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Fei J, Jadaliha M, Harmon TS, Li ITS, Hua B, Hao Q, Holehouse AS, Reyer M, Sun Q, Freier SM, Pappu RV, Prasanth KV, Ha T. Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution. J Cell Sci 2017; 130:4180-4192. [PMID: 29133588 DOI: 10.1242/jcs.206854] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/01/2017] [Indexed: 12/30/2022] Open
Abstract
Nuclear speckles are self-assembled organelles composed of RNAs and proteins. They are proposed to act as structural domains that control distinct steps in gene expression, including transcription, splicing and mRNA export. Earlier studies identified differential localization of a few components within the speckles. It was speculated that the spatial organization of speckle components might contribute directly to the order of operations that coordinate distinct processes. Here, by performing multi-color structured illumination microscopy, we characterized the multilayer organization of speckles at a higher resolution. We found that SON and SC35 (also known as SRSF2) localize to the central region of the speckle, whereas MALAT1 and small nuclear (sn)RNAs are enriched at the speckle periphery. Coarse-grained simulations indicate that the non-random organization arises due to the interplay between favorable sequence-encoded intermolecular interactions of speckle-resident proteins and RNAs. Finally, we observe positive correlation between the total amount of RNA present within a speckle and the speckle size. These results imply that speckle size may be regulated to accommodate RNA accumulation and processing. Accumulation of RNA from various actively transcribed speckle-associated genes could contribute to the observed speckle size variations within a single cell.
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Affiliation(s)
- Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA .,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Mahdieh Jadaliha
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tyler S Harmon
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Isaac T S Li
- Department of Chemistry, University of British Columbia Okanagan, Kelowna, British Columbia, Canada, V1V 1V7
| | - Boyang Hua
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew Reyer
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taekjip Ha
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA
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53
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Hernandez-Segura A, de Jong TV, Melov S, Guryev V, Campisi J, Demaria M. Unmasking Transcriptional Heterogeneity in Senescent Cells. Curr Biol 2017; 27:2652-2660.e4. [PMID: 28844647 DOI: 10.1016/j.cub.2017.07.033] [Citation(s) in RCA: 486] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 06/22/2017] [Accepted: 07/13/2017] [Indexed: 12/31/2022]
Abstract
Cellular senescence is a state of irreversibly arrested proliferation, often induced by genotoxic stress [1]. Senescent cells participate in a variety of physiological and pathological conditions, including tumor suppression [2], embryonic development [3, 4], tissue repair [5-8], and organismal aging [9]. The senescence program is variably characterized by several non-exclusive markers, including constitutive DNA damage response (DDR) signaling, senescence-associated β-galactosidase (SA-βgal) activity, increased expression of the cyclin-dependent kinase (CDK) inhibitors p16INK4A (CDKN2A) and p21CIP1 (CDKN1A), increased secretion of many bio-active factors (the senescence-associated secretory phenotype, or SASP), and reduced expression of the nuclear lamina protein LaminB1 (LMNB1) [1]. Many senescence-associated markers result from altered transcription, but the senescent phenotype is variable, and methods for clearly identifying senescent cells are lacking [10]. Here, we characterize the heterogeneity of the senescence program using numerous whole-transcriptome datasets generated by us or publicly available. We identify transcriptome signatures associated with specific senescence-inducing stresses or senescent cell types and identify and validate genes that are commonly differentially regulated. We also show that the senescent phenotype is dynamic, changing at varying intervals after senescence induction. Identifying novel transcriptome signatures to detect any type of senescent cell or to discriminate among diverse senescence programs is an attractive strategy for determining the diverse biological roles of senescent cells and developing specific drug targets.
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Affiliation(s)
- Alejandra Hernandez-Segura
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Tristan V de Jong
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Simon Melov
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, 94945 Novato CA, USA
| | - Victor Guryev
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Judith Campisi
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, 94945 Novato CA, USA; Lawrence Berkeley National Laboratory, Life Sciences Division, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Marco Demaria
- European Research Institute for the Biology of Aging, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands.
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Stegeman R, Weake VM. Transcriptional Signatures of Aging. J Mol Biol 2017; 429:2427-2437. [PMID: 28684248 DOI: 10.1016/j.jmb.2017.06.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/02/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022]
Abstract
Genome-wide studies of aging have identified subsets of genes that show age-related changes in expression. Although the types of genes that are age regulated vary among different tissues and organisms, some patterns emerge from these large data sets. First, aging is associated with a broad induction of stress response pathways, although the specific genes and pathways involved differ depending on cell type and species. In contrast, a wide variety of functional classes of genes are downregulated with age, often including tissue-specific genes. Although the upregulation of age-regulated genes is likely to be governed by stress-responsive transcription factors, questions remain as to why particular genes are susceptible to age-related transcriptional decline. Here, we discuss recent findings showing that splicing is misregulated with age. While defects in splicing could lead to changes in protein isoform levels, they could also impact gene expression through nonsense-mediated decay of intron-retained transcripts. The discovery that splicing is misregulated with age suggests that other aspects of gene expression, such as transcription elongation, termination, and polyadenylation, must also be considered as potential mechanisms for age-related changes in transcript levels. Moreover, the considerable variation between genome-wide aging expression studies indicates that there is a critical need to analyze the transcriptional signatures of aging in single-cell types rather than whole tissues. Since age-associated decreases in gene expression could contribute to a progressive decline in cellular function, understanding the mechanisms that determine the aging transcriptome provides a potential target to extend healthy cellular lifespan.
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Affiliation(s)
- R Stegeman
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - V M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN 47907, USA.
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Senescence-associated microRNAs target cell cycle regulatory genes in normal human lung fibroblasts. Exp Gerontol 2017; 96:110-122. [PMID: 28658612 DOI: 10.1016/j.exger.2017.06.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 06/19/2017] [Accepted: 06/24/2017] [Indexed: 12/20/2022]
Abstract
Senescence recapitulates the ageing process at the cell level. A senescent cell stops dividing and exits the cell cycle. MicroRNAs (miRNAs) acting as master regulators of transcription, have been implicated in senescence. In the current study we investigated and compared the expression of miRNAs in young versus senescent human fibroblasts (HDFs), and analysed the role of mRNAs expressed in replicative senescent HFL-1 HDFs. Cell cycle analysis confirmed that HDFs accumulated in G1/S cell cycle phase. Nanostring analysis of isolated miRNAs from young and senescent HFL-1 showed that a distinct set of 15 miRNAs were significantly up-regulated in senescent cells including hsa-let-7d-5p, hsa-let-7e-5p, hsa-miR-23a-3p, hsa-miR-34a-5p, hsa-miR-122-5p, hsa-miR-125a-3p, hsa-miR-125a-5p, hsa-miR-125b-5p, hsa-miR-181a-5p, hsa-miR-221-3p, hsa-miR-222-3p, hsa-miR-503-5p, hsa-miR-574-3p, hsa-miR-574-5p and hsa-miR-4454. Importantly, pathway analysis of miRNA target genes down-regulated during replicative senescence in a public RNA-seq data set revealed a significant high number of genes regulating cell cycle progression, both G1/S and G2/M cell cycle phase transitions and telomere maintenance. The reduced expression of selected miRNA targets, upon replicative and oxidative-stress induced senescence, such as the cell cycle effectors E2F1, CcnE, Cdc6, CcnB1 and Cdc25C was verified at the protein and/or RNA levels. Induction of G1/S cell cycle phase arrest and down-regulation of cell cycle effectors correlated with the up-regulation of miR-221 upon both replicative and oxidative stress-induced senescence. Transient expression of miR-221/222 in HDFs promoted the accumulation of HDFs in G1/S cell cycle phase. We propose that miRNAs up-regulated during replicative senescence may act in concert to induce cell cycle phase arrest and telomere erosion, establishing a senescent phenotype.
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Mitochondrial DNA Hypomethylation Is a Biomarker Associated with Induced Senescence in Human Fetal Heart Mesenchymal Stem Cells. Stem Cells Int 2017; 2017:1764549. [PMID: 28484495 PMCID: PMC5397648 DOI: 10.1155/2017/1764549] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/05/2017] [Accepted: 01/16/2017] [Indexed: 02/07/2023] Open
Abstract
Background. Fetal heart can regenerate to restore its normal anatomy and function in response to injury, but this regenerative capacity is lost within the first week of postnatal life. Although the specific molecular mechanisms remain to be defined, it is presumed that aging of cardiac stem or progenitor cells may contribute to the loss of regenerative potential. Methods. To study this aging-related dysfunction, we cultured mesenchymal stem cells (MSCs) from human fetal heart tissues. Senescence was induced by exposing cells to chronic oxidative stress/low serum. Mitochondrial DNA methylation was examined during the period of senescence. Results. Senescent MSCs exhibited flattened and enlarged morphology and were positive for the senescence-associated beta-galactosidase (SA-β-Gal). By scanning the entire mitochondrial genome, we found that four CpG islands were hypomethylated in close association with senescence in MSCs. The mitochondrial COX1 gene, which encodes the main subunit of the cytochrome c oxidase complex and contains the differentially methylated CpG island 4, was upregulated in MSCs in parallel with the onset of senescence. Knockdown of DNA methyltransferases (DNMT1, DNMT3a, and DNMT3B) also upregulated COX1 expression and induced cellular senescence in MSCs. Conclusions. This study demonstrates that mitochondrial CpG hypomethylation may serve as a critical biomarker associated with cellular senescence induced by chronic oxidative stress.
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Eberhardt K, Beleites C, Marthandan S, Matthäus C, Diekmann S, Popp J. Raman and Infrared Spectroscopy Distinguishing Replicative Senescent from Proliferating Primary Human Fibroblast Cells by Detecting Spectral Differences Mainly Due to Biomolecular Alterations. Anal Chem 2017; 89:2937-2947. [DOI: 10.1021/acs.analchem.6b04264] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Katharina Eberhardt
- Leibniz Institute of Photonic Technology e. V., Albert-Einstein-Str. 9, 07745 Jena, Germany
- Institute
for Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Claudia Beleites
- Leibniz Institute of Photonic Technology e. V., Albert-Einstein-Str. 9, 07745 Jena, Germany
- Chemometric Consulting and Chemometrix GmbH, Södeler Weg 19, 61200 Wölfersheim, Germany
| | - Shiva Marthandan
- Department
of Molecular Biology, Leibniz Institute on Aging − Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany
| | - Christian Matthäus
- Leibniz Institute of Photonic Technology e. V., Albert-Einstein-Str. 9, 07745 Jena, Germany
- Institute
for Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Stephan Diekmann
- Department
of Molecular Biology, Leibniz Institute on Aging − Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology e. V., Albert-Einstein-Str. 9, 07745 Jena, Germany
- Institute
for Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
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Eberhardt K, Matthäus C, Winter D, Wiegand C, Hipler UC, Diekmann S, Popp J. Raman and infrared spectroscopy differentiate senescent from proliferating cells in a human dermal fibroblast 3D skin model. Analyst 2017; 142:4405-4414. [DOI: 10.1039/c7an00592j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Senescence-associated alterations were detected in biomolecules of 3D cultured cells and these cells were distinguished from 2D cultured cells.
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Affiliation(s)
- Katharina Eberhardt
- Leibniz Institute of Photonic Technology Jena
- 07745 Jena
- Germany
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
| | - Christian Matthäus
- Leibniz Institute of Photonic Technology Jena
- 07745 Jena
- Germany
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
| | - Doreen Winter
- University Hospital Jena
- Department of Dermatology
- 07740 Jena
- Germany
| | - Cornelia Wiegand
- University Hospital Jena
- Department of Dermatology
- 07740 Jena
- Germany
| | | | - Stephan Diekmann
- Leibniz Institute on Aging – Fritz Lipmann Institute
- Department of Molecular Biology
- 07745 Jena
- Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology Jena
- 07745 Jena
- Germany
- Institute for Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
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Chan KT, Paavolainen L, Hannan KM, George AJ, Hannan RD, Simpson KJ, Horvath P, Pearson RB. Combining High-Content Imaging and Phenotypic Classification Analysis of Senescence-Associated Beta-Galactosidase Staining to Identify Regulators of Oncogene-Induced Senescence. Assay Drug Dev Technol 2016; 14:416-28. [DOI: 10.1089/adt.2016.739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Keefe T. Chan
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Lassi Paavolainen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Katherine M. Hannan
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - Amee J. George
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Ross D. Hannan
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Kaylene J. Simpson
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Peter Horvath
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Szeged, Hungary
| | - Richard B. Pearson
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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Marthandan S, Menzel U, Priebe S, Groth M, Guthke R, Platzer M, Hemmerich P, Kaether C, Diekmann S. Conserved genes and pathways in primary human fibroblast strains undergoing replicative and radiation induced senescence. Biol Res 2016; 49:34. [PMID: 27464526 PMCID: PMC4963952 DOI: 10.1186/s40659-016-0095-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023] Open
Abstract
Background Cellular senescence is induced either internally, for example by replication exhaustion and cell division, or externally, for example by irradiation. In both cases, cellular damages accumulate which, if not successfully repaired, can result in senescence induction. Recently, we determined the transcriptional changes combined with the transition into replicative senescence in primary human fibroblast strains. Here, by γ-irradiation we induced premature cellular senescence in the fibroblast cell strains (HFF and MRC-5) and determined the corresponding transcriptional changes by high-throughput RNA sequencing. Results Comparing the transcriptomes, we found a high degree of similarity in differential gene expression in replicative as well as in irradiation induced senescence for both cell strains suggesting, in each cell strain, a common cellular response to error accumulation. On the functional pathway level, “Cell cycle” was the only pathway commonly down-regulated in replicative and irradiation-induced senescence in both fibroblast strains, confirming the tight link between DNA repair and cell cycle regulation. However, “DNA repair” and “replication” pathways were down-regulated more strongly in fibroblasts undergoing replicative exhaustion. We also retrieved genes and pathways in each of the cell strains specific for irradiation induced senescence. Conclusion We found the pathways associated with “DNA repair” and “replication” less stringently regulated in irradiation induced compared to replicative senescence. The strong regulation of these pathways in replicative senescence highlights the importance of replication errors for its induction. Electronic supplementary material The online version of this article (doi:10.1186/s40659-016-0095-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiva Marthandan
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
| | - Uwe Menzel
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Steffen Priebe
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Marco Groth
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute e.V. (HKI), Jena, Germany
| | - Matthias Platzer
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Peter Hemmerich
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaether
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Stephan Diekmann
- Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
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