023]
Abstract
Nuclear actin polymerization plays an indispensable role in the nuclear assembly of baculovirus nucleocapsid, but the underlying viral infection-mediated mechanism remains unclear. VP39 is the major protein in baculovirus capsid, which builds the skeleton of the capsid tubular structure. VP39 is suggested in previous studies to interact with cellular actin and mediate actin polymerization. However, it is unclear about the role of VP39 in mediating nuclear actin polymerization. Results in this study indicated that vp39 deletion abolished nuclear actin polymerization, which was recovered after vp39 repair, revealing the essential part of VP39 in nuclear actin polymerization. Furthermore, a series of mutants with vp39 deletions were constructed to analyze the important region responsible for nuclear actin polymerization. In addition, intracellular localization analysis demonstrated that the amino acids 192-286 in VP39 C-terminal are responsible for nuclear actin polymerization.
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Affiliation(s)
- Jianjia Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yang Li
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shudi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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36
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Dymek AM, Pecio A. Spermatogenesis in the inseminating African butterflyfish Pantodon buchholzi (Teleostei: Osteoglossiformes: Pantodontidae) with the revision of residual bodies formation. J Fish Biol 2020; 97:1491-1506. [PMID: 32869341 DOI: 10.1111/jfb.14518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
The aim of this study was to analyse spermatogenesis in the African butterflyfish, Pantodon buchholzi, using transmission electron microscopy and scanning electron microscopy. P. buchholzi is the most basal teleost that exhibits insemination and produces a highly complex introsperm with the most elongate midpiece known in teleost fishes. Their early stages (spermatogonia and spermatocytes) do not differ greatly from those of other fishes, with the exception of Golgi apparatus degradation appearing as spindle-shaped bodies (SSBs). In round, early spermatids, the development of the flagellum begins after the migration of the centriolar complex towards the nucleus. Later, the elongation of the midpiece coincides with the displacement of the mitochondria and their fusion to produce nine mitochondrial derivatives (MDs). In these spermatids, the nucleus is situated laterally to the midpiece, with condensing chromatin in the centre of the nucleus. Within the midpiece, the flagellum is located within a cytoplasmic canal and is surrounded by a cytoplasmic sleeve containing fibres, MDs and a great amount of cytoplasm located on one side. During the next phase, nuclear rotation, the highly condensed chromatin is displaced to a position above the centriolar apparatus, whereas chromatin-free nucleoplasm is transferred to the cytoplasm. Later, this nucleoplasm, still surrounded by the nuclear membrane, is eliminated into the cyst lumen as the nucleoplasmic packet. Within the highly elongate spermatids, other excess organelles (SSBs, endoplasmic reticulum and mitochondria) are eliminated as residual bodies (RBs). Fully developed spermatozoa, which contain conical-shaped nuclei, eventually coalesce to form unencapsulated sperm packets (spermatozeugmata) that are surrounded by RBs at the level of the extremely elongate midpieces. Later, RBs are removed at the periphery of the cyst by means of phagocytosis by Sertoli cells.
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Affiliation(s)
- Anna M Dymek
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, Cracow, Poland
| | - Anna Pecio
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, Cracow, Poland
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37
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MacDonald KM, Benguerfi S, Harding SM. Alerting the immune system to DNA damage: micronuclei as mediators. Essays Biochem 2020; 64:753-764. [PMID: 32844183 PMCID: PMC7588664 DOI: 10.1042/ebc20200016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/01/2020] [Accepted: 08/13/2020] [Indexed: 12/18/2022]
Abstract
Healthy cells experience thousands of DNA lesions per day during normal cellular metabolism, and ionizing radiation and chemotherapeutic drugs rely on DNA damage to kill cancer cells. In response to such lesions, the DNA damage response (DDR) activates cell-cycle checkpoints, initiates DNA repair mechanisms, or promotes the clearance of irreparable cells. Work over the past decade has revealed broader influences of the DDR, involving inflammatory gene expression following unresolved DNA damage, and immune surveillance of damaged or mutated cells. Subcellular structures called micronuclei, containing broken fragments of DNA or whole chromosomes that have been isolated away from the rest of the genome, are now recognized as one mediator of DDR-associated immune recognition. Micronuclei can initiate pro-inflammatory signaling cascades, or massively degrade to invoke distinct forms of genomic instability. In this mini-review, we aim to provide an overview of the current evidence linking the DDR to activation of the immune response through micronuclei formation, identifying key areas of interest, open questions, and emerging implications.
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Affiliation(s)
- Kate M MacDonald
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Soraya Benguerfi
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Shane M Harding
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology and Immunology, University of Toronto, Toronto, ON, Canada
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38
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Ohta S, Oshimo S, Ohta E, Nehira T, Ômura H, Uy MM, Ishihara Y. Asaroidoxazines from the Roots of Asarum asaroides Induce Apoptosis in Human Neuroblastoma Cells. J Nat Prod 2020; 83:3050-3057. [PMID: 32955260 DOI: 10.1021/acs.jnatprod.0c00574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Plants in the family Aristolochiaceae contain phenanthrene skeleton-containing chemical constituents that exhibit nephrotoxic, carcinogenic, mutagenic, anti-inflammatory, and cytotoxic effects. Two new phenanthrene-containing 1,2-oxazin-6-ones, designated as asaroidoxazine A (1) and asaroidoxazine B (2), and a known aristolactam, 5-methoxyaristololactam I (3), were isolated from the roots of Asarum asaroides. The structures of compounds 1 and 2 were determined using spectroscopic methods and X-ray crystallography. Treatment of SH-SY5Y human neuroblastoma cells with 1 μM of asaroidoxazine A (1) induced nuclear condensation as well as caspase-3/7 activation, indicating that this compound is a strong apoptosis inducer in neuronal cells. This is the first report of apoptosis induction by phenanthrene-containing oxazines.
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Affiliation(s)
- Shinji Ohta
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan
| | - Shiori Oshimo
- Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan
| | - Emi Ohta
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan
| | - Tatsuo Nehira
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan
| | - Hisashi Ômura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan
| | - Mylene M Uy
- Department of Chemistry, Mindanao State University-Iligan Institute of Technology, Iligan City 9200, Philippines
| | - Yasuhiro Ishihara
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan
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Pérez-Rodriguez S, de Jesús Ramírez-Lira M, Wulff T, Voldbor BG, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Enrichment of microsomes from Chinese hamster ovary cells by subcellular fractionation for its use in proteomic analysis. PLoS One 2020; 15:e0237930. [PMID: 32841274 PMCID: PMC7447005 DOI: 10.1371/journal.pone.0237930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/06/2020] [Indexed: 11/19/2022] Open
Abstract
Chinese hamster ovary cells have been the workhorse for the production of recombinant proteins in mammalian cells. Since biochemical, cellular and omics studies are usually affected by the lack of suitable fractionation procedures to isolate compartments from these cells, differential and isopycnic centrifugation based techniques were characterized and developed specially for them. Enriched fractions in intact nuclei, mitochondria, peroxisomes, cis-Golgi, trans-Golgi and endoplasmic reticulum (ER) were obtained in differential centrifugation steps and subsequently separated in discontinuous sucrose gradients. Nuclei, mitochondria, cis-Golgi, peroxisomes and smooth ER fractions were obtained as defined bands in 30-60% gradients. Despite the low percentage represented by the microsomes of the total cell homogenate (1.7%), their separation in a novel sucrose gradient (10-60%) showed enough resolution and efficiency to quantitatively separate their components into enriched fractions in trans-Golgi, cis-Golgi and ER. The identity of these organelles belonging to the classical secretion pathway that came from 10-60% gradients was confirmed by proteomics. Data are available via ProteomeXchange with identifier PXD019778. Components from ER and plasma membrane were the most frequent contaminants in almost all obtained fractions. The improved sucrose gradient for microsomal samples proved being successful in obtaining enriched fractions of low abundance organelles, such as Golgi apparatus and ER components, for biochemical and molecular studies, and suitable for proteomic research, which makes it a useful tool for future studies of this and other mammalian cell lines.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - María de Jesús Ramírez-Lira
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bjørn Gunnar Voldbor
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Octavio T. Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Mauricio A. Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
| | - Norma A. Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
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Abstract
RATIONALE Ovarian microcystic stromal tumor is a relatively rare tumor type, which is characterized by morphology with microcyst structure, solid cellular areas, and hyalinized fibrous stroma. The most reported tumors were stage I with good prognosis. PATIENT CONCERNS We report a case of a 33-year-old woman with primary ovarian microcystic stromal tumor with significant bizarre nuclei. We describe the clinical, histopathological, and immunohistochemical findings and review the English literatures. So far, as we know, the patient presented here is a rare case of ovarian microcystic stromal tumor with prominent bizarre nuclei accounting for about 50% of the tumor cells. DIAGNOSES She was diagnosed with ovarian microcystic stromal tumor with significant bizarre nuclei. INTERVENTIONS The right ovarian tumor was resected laparoscopically on October 19, 2018. OUTCOMES Up to now, the patient is free of disease at 19 months of follow-up. LESSONS This is a rare case of ovarian microcystic stromal tumor with obvious bizarre nuclei. This report will contribute to expand the morphological spectrum of ovarian microcystic stromal tumor.
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Affiliation(s)
- Ying He
- Department of Pathology, West China Second Hospital of Sichuan University
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Lian Xu
- Department of Pathology, West China Second Hospital of Sichuan University
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Min Feng
- Department of Pathology, West China Second Hospital of Sichuan University
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
| | - Wei Wang
- Department of Pathology, West China Second Hospital of Sichuan University
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Sichuan, China
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41
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Guo X, Dai X, Wu X, Zhou T, Ni J, Xue J, Wang X. Understanding the birth of rupture-prone and irreparable micronuclei. Chromosoma 2020; 129:181-200. [PMID: 32671520 DOI: 10.1007/s00412-020-00741-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022]
Abstract
Micronuclei are extra-nuclear bodies mainly derived from ana-telophase lagging chromosomes/chromatins (LCs) that are not incorporated into primary nuclei at mitotic exit. Unlike primary nuclei, most micronuclei are enclosed by nuclear envelope (NE) that is highly susceptible to spontaneous and irreparable rupture. Ruptured micronuclei act as triggers of chromothripsis-like chaotic chromosomal rearrangements and cGAS-mediated innate immunity and inflammation, raising the view that micronuclei play active roles in human aging and tumorigenesis. Thus, understanding the ways in which micronuclear envelope (mNE) goes awry acquires increased importance. Here, we review the data to present a general framework for this question. We firstly describe NE reassembly after mitosis and NE repair during interphase. Simultaneously, we briefly discuss how mNE is organized and how mNE rupture controls the fate of micronuclei and micronucleated cells. As a focus of this review, we highlight current knowledge about why mNE is rupture-prone and irreparable. For this, we survey observations from a series of elegant studies to provide a systematic overview. We conclude that the birth of rupture-prone and irreparable micronuclei may be the cumulative effects of their intracellular geographic origins, biophysical properties, and specific mNE features. We propose that DNA damage and immunogenicity in micronuclei increase stepwise from altered mNE components, mNE rupture, and refractory to repair. Throughout our discussion, we note interesting issues in mNE fragility that have yet to be resolved.
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Affiliation(s)
- Xihan Guo
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Xueqin Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue Wu
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Tao Zhou
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Juan Ni
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Jinglun Xue
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xu Wang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, 650500, Yunnan, China.
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García Manzano MF, Joray MB, Laiolo J, Palacios SM, Carpinella MC. Cytotoxic Activity of Germacrane-Type Sesquiterpene Lactones from Dimerostemma aspilioides. J Nat Prod 2020; 83:1909-1918. [PMID: 32496057 DOI: 10.1021/acs.jnatprod.0c00115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The need for effective candidates as cytotoxic drugs that at the same time challenge cancer multidrug resistance encouraged a search for these in plants of central Argentina. Bioassay-guided fractionation of the cytotoxic extract from Dimerostemma aspilioides led to the isolation of the germacranolide tomenphantin A (1), along with three new analogues (2-4). These efficiently inhibited the proliferation of the leukemia cell lines K562 and CCRF-CEM and their resistant variants, Lucena 1 and CEM/ADR5000, respectively, with IC50 values ranging from 0.40 to 7.7 μM. The structures and relative configurations of compounds 1-4 were elucidated by analysis of the spectroscopic data, in particular NMR spectroscopy. The most active among these was compound 1 (IC50 = 0.40-5.1 μM), and, therefore, this was selected as a model for a mechanistic study, which revealed that its antiproliferative effect was mediated by cell cycle arrest in the G2/M phase followed by apoptosis. The activity of compound 1 was selective, given the absence of cytotoxicity toward peripheral blood mononuclear cells. The results show the potential of these compounds, and in particular of compound 1, as leads for the development of drug candidates to fight sensitive and resistant leukemia cells.
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Affiliation(s)
- María F García Manzano
- Fine Chemical and Natural Products Laboratory, Research Institute of Natural Resources and Sustainability José Sánchez Labrador S.J. (IRNASUS-CONICET), School of Chemistry, Catholic University of Córdoba, Córdoba X5016DHK, Argentina
| | - Mariana B Joray
- Fine Chemical and Natural Products Laboratory, Research Institute of Natural Resources and Sustainability José Sánchez Labrador S.J. (IRNASUS-CONICET), School of Chemistry, Catholic University of Córdoba, Córdoba X5016DHK, Argentina
| | - Jerónimo Laiolo
- Fine Chemical and Natural Products Laboratory, Research Institute of Natural Resources and Sustainability José Sánchez Labrador S.J. (IRNASUS-CONICET), School of Chemistry, Catholic University of Córdoba, Córdoba X5016DHK, Argentina
| | - Sara M Palacios
- Fine Chemical and Natural Products Laboratory, Research Institute of Natural Resources and Sustainability José Sánchez Labrador S.J. (IRNASUS-CONICET), School of Chemistry, Catholic University of Córdoba, Córdoba X5016DHK, Argentina
| | - María C Carpinella
- Fine Chemical and Natural Products Laboratory, Research Institute of Natural Resources and Sustainability José Sánchez Labrador S.J. (IRNASUS-CONICET), School of Chemistry, Catholic University of Córdoba, Córdoba X5016DHK, Argentina
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43
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Yu H, Hu W, Song X, Zhao Y. Generation of Multipotent Stem Cells from Adult Human Peripheral Blood Following the Treatment with Platelet-Derived Mitochondria. Cells 2020; 9:cells9061350. [PMID: 32485922 PMCID: PMC7349571 DOI: 10.3390/cells9061350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022] Open
Abstract
Autologous stem cells are highly preferred for cellular therapy to treat human diseases. Mitochondria are organelles normally located in cytoplasm. Our recent studies demonstrated the differentiation of adult peripheral blood-derived insulin-producing cells (designated PB-IPC) into hematopoietic-like cells after the treatment with platelet-derived mitochondria. To further explore the molecular mechanism and their therapeutic potentials, through confocal and electron microscopy, we found that mitochondria enter cells and directly penetrate the nucleus of PB-IPC after the treatment with platelet-derived mitochondria, where they can produce profound epigenetic changes as demonstrated by RNA-seq and PCR array. Ex vivo functional studies established that mitochondrion-induced PB-IPC (miPB-IPC) can give rise to retinal pigment epithelium (RPE) cells and neuronal cells in the presence of different inducers. Further colony analysis highlighted the multipotent capability of the differentiation of PB-IPC into three-germ layer-derived cells. Therefore, these data indicate a novel function of mitochondria in cellular reprogramming, leading to the generation of autologous multipotent stem cells for clinical applications.
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Affiliation(s)
| | | | | | - Yong Zhao
- Correspondence: ; Tel.: +201-880-3460
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Affiliation(s)
- Aminder Singh
- Pathology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Neena Sood
- Pathology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Vikram Narang
- Pathology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Abhishek Goyal
- Department of Cardiology, Dayanand Medical College and Hospital, Ludhiana, India
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45
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Li M, Nopparat J, Aguilar BJ, Chen YH, Zhang J, Du J, Ai X, Luo Y, Jiang Y, Boykin C, Lu Q. Intratumor δ-catenin heterogeneity driven by genomic rearrangement dictates growth factor dependent prostate cancer progression. Oncogene 2020; 39:4358-4374. [PMID: 32313227 PMCID: PMC10493073 DOI: 10.1038/s41388-020-1281-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022]
Abstract
Only a small number of genes are bona fide oncogenes and tumor suppressors such as Ras, Myc, β-catenin, p53, and APC. However, targeting these cancer drivers frequently fail to demonstrate sustained cancer remission. Tumor heterogeneity and evolution contribute to cancer resistance and pose challenges for cancer therapy due to differential genomic rearrangement and expression driving distinct tumor responses to treatments. Here we report that intratumor heterogeneity of Wnt/β-catenin modulator δ-catenin controls individual cell behavior to promote cancer. The differential intratumor subcellular localization of δ-catenin mirrors its compartmentalization in prostate cancer xenograft cultures as result of mutation-rendered δ-catenin truncations. Wild-type and δ-catenin mutants displayed distinct protein interactomes that highlight rewiring of signal networks. Localization specific δ-catenin mutants influenced p120ctn-dependent Rho GTPase phosphorylation and shifted cells towards differential bFGF-responsive growth and motility, a known signal to bypass androgen receptor dependence. Mutant δ-catenin promoted Myc-induced prostate tumorigenesis while increasing bFGF-p38 MAP kinase signaling, β-catenin-HIF-1α expression, and the nuclear size. Therefore, intratumor δ-catenin heterogeneity originated from genetic remodeling promotes prostate cancer expansion towards androgen independent signaling, supporting a neomorphism model paradigm for targeting tumor progression.
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Affiliation(s)
- Mingchuan Li
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Jongdee Nopparat
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Anatomy, Prince of Songkla University, Songkhla, Thailand
| | - Byron J. Aguilar
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Yan-hua Chen
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Jiao Zhang
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Jie Du
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Xin Ai
- Dept. of Urology, PLA Army General Hospital, Beijing, China
| | - Yong Luo
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Yongguang Jiang
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Christi Boykin
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Qun Lu
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
- The Harriet and John Wooten Laboratory for Alzheimer’s and Neurodegenerative Diseases Research, The Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
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Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, Śliwińska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczyński D, Ruan Y, Wilczyński GM. Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization. Nat Commun 2020; 11:2120. [PMID: 32358536 PMCID: PMC7195386 DOI: 10.1038/s41467-020-15987-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of an electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5 × 5 × 30 nm in xyz dimensions) that is superior to the current super-resolution by fluorescence light microscopy. We apply 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualize a large number of distinctive 3D chromatin folding structures in ultra-resolution. We further quantitatively characterize the reconstituted chromatin folding structures by identifying sub-domains, and uncover a high level heterogeneity of chromatin folding ultrastructures in individual nuclei, suggestive of extensive dynamic fluidity in 3D chromatin states.
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Affiliation(s)
- Paweł Trzaskoma
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Błażej Ruszczycki
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington, CT, 06032, USA
| | - Katarzyna K Pels
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Katarzyna Krawczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Grzegorz Bokota
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Andrzej A Szczepankiewicz
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Jesse Aaron
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA, 20147, USA
| | - Agnieszka Walczak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 6 Uniwersytetu Poznanskiego St, 61-614, Poznan, Poland
| | - Małgorzata A Śliwińska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Adriana Magalska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Michal Kadlof
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Artur Wolny
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland
| | - Zofia Parteka
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
| | - Sebastian Arabasz
- Łukasiewicz Research NETWORK - PORT Polish Center for Technology Development, 147 Stablowicka St, 54-066, Wroclaw, Poland
| | - Magdalena Kiss-Arabasz
- Łukasiewicz Research NETWORK - PORT Polish Center for Technology Development, 147 Stablowicka St, 54-066, Wroclaw, Poland
| | - Dariusz Plewczyński
- Center of New Technologies, University of Warsaw, 2c Banacha St, 02-097, Warsaw, Poland
- Mathematics and Information Science, Warsaw Technical University, 75 Koszykowa St, 00-662, Warsaw, Poland
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington, CT, 06032, USA.
| | - Grzegorz M Wilczyński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093, Warsaw, Poland.
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47
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Xiong F, Duan CY, Liu HH, Wu JH, Zhang ZH, Li S, Zhang Y. Arabidopsis KETCH1 Is Critical for the Nuclear Accumulation of Ribosomal Proteins and Gametogenesis. Plant Cell 2020; 32:1270-1284. [PMID: 32086364 PMCID: PMC7145482 DOI: 10.1105/tpc.19.00791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/02/2020] [Accepted: 02/21/2020] [Indexed: 05/19/2023]
Abstract
Male and female gametophytes are generated from micro- or megaspore mother cells through consecutive meiotic and mitotic cell divisions. Defects in these divisions often result in gametophytic lethality. Gametophytic lethality was also reported when genes encoding ribosome-related proteins were mutated. Although numerous ribosomal proteins (RPs) have been identified in plants based on homology with their yeast and metazoan counterparts, how RPs are regulated, e.g., through dynamic subcellular targeting, is unknown. We report here that an Arabidopsis (Arabidopsis thaliana) importin β, KETCH1 (karyopherin enabling the transport of the cytoplasmic HYL1), is critical for gametogenesis. Karyopherins are molecular chaperones mediating nucleocytoplasmic protein transport. However, the role of KETCH1 during gametogenesis is independent of HYPONASTIC LEAVES 1 (HYL1), a previously reported KETCH1 cargo. Instead, KETCH1 interacts with several RPs and is critical for the nuclear accumulation of RPL27a, whose mutations caused similar gametophytic defects. We further showed that knocking down KETCH1 caused reduced ribosome biogenesis and translational capacity, which may trigger the arrest of mitotic cell cycle progression and lead to gametophytic lethality.
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Affiliation(s)
- Feng Xiong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Cun-Ying Duan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Hai-Hong Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Ju-Hua Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Zhong-Hui Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Sha Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yan Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
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Di Stefano M, Di Giovanni F, Pozharskaia V, Gomar-Alba M, Baù D, Carey LB, Marti-Renom MA, Mendoza M. Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast. Genetics 2020; 214:651-667. [PMID: 31907200 PMCID: PMC7054015 DOI: 10.1534/genetics.119.302978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/01/2020] [Indexed: 12/03/2022] Open
Abstract
The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.
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Affiliation(s)
- Marco Di Stefano
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Francesca Di Giovanni
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Vasilisa Pozharskaia
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Davide Baù
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Lucas B Carey
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871 Beijing, China
- Peking-Tsinghua Center for the Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871 Beijing, China
| | - Marc A Marti-Renom
- CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- ICREA, 08010 Barcelona, Spain
| | - Manuel Mendoza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
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49
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Zhang Y, Zhang X, Shi Y, Sun C, Zhou N, Wen H. The Synthesis and Functional Study of Multicolor Nitrogen-Doped Carbon Dots for Live Cell Nuclear Imaging. Molecules 2020; 25:molecules25020306. [PMID: 31940913 PMCID: PMC7024153 DOI: 10.3390/molecules25020306] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/16/2022] Open
Abstract
The nitrogen-doped carbon dots (N-CQDs) were synthesized by citric acid as a raw material and propylene diamine as a passivation agent. Structure, optical properties and biocompatibility of N-CQDs were analyzed. It was found that the N-CQDs possessed concentration-dependent, multicolor photoluminescence and low toxicity. As demonstrated in the imaging of bioluminescence, by adjusting the concentration of N-CQDs, the cell imaging effect can be adjusted. The internalized N-CQDs were concentrated in the nucleus. A novel tool for studying the nuclear changes during the cell cycle was developed.
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Affiliation(s)
- Yanan Zhang
- Department of Physiology, Harbin Medical University, Harbin 150081, China;
| | - Xingwei Zhang
- Department of Chemistry, Northeast Agricultural University, Harbin 150025, China; (X.Z.); (Y.S.); (C.S.)
| | - Yanping Shi
- Department of Chemistry, Northeast Agricultural University, Harbin 150025, China; (X.Z.); (Y.S.); (C.S.)
| | - Chao Sun
- Department of Chemistry, Northeast Agricultural University, Harbin 150025, China; (X.Z.); (Y.S.); (C.S.)
| | - Nan Zhou
- Department of Chemistry, Northeast Agricultural University, Harbin 150025, China; (X.Z.); (Y.S.); (C.S.)
- Correspondence: (H.W.); (N.Z.); Tel.: +86-13766873464 (N.Z.)
| | - Haixia Wen
- Department of Physiology, Harbin Medical University, Harbin 150081, China;
- Correspondence: (H.W.); (N.Z.); Tel.: +86-13766873464 (N.Z.)
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50
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Smetana K, Klamová H, Mikulenková D. Dominant Nucleolus in the Progenitor Cell Using Human Bone Marrow Erythroid and Granulocytic Cell Lineages as a Model. A Morphological and Cytochemical Note. Folia Biol (Praha) 2020; 66:111-115. [PMID: 33069190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Progenitor cells of the human erythroid and granulocytic cell lineages are characterized by the presence of several nucleoli. One of these nucleoli is larger and possesses more fibrillar centres than others. Such nucleolus is apparently dominant in respect of both size and main nucleolar function such as nucleolar-ribosomal RNA transcription. Such nucleolus is also visible in specimens using conventional visualization procedures, in contrast to smaller nucleoli. In the terminal differentiation nucleated stages of the erythroid and granulocytic development, dominant nucleoli apparently disappeared, since these cells mostly contained very small nucleoli of a similar size with one fibrillar centre. Thus, the easily visible dominant nucleoli appear to be useful markers of the progenitor cell state, such as proliferation, and differentiation potential.
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Affiliation(s)
- K Smetana
- Institute of Haematology and Blood Transfusion, Prague, Czech Republic
| | - H Klamová
- Institute of Haematology and Blood Transfusion, Prague, Czech Republic
| | - D Mikulenková
- Institute of Haematology and Blood Transfusion, Prague, Czech Republic
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