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Cathcart B, Cheedipudi SM, Rouhi L, Zhao Z, Gurha P, Marian AJ. DNA double-stranded breaks, a hallmark of aging, defined at the nucleotide resolution, are increased and associated with transcription in the cardiac myocytes in LMNA-cardiomyopathy. Cardiovasc Res 2024:cvae063. [PMID: 38577741 DOI: 10.1093/cvr/cvae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
AIMS An intrinsic feature of gene transcription is the formation of DNA superhelices near the transcription bubble, which are resolved upon induction of transient double-stranded breaks (DSBs) by topoisomerases. Unrepaired DSBs are pathogenic as they lead to cell cycle arrest, senescence, inflammation, and organ dysfunction. We posit that DSBs would be more prevalent at the genomic sites that are associated with gene expression. The objectives were to identify and characterize genome-wide DSBs at the nucleotide resolution and determine the association of DSBs with transcription in cardiac myocytes. METHODS AND RESULTS We identified the genome-wide DSBs in ∼1 million cardiac myocytes per heart in three wild-type and three myocyte-specific LMNA-deficient (Myh6-Cre:LmnaF/F) mice by END-Sequencing. The prevalence of DSBs was 0.8% and 2.2% in the wild-type and Myh6-Cre:LmnaF/F myocytes, respectively. The END-Seq signals were enriched for 8 and 6764 DSBs in the wild-type and Myh6-Cre:LmnaF/F myocytes, respectively (q < 0.05). The DSBs were preferentially localized to the gene regions, transcription initiation sites, cardiac transcription factor motifs, and the G quadruplex forming structures. Because LMNA regulates transcription through the lamin-associated domains (LADs), we defined the LADs in cardiac myocytes by a Cleavage Under Targets & Release Using Nuclease (CUT&RUN) assay (N = 5). On average there were 818 LADs per myocyte. Constitutive LADs (cLADs), defined as LADs that were shared by at least three genomes (N = 2572), comprised about a third of the mouse cardiac myocyte genomes. Transcript levels of the protein-coding genes located at the cLADs (N = 3975) were ∼16-fold lower than those at the non-LAD regions (N = ∼17 778). The prevalence of DSBs was higher in the non-LAD as compared to the cLAD regions. Likewise, DSBs were more common in the loss-of-LAD regions, defined as the genomic regions in the Myh6-Cre:LmnaF/F that were juxtaposed to the LAD regions in the wild-type myocytes. CONCLUSION To our knowledge, this is the first identification of the DSBs, at the nucleotide resolution in the cardiovascular system. The prevalence of DSBs was higher in the genomic regions associated with transcription. Because transcription is pervasive, DSBs are expected to be common and pathogenic in various states and aging.
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Affiliation(s)
- Benjamin Cathcart
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Sirisha M Cheedipudi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Leila Rouhi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics and School of Public Health, UTHealth, Houston, TX 77030, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Ali J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
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2
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Rai R, Sodeinde T, Boston A, Chang S. Telomeres cooperate with the nuclear envelope to maintain genome stability. Bioessays 2024; 46:e2300184. [PMID: 38047499 DOI: 10.1002/bies.202300184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023]
Abstract
Mammalian telomeres have evolved safeguards to prevent their recognition as DNA double-stranded breaks by suppressing the activation of various DNA sensing and repair proteins. We have shown that the telomere-binding proteins TRF2 and RAP1 cooperate to prevent telomeres from undergoing aberrant homology-directed recombination by mediating t-loop protection. Our recent findings also suggest that mammalian telomere-binding proteins interact with the nuclear envelope to maintain chromosome stability. RAP1 interacts with nuclear lamins through KU70/KU80, and disruption of RAP1 and TRF2 function result in nuclear envelope rupture, promoting telomere-telomere recombination to form structures termed ultrabright telomeres. In this review, we discuss the importance of the interactions between shelterin components and the nuclear envelope to maintain telomere homeostasis and genome stability.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ava Boston
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
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3
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Elzamzami FD, Samal A, Arun AS, Dharmaraj T, Prasad NR, Rendon-Jonguitud A, DeVine L, Walston JD, Cole RN, Wilson KL. Native lamin A/C proteomes and novel partners from heart and skeletal muscle in a mouse chronic inflammation model of human frailty. Front Cell Dev Biol 2023; 11:1240285. [PMID: 37936983 PMCID: PMC10626543 DOI: 10.3389/fcell.2023.1240285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
Clinical frailty affects ∼10% of people over age 65 and is studied in a chronically inflamed (Interleukin-10 knockout; "IL10-KO") mouse model. Frailty phenotypes overlap the spectrum of diseases ("laminopathies") caused by mutations in LMNA. LMNA encodes nuclear intermediate filament proteins lamin A and lamin C ("lamin A/C"), important for tissue-specific signaling, metabolism and chromatin regulation. We hypothesized that wildtype lamin A/C associations with tissue-specific partners are perturbed by chronic inflammation, potentially contributing to dysfunction in frailty. To test this idea we immunoprecipitated native lamin A/C and associated proteins from skeletal muscle, hearts and brains of old (21-22 months) IL10-KO versus control C57Bl/6 female mice, and labeled with Tandem Mass Tags for identification and quantitation by mass spectrometry. We identified 502 candidate lamin-binding proteins from skeletal muscle, and 340 from heart, including 62 proteins identified in both tissues. Candidates included frailty phenotype-relevant proteins Perm1 and Fam210a, and nuclear membrane protein Tmem38a, required for muscle-specific genome organization. These and most other candidates were unaffected by IL10-KO, but still important as potential lamin A/C-binding proteins in native heart or muscle. A subset of candidates (21 in skeletal muscle, 30 in heart) showed significantly different lamin A/C-association in an IL10-KO tissue (p < 0.05), including AldoA and Gins3 affected in heart, and Lmcd1 and Fabp4 affected in skeletal muscle. To screen for binding, eleven candidates plus prelamin A and emerin controls were arrayed as synthetic 20-mer peptides (7-residue stagger) and incubated with recombinant purified lamin A "tail" residues 385-646 under relatively stringent conditions. We detected strong lamin A binding to peptides solvent exposed in Lmcd1, AldoA, Perm1, and Tmem38a, and plausible binding to Csrp3 (muscle LIM protein). These results validated both proteomes as sources for native lamin A/C-binding proteins in heart and muscle, identified four candidate genes for Emery-Dreifuss muscular dystrophy (CSRP3, LMCD1, ALDOA, and PERM1), support a lamin A-interactive molecular role for Tmem38A, and supported the hypothesis that lamin A/C interactions with at least two partners (AldoA in heart, transcription factor Lmcd1 in muscle) are altered in the IL10-KO model of frailty.
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Affiliation(s)
- Fatima D. Elzamzami
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Arushi Samal
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Adith S. Arun
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tejas Dharmaraj
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Neeti R. Prasad
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alex Rendon-Jonguitud
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lauren DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeremy D. Walston
- Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert N. Cole
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Katherine L. Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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4
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Pande S, Ghosh DK. Nuclear proteostasis imbalance in laminopathy-associated premature aging diseases. FASEB J 2023; 37:e23116. [PMID: 37498235 DOI: 10.1096/fj.202300878r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/15/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
Laminopathies are a group of rare genetic disorders with heterogeneous clinical phenotypes such as premature aging, cardiomyopathy, lipodystrophy, muscular dystrophy, microcephaly, epilepsy, and so on. The cellular phenomena associated with laminopathy invariably show disruption of nucleoskeleton of lamina due to deregulated expression, localization, function, and interaction of mutant lamin proteins. Impaired spatial and temporal tethering of lamin proteins to the lamina or nucleoplasmic aggregation of lamins are the primary molecular events that can trigger nuclear proteotoxicity by modulating differential protein-protein interactions, sequestering quality control proteins, and initiating a cascade of abnormal post-translational modifications. Clearly, laminopathic cells exhibit moderate to high nuclear proteotoxicity, raising the question of whether an imbalance in nuclear proteostasis is involved in laminopathic diseases, particularly in diseases of early aging such as HGPS and laminopathy-associated premature aging. Here, we review nuclear proteostasis and its deregulation in the context of lamin proteins and laminopathies.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Debasish Kumar Ghosh
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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5
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Rai R, Biju K, Sun W, Sodeinde T, Al-Hiyasat A, Morgan J, Ye X, Li X, Chen Y, Chang S. Homology directed telomere clustering, ultrabright telomere formation and nuclear envelope rupture in cells lacking TRF2 B and RAP1. Nat Commun 2023; 14:2144. [PMID: 37059728 PMCID: PMC10104862 DOI: 10.1038/s41467-023-37761-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
Double-strand breaks (DSBs) due to genotoxic stress represent potential threats to genome stability. Dysfunctional telomeres are recognized as DSBs and are repaired by distinct DNA repair mechanisms. RAP1 and TRF2 are telomere binding proteins essential to protect telomeres from engaging in homology directed repair (HDR), but how this occurs remains unclear. In this study, we examined how the basic domain of TRF2 (TRF2B) and RAP1 cooperate to repress HDR at telomeres. Telomeres lacking TRF2B and RAP1 cluster into structures termed ultrabright telomeres (UTs). HDR factors localize to UTs, and UT formation is abolished by RNaseH1, DDX21 and ADAR1p110, suggesting that they contain DNA-RNA hybrids. Interaction between the BRCT domain of RAP1 and KU70/KU80 is also required to repress UT formation. Expressing TRF2∆B in Rap1-/- cells resulted in aberrant lamin A localization in the nuclear envelope and dramatically increased UT formation. Expressing lamin A phosphomimetic mutants induced nuclear envelope rupturing and aberrant HDR-mediated UT formation. Our results highlight the importance of shelterin and proteins in the nuclear envelope in repressing aberrant telomere-telomere recombination to maintain telomere homeostasis.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
| | - Kevin Biju
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wenqi Sun
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Amer Al-Hiyasat
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Jaida Morgan
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Xianwen Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Xueqing Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
- Department of Pathology, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
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Genotype-Phenotype Correlations in Human Diseases Caused by Mutations of LINC Complex-Associated Genes: A Systematic Review and Meta-Summary. Cells 2022; 11:cells11244065. [PMID: 36552829 PMCID: PMC9777268 DOI: 10.3390/cells11244065] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Mutations in genes encoding proteins associated with the linker of nucleoskeleton and cytoskeleton (LINC) complex within the nuclear envelope cause different diseases with varying phenotypes including skeletal muscle, cardiac, metabolic, or nervous system pathologies. There is some understanding of the structure of LINC complex-associated proteins and how they interact, but it is unclear how mutations in genes encoding them can cause the same disease, and different diseases with different phenotypes. Here, published mutations in LINC complex-associated proteins were systematically reviewed and analyzed to ascertain whether patterns exist between the genetic sequence variants and clinical phenotypes. This revealed LMNA is the only LINC complex-associated gene in which mutations commonly cause distinct conditions, and there are no clear genotype-phenotype correlations. Clusters of LMNA variants causing striated muscle disease are located in exons 1 and 6, and metabolic disease-associated LMNA variants are frequently found in the tail of lamin A/C. Additionally, exon 6 of the emerin gene, EMD, may be a mutation "hot-spot", and diseases related to SYNE1, encoding nesprin-1, are most often caused by nonsense type mutations. These results provide insight into the diverse roles of LINC-complex proteins in human disease and provide direction for future gene-targeted therapy development.
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La Torre M, Merigliano C, Maccaroni K, Chojnowski A, Goh WI, Giubettini M, Vernì F, Capanni C, Rhodes D, Wright G, Burke B, Soddu S, Burla R, Saggio I. Combined alteration of lamin and nuclear morphology influences the localization of the tumor-associated factor AKTIP. J Exp Clin Cancer Res 2022; 41:273. [PMID: 36096808 PMCID: PMC9469526 DOI: 10.1186/s13046-022-02480-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Lamins, key nuclear lamina components, have been proposed as candidate risk biomarkers in different types of cancer but their accuracy is still debated. AKTIP is a telomeric protein with the property of being enriched at the nuclear lamina. AKTIP has similarity with the tumor susceptibility gene TSG101. AKTIP deficiency generates genome instability and, in p53−/− mice, the reduction of the mouse counterpart of AKTIP induces the exacerbation of lymphomas. Here, we asked whether the distribution of AKTIP is altered in cancer cells and whether this is associated with alterations of lamins. Methods We performed super-resolution imaging, quantification of lamin expression and nuclear morphology on HeLa, MCF7, and A549 tumor cells, and on non-transformed fibroblasts from healthy donor and HGPS (LMNA c.1824C > T p.Gly608Gly) and EDMD2 (LMNA c.775 T > G) patients. As proof of principle model combining a defined lamin alteration with a tumor cell setting, we produced HeLa cells exogenously expressing the HGPS lamin mutant progerin that alters nuclear morphology. Results In HeLa cells, AKTIP locates at less than 0.5 µm from the nuclear rim and co-localizes with lamin A/C. As compared to HeLa, there is a reduced co-localization of AKTIP with lamin A/C in both MCF7 and A549. Additionally, MCF7 display lower amounts of AKTIP at the rim. The analyses in non-transformed fibroblasts show that AKTIP mislocalizes in HGPS cells but not in EDMD2. The integrated analysis of lamin expression, nuclear morphology, and AKTIP topology shows that positioning of AKTIP is influenced not only by lamin expression, but also by nuclear morphology. This conclusion is validated by progerin-expressing HeLa cells in which nuclei are morphologically altered and AKTIP is mislocalized. Conclusions Our data show that the combined alteration of lamin and nuclear morphology influences the localization of the tumor-associated factor AKTIP. The results also point to the fact that lamin alterations per se are not predictive of AKTIP mislocalization, in both non-transformed and tumor cells. In more general terms, this study supports the thesis that a combined analytical approach should be preferred to predict lamin-associated changes in tumor cells. This paves the way of next translational evaluation to validate the use of this combined analytical approach as risk biomarker. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02480-5.
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8
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Neumann-Staubitz P, Kitsberg D, Buxboim A, Neumann H. A method to map the interaction network of the nuclear lamina with genetically encoded photo-crosslinkers in vivo. Front Chem 2022; 10:905794. [PMID: 36110135 PMCID: PMC9468544 DOI: 10.3389/fchem.2022.905794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
Lamins are intermediate filaments that assemble in a meshwork at the inner nuclear periphery of metazoan cells. The nuclear periphery fulfils important functions by providing stability to the nuclear membrane, connecting the cytoskeleton with chromatin, and participating in signal transduction. Mutations in lamins interfere with these functions and cause severe, phenotypically diverse diseases collectively referred to as laminopathies. The molecular consequences of these mutations are largely unclear but likely include alterations in lamin-protein and lamin-chromatin interactions. These interactions are challenging to study biochemically mainly because the lamina is resistant to high salt and detergent concentrations and co-immunoprecipitation are susceptible to artefacts. Here, we used genetic code expansion to install photo-activated crosslinkers to capture direct lamin-protein interactions in vivo. Mapping the Ig-fold of laminC for interactions, we identified laminC-crosslink products with laminB1, LAP2, and TRIM28. We observed significant changes in the crosslink intensities between laminC mutants mimicking different phosphorylation states. Similarly, we found variations in laminC crosslink product intensities comparing asynchronous cells and cells synchronized in prophase. This method can be extended to other laminC domains or other lamins to reveal changes in their interactome as a result of mutations or cell cycle stages.
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Affiliation(s)
| | - Daniel Kitsberg
- Institute of Life Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amnon Buxboim
- Institute of Life Science, Hebrew University of Jerusalem, Jerusalem, Israel
- Rachel and Selim Benin School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem, Israel
- Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Heinz Neumann
- University of Applied Sciences Darmstadt, Darmstadt, Germany
- *Correspondence: Heinz Neumann,
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9
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Kim BH, Woo TG, Kang SM, Park S, Park BJ. Splicing Variants, Protein-Protein Interactions, and Drug Targeting in Hutchinson-Gilford Progeria Syndrome and Small Cell Lung Cancer. Genes (Basel) 2022; 13:genes13020165. [PMID: 35205210 PMCID: PMC8871687 DOI: 10.3390/genes13020165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) is a biological operation that enables a messenger RNA to encode protein variants (isoforms) that give one gene several functions or properties. This process provides one of the major sources of use for understanding the proteomic diversity of multicellular organisms. In combination with post-translational modifications, it contributes to generating a variety of protein–protein interactions (PPIs) that are essential to cellular homeostasis or proteostasis. However, cells exposed to many kinds of stresses (aging, genetic changes, carcinogens, etc.) sometimes derive cancer or disease onset from aberrant PPIs caused by DNA mutations. In this review, we summarize how splicing variants may form a neomorphic protein complex and cause diseases such as Hutchinson-Gilford progeria syndrome (HGPS) and small cell lung cancer (SCLC), and we discuss how protein–protein interfaces obtained from the variants may represent efficient therapeutic target sites to treat HGPS and SCLC.
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Affiliation(s)
- Bae-Hoon Kim
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
| | - Tae-Gyun Woo
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
| | - So-Mi Kang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
| | - Soyoung Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
| | - Bum-Joon Park
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
- Correspondence:
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Rahman MM, Ferdous KS, Ahmed M, Islam MT, Khan MR, Perveen A, Ashraf GM, Uddin MS. Hutchinson-Gilford Progeria Syndrome: An Overview of the Molecular Mechanism, Pathophysiology and Therapeutic Approach. Curr Gene Ther 2021; 21:216-229. [PMID: 33655857 DOI: 10.2174/1566523221666210303100805] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 12/29/2022]
Abstract
Lamin A/C encoded by the LMNA gene is an essential component for maintaining the nuclear structure. Mutation in the lamin A/C leads to a group of inherited disorders is known as laminopathies. In the human body, there are several mutations in the LMNA gene that have been identified. It can affect diverse organs or tissues or can be systemic, causing different diseases. In this review, we mainly focused on one of the most severe laminopathies, Hutchinson-Gilford progeria syndrome (HGPS). HGPS is an immensely uncommon, deadly, metameric ill-timed laminopathies caused by the abnormal splicing of the LMNA gene and production of an aberrant protein known as progerin. Here, we also presented the currently available data on the molecular mechanism, pathophysiology, available treatment, and future approaches to this deadly disease. Due to the production of progerin, an abnormal protein leads to an abnormality in nuclear structure, defects in DNA repair, shortening of telomere, and impairment in gene regulation which ultimately results in aging in the early stage of life. Now some treatment options are available for this disease, but a proper understanding of the molecular mechanism of this disease will help to develop a more appropriate treatment which makes it an emerging area of research.
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Affiliation(s)
- Md Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Kazi Sayma Ferdous
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Muniruddin Ahmed
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Mohammad Touhidul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md Robin Khan
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Saharanpur, India
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
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11
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Herrera A, Menendez A, Torroba B, Ochoa A, Pons S. Dbnl and β-catenin promote pro-N-cadherin processing to maintain apico-basal polarity. J Cell Biol 2021; 220:212044. [PMID: 33939796 PMCID: PMC8097490 DOI: 10.1083/jcb.202007055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 02/15/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
The neural tube forms when neural stem cells arrange into a pseudostratified, single-cell–layered epithelium, with a marked apico-basal polarity, and in which adherens junctions (AJs) concentrate in the subapical domain. We previously reported that sustained β-catenin expression promotes the formation of enlarged apical complexes (ACs), enhancing apico-basal polarity, although the mechanism through which this occurs remained unclear. Here, we show that β-catenin interacts with phosphorylated pro-N-cadherin early in its transit through the Golgi apparatus, promoting propeptide excision and the final maturation of N-cadherin. We describe a new β-catenin–dependent interaction of N-cadherin with Drebrin-like (Dbnl), an actin-binding protein that is involved in anterograde Golgi trafficking of proteins. Notably, Dbnl knockdown led to pro-N-cadherin accumulation and limited AJ formation. In brief, we demonstrate that Dbnl and β-catenin assist in the maturation of pro-N-cadherin, which is critical for AJ formation and for the recruitment AC components like aPKC and, consequently, for the maintenance of apico-basal polarity.
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Affiliation(s)
- Antonio Herrera
- Instituto de Biología Molecular de Barcelona, Parc Científic de Barcelona, Barcelona, Spain
| | - Anghara Menendez
- Instituto de Biología Molecular de Barcelona, Parc Científic de Barcelona, Barcelona, Spain
| | - Blanca Torroba
- Instituto de Biología Molecular de Barcelona, Parc Científic de Barcelona, Barcelona, Spain
| | - Andrea Ochoa
- Instituto de Biología Molecular de Barcelona, Parc Científic de Barcelona, Barcelona, Spain
| | - Sebastián Pons
- Instituto de Biología Molecular de Barcelona, Parc Científic de Barcelona, Barcelona, Spain
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12
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Wong X, Cutler JA, Hoskins VE, Gordon M, Madugundu AK, Pandey A, Reddy KL. Mapping the micro-proteome of the nuclear lamina and lamina-associated domains. Life Sci Alliance 2021; 4:e202000774. [PMID: 33758005 PMCID: PMC8008952 DOI: 10.26508/lsa.202000774] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 01/13/2023] Open
Abstract
The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, the so-called lamina-associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2β to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin-directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify both LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina, identified putative LAD proximal proteins and found several proteins that appear to interface with both micro-proteomes. Importantly, several proteins essential for LAD function, including heterochromatin regulating proteins related to H3K9 methylation, were identified in this study.
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Affiliation(s)
- Xianrong Wong
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Developmental and Regenerative Biology, Institute of Medical Biology, Agency for Science, Technology and Research (A∗STAR), Immunos, Singapore
| | - Jevon A Cutler
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Victoria E Hoskins
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Molly Gordon
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anil K Madugundu
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHNS), Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHNS), Bangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen L Reddy
- Department of Biological Chemistry, Johns Hopkins University of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Cancer Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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13
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Willaume S, Rass E, Fontanilla-Ramirez P, Moussa A, Wanschoor P, Bertrand P. A Link between Replicative Stress, Lamin Proteins, and Inflammation. Genes (Basel) 2021; 12:genes12040552. [PMID: 33918867 PMCID: PMC8070205 DOI: 10.3390/genes12040552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Double-stranded breaks (DSB), the most toxic DNA lesions, are either a consequence of cellular metabolism, programmed as in during V(D)J recombination, or induced by anti-tumoral therapies or accidental genotoxic exposure. One origin of DSB sources is replicative stress, a major source of genome instability, especially when the integrity of the replication forks is not properly guaranteed. To complete stalled replication, restarting the fork requires complex molecular mechanisms, such as protection, remodeling, and processing. Recently, a link has been made between DNA damage accumulation and inflammation. Indeed, defects in DNA repair or in replication can lead to the release of DNA fragments in the cytosol. The recognition of this self-DNA by DNA sensors leads to the production of inflammatory factors. This beneficial response activating an innate immune response and destruction of cells bearing DNA damage may be considered as a novel part of DNA damage response. However, upon accumulation of DNA damage, a chronic inflammatory cellular microenvironment may lead to inflammatory pathologies, aging, and progression of tumor cells. Progress in understanding the molecular mechanisms of DNA damage repair, replication stress, and cytosolic DNA production would allow to propose new therapeutical strategies against cancer or inflammatory diseases associated with aging. In this review, we describe the mechanisms involved in DSB repair, the replicative stress management, and its consequences. We also focus on new emerging links between key components of the nuclear envelope, the lamins, and DNA repair, management of replicative stress, and inflammation.
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14
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Tran JR, Paulson DI, Moresco JJ, Adam SA, Yates JR, Goldman RD, Zheng Y. An APEX2 proximity ligation method for mapping interactions with the nuclear lamina. J Cell Biol 2021; 220:e202002129. [PMID: 33306092 PMCID: PMC7737704 DOI: 10.1083/jcb.202002129] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 01/13/2023] Open
Abstract
The nuclear lamina (NL) is a meshwork found beneath the inner nuclear membrane. The study of the NL is hindered by the insolubility of the meshwork and has driven the development of proximity ligation methods to identify the NL-associated/proximal proteins, RNA, and DNA. To simplify and improve temporal labeling, we fused APEX2 to the NL protein lamin-B1 to map proteins, RNA, and DNA. The identified NL-interacting/proximal RNAs show a long 3' UTR bias, a finding consistent with an observed bias toward longer 3' UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 3' UTR. Our APEX2-based proteomics identifies a C-rich motif binding regulatory protein that exhibits altered localization in lamin-null cells. Finally, we use APEX2 to map lamina-associated domains (LADs) during the cell cycle and uncover short, H3K27me3-rich variable LADs. Thus, the APEX2-based tools presented here permit identification of proteomes, transcriptomes, and genome elements associated with or proximal to the NL.
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Affiliation(s)
- Joseph R. Tran
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
| | - Danielle I. Paulson
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
- Horace Mann School, The Bronx, NY
| | - James J. Moresco
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Stephen A. Adam
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - John R. Yates
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Robert D. Goldman
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - Yixian Zheng
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
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15
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Maynard S, Keijzers G, Akbari M, Ezra MB, Hall A, Morevati M, Scheibye-Knudsen M, Gonzalo S, Bartek J, Bohr VA. Lamin A/C promotes DNA base excision repair. Nucleic Acids Res 2020; 47:11709-11728. [PMID: 31647095 DOI: 10.1093/nar/gkz912] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/25/2019] [Accepted: 10/02/2019] [Indexed: 12/17/2022] Open
Abstract
The A-type lamins (lamin A/C), encoded by the LMNA gene, are important structural components of the nuclear lamina. LMNA mutations lead to degenerative disorders known as laminopathies, including the premature aging disease Hutchinson-Gilford progeria syndrome. In addition, altered lamin A/C expression is found in various cancers. Reports indicate that lamin A/C plays a role in DNA double strand break repair, but a role in DNA base excision repair (BER) has not been described. We provide evidence for reduced BER efficiency in lamin A/C-depleted cells (Lmna null MEFs and lamin A/C-knockdown U2OS). The mechanism involves impairment of the APE1 and POLβ BER activities, partly effectuated by associated reduction in poly-ADP-ribose chain formation. Also, Lmna null MEFs displayed reduced expression of several core BER enzymes (PARP1, LIG3 and POLβ). Absence of Lmna led to accumulation of 8-oxoguanine (8-oxoG) lesions, and to an increased frequency of substitution mutations induced by chronic oxidative stress including GC>TA transversions (a fingerprint of 8-oxoG:A mismatches). Collectively, our results provide novel insights into the functional interplay between the nuclear lamina and cellular defenses against oxidative DNA damage, with implications for cancer and aging.
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Affiliation(s)
- Scott Maynard
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Guido Keijzers
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Mansour Akbari
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michael Ben Ezra
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Arnaldur Hall
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Marya Morevati
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Morten Scheibye-Knudsen
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Susana Gonzalo
- Department of Biochemistry and Molecular Biology, Saint Louis University, School of Medicine, Saint Louis, MO 63104, USA
| | - Jiri Bartek
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.,Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, SE-17177 Stockholm, Sweden
| | - Vilhelm A Bohr
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark.,Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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16
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Lessel I, Chen MJ, Lüttgen S, Arndt F, Fuchs S, Meien S, Thiele H, Jones JR, Shaw BR, Crossman DK, Nürnberg P, Korf BR, Kubisch C, Lessel D. Two novel cases further expand the phenotype of TOR1AIP1-associated nuclear envelopathies. Hum Genet 2020; 139:483-498. [PMID: 32055997 PMCID: PMC7078146 DOI: 10.1007/s00439-019-02105-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 12/22/2019] [Indexed: 12/19/2022]
Abstract
Biallelic variants in TOR1AIP1, encoding the integral nuclear membrane protein LAP1 (lamina-associated polypeptide 1) with two functional isoforms LAP1B and LAP1C, have initially been linked to muscular dystrophies with variable cardiac and neurological impairment. Furthermore, a recurrent homozygous nonsense alteration, resulting in loss of both LAP1 isoforms, was identified in seven likely related individuals affected by multisystem anomalies with progeroid-like appearance and lethality within the 1st decade of life. Here, we have identified compound heterozygosity in TOR1AIP1 affecting both LAP1 isoforms in two unrelated individuals affected by congenital bilateral hearing loss, ventricular septal defect, bilateral cataracts, mild to moderate developmental delay, microcephaly, mandibular hypoplasia, short stature, progressive muscular atrophy, joint contractures and severe chronic heart failure, with much longer survival. Cellular characterization of primary fibroblasts of one affected individual revealed absence of both LAP1B and LAP1C, constitutively low lamin A/C levels, aberrant nuclear morphology including nuclear cytoplasmic channels, and premature senescence, comparable to findings in other progeroid forms of nuclear envelopathies. We additionally observed an abnormal activation of the extracellular signal-regulated kinase 1/2 (ERK 1/2). Ectopic expression of wild-type TOR1AIP1 mitigated these cellular phenotypes, providing further evidence for the causal role of identified genetic variants. Altogether, we thus further expand the TOR1AIP1-associated phenotype by identifying individuals with biallelic loss-of-function variants who survived beyond the 1st decade of life and reveal novel molecular consequences underlying the TOR1AIP1-associated disorders.
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Affiliation(s)
- Ivana Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Mei-Jan Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 36394, USA
| | - Sabine Lüttgen
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Florian Arndt
- Department for Pediatric Cardiology, University Heart Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Sigrid Fuchs
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Stefanie Meien
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Julie R Jones
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Brandon R Shaw
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 36394, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 36394, USA
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931, Cologne, Germany
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 36394, USA
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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17
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Šoltić D, Shorrock HK, Allardyce H, Wilson EL, Holt I, Synowsky SA, Shirran SL, Parson SH, Gillingwater TH, Fuller HR. Lamin A/C dysregulation contributes to cardiac pathology in a mouse model of severe spinal muscular atrophy. Hum Mol Genet 2019; 28:3515-3527. [PMID: 31397869 PMCID: PMC6927462 DOI: 10.1093/hmg/ddz195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 12/21/2022] Open
Abstract
Cardiac pathology is emerging as a prominent systemic feature of spinal muscular atrophy (SMA), but little is known about the underlying molecular pathways. Using quantitative proteomics analysis, we demonstrate widespread molecular defects in heart tissue from the Taiwanese mouse model of severe SMA. We identify increased levels of lamin A/C as a robust molecular phenotype in the heart of SMA mice and show that lamin A/C dysregulation is also apparent in SMA patient fibroblast cells and other tissues from SMA mice. Lamin A/C expression was regulated in vitro by knockdown of the E1 ubiquitination factor ubiquitin-like modifier activating enzyme 1, a key downstream mediator of SMN-dependent disease pathways, converging on β-catenin signaling. Increased levels of lamin A are known to increase the rigidity of nuclei, inevitably disrupting contractile activity in cardiomyocytes. The increased lamin A/C levels in the hearts of SMA mice therefore provide a likely mechanism explaining morphological and functional cardiac defects, leading to blood pooling. Therapeutic strategies directed at lamin A/C may therefore offer a new approach to target cardiac pathology in SMA.
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Affiliation(s)
- Darija Šoltić
- Institute for Science and Technology in Medicine, Keele University, Keele ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Hannah K Shorrock
- Edinburgh Medical School: Biomedical Sciences
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Hazel Allardyce
- Institute of Education for Medical and Dental Science, College of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Emma L Wilson
- Chester Medical School, University of Chester, Chester CH1 4BJ, UK
| | - Ian Holt
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Silvia A Synowsky
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, St Andrews KY16 9ST, UK
| | - Sally L Shirran
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, St Andrews KY16 9ST, UK
| | - Simon H Parson
- Institute of Education for Medical and Dental Science, College of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Thomas H Gillingwater
- Edinburgh Medical School: Biomedical Sciences
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Heidi R Fuller
- Institute for Science and Technology in Medicine, Keele University, Keele ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
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18
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The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nat Cell Biol 2019; 21:1248-1260. [PMID: 31576060 DOI: 10.1038/s41556-019-0397-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022]
Abstract
While nuclear lamina abnormalities are hallmarks of human diseases, their interplay with epigenetic regulators and precise epigenetic landscape remain poorly understood. Here, we show that loss of the lysine acetyltransferase MOF or its associated NSL-complex members KANSL2 or KANSL3 leads to a stochastic accumulation of nuclear abnormalities with genomic instability patterns including chromothripsis. SILAC-based MOF and KANSL2 acetylomes identified lamin A/C as an acetylation target of MOF. HDAC inhibition or acetylation-mimicking lamin A derivatives rescue nuclear abnormalities observed in MOF-deficient cells. Mechanistically, loss of lamin A/C acetylation resulted in its increased solubility, defective phosphorylation dynamics and impaired nuclear mechanostability. We found that nuclear abnormalities include EZH2-dependent histone H3 Lys 27 trimethylation and loss of nascent transcription. We term this altered epigenetic landscape "heterochromatin enrichment in nuclear abnormalities" (HENA). Collectively, the NSL-complex-dependent lamin A/C acetylation provides a mechanism that maintains nuclear architecture and genome integrity.
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19
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Graziano S, Kreienkamp R, Coll-Bonfill N, Gonzalo S. Causes and consequences of genomic instability in laminopathies: Replication stress and interferon response. Nucleus 2019; 9:258-275. [PMID: 29637811 PMCID: PMC5973265 DOI: 10.1080/19491034.2018.1454168] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mammalian nuclei are equipped with a framework of intermediate filaments that function as a karyoskeleton. This nuclear scaffold, formed primarily by lamins (A-type and B-type), maintains the spatial and functional organization of the genome and of sub-nuclear compartments. Over the past decade, a body of evidence has highlighted the significance of these structural nuclear proteins in the maintenance of nuclear architecture and mechanical stability, as well as genome function and integrity. The importance of these structures is now unquestioned given the wide range of degenerative diseases that stem from LMNA gene mutations, including muscular dystrophy disorders, peripheral neuropathies, lipodystrophies, and premature aging syndromes. Here, we review our knowledge about how alterations in nuclear lamins, either by mutation or reduced expression, impact cellular mechanisms that maintain genome integrity. Despite the fact that DNA replication is the major source of DNA damage and genomic instability in dividing cells, how alterations in lamins function impact replication remains minimally explored. We summarize recent studies showing that lamins play a role in DNA replication, and that the DNA damage that accumulates upon lamins dysfunction is elicited in part by deprotection of replication forks. We also discuss the emerging model that DNA damage and replication stress are “sensed” at the cytoplasm by proteins that normally survey this space in search of foreign nucleic acids. In turn, these cytosolic sensors activate innate immune responses, which are materializing as important players in aging and cancer, as well as in the response to cancer immunotherapy.
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Affiliation(s)
- Simona Graziano
- a Edward A. Doisy Department of Biochemistry and Molecular Biology , Saint Louis University School of Medicine , St. Louis , MO , USA
| | - Ray Kreienkamp
- a Edward A. Doisy Department of Biochemistry and Molecular Biology , Saint Louis University School of Medicine , St. Louis , MO , USA
| | - Nuria Coll-Bonfill
- a Edward A. Doisy Department of Biochemistry and Molecular Biology , Saint Louis University School of Medicine , St. Louis , MO , USA
| | - Susana Gonzalo
- a Edward A. Doisy Department of Biochemistry and Molecular Biology , Saint Louis University School of Medicine , St. Louis , MO , USA
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20
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Genomic instability and innate immune responses to self-DNA in progeria. GeroScience 2019; 41:255-266. [PMID: 31280482 DOI: 10.1007/s11357-019-00082-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022] Open
Abstract
In the last decade, we have seen increasing evidence of the importance of structural nuclear proteins such as lamins in nuclear architecture and compartmentalization of genome function and in the maintenance of mechanical stability and genome integrity. With over 400 mutations identified in the LMNA gene (encoding for A-type lamins) associated with more than ten distinct degenerative disorders, the role of lamins as genome caretakers and the contribution of lamins dysfunction to disease are unarguable. However, the molecular mechanisms whereby lamins mutations cause pathologies remain less understood. Here, we review pathways and mechanisms recently identified as playing a role in the pathophysiology of laminopathies, with special emphasis in Hutchinson Gilford Progeria Syndrome (HGPS). This devastating incurable accelerated aging disease is caused by a silent mutation in the LMNA gene that generates a truncated lamin A protein "progerin" that exerts profound cellular toxicity and organismal decline. Patients usually die in their teens due to cardiovascular complications such as myocardial infarction or stroke. To date, there are no efficient therapies that ameliorate disease progression, stressing the need to understand molecularly disease mechanisms that can be targeted therapeutically. We will summarize data supporting that replication stress is a major cause of genomic instability in laminopathies, which contributes to the activation of innate immune responses to self-DNA that in turn accelerate the aging process.
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21
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Jiang Z, Chen W, Zhou J, Peng Q, Zheng H, Yuan Y, Cui H, Zhao W, Sun X, Zhou Z, Liu X. Identification of COMMD1 as a novel lamin A binding partner. Mol Med Rep 2019; 20:1790-1796. [PMID: 31257505 PMCID: PMC6625409 DOI: 10.3892/mmr.2019.10419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 05/20/2019] [Indexed: 01/28/2023] Open
Abstract
Lamin A, which is encoded by the LMNA gene, regulates gene expression and genome stability through interactions with a variety of proteins. Mutations in LMNA lead to a diverse set of inherited human diseases, collectively referred to as laminopathies. To gain insight into the protein interactions of lamin A, a yeast two-hybrid screen was conducted using the carboxy-terminus of lamin A. The screen identified copper metabolism MURR1 domain-containing 1 (COMMD1) as a novel lamin A binding partner. Colocalization experiments using fluorescent confocal microscopy revealed that COMMD1 colocalized with lamin A in 293 cells. Furthermore, the COMMD1-lamin A protein interaction was also demonstrated in co-immunoprecipitation experiments. Collectively, the present study demonstrated a physical interaction between COMMD1 and lamin A, which may aid to elucidate the mechanisms of lamin A in the aging process.
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Affiliation(s)
- Zhiwen Jiang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Weichun Chen
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Jing Zhou
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Qi Peng
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Huiling Zheng
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Yuan Yuan
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Hongjing Cui
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Wei Zhao
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Xuerong Sun
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Zhongjun Zhou
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Xinguang Liu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
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22
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Kreienkamp R, Gonzalo S. Hutchinson-Gilford Progeria Syndrome: Challenges at Bench and Bedside. Subcell Biochem 2019; 91:435-451. [PMID: 30888661 DOI: 10.1007/978-981-13-3681-2_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The structural nuclear proteins known as "lamins" (A-type and B-type) provide a scaffold for the compartmentalization of genome function that is important to maintain genome stability. Mutations in the LMNA gene -encoding for A-type lamins- are associated with over a dozen of degenerative disorders termed laminopathies, which include muscular dystrophies, lipodystrophies, neuropathies, and premature ageing diseases such as Hutchinson Gilford Progeria Syndrome (HGPS). This devastating disease is caused by the expression of a truncated lamin A protein named "progerin". To date, there is no effective treatment for HGPS patients, who die in their teens from cardiovascular disease. At a cellular level, progerin expression impacts nuclear architecture, chromatin organization, response to mechanical stress, and DNA transactions such as transcription, replication and repair. However, the current view is that key mechanisms behind progerin toxicity still remain to be discovered. Here, we discuss new findings about pathological mechanisms in HGPS, especially the contribution of replication stress to cellular decline, and therapeutic strategies to ameliorate progerin toxicity. In particular, we present evidence for retinoids and calcitriol (hormonal vitamin D metabolite) being among the most potent compounds to ameliorate HGPS cellular phenotypes in vitro, providing the rationale for testing these compounds in preclinical models of the disease in the near term, and in patients in the future.
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Affiliation(s)
- Ray Kreienkamp
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Doisy Research Center, St Louis University School of Medicine, St. Louis, MO, USA
| | - Susana Gonzalo
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Doisy Research Center, St Louis University School of Medicine, St. Louis, MO, USA.
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Sola-Carvajal A, Revêchon G, Helgadottir HT, Whisenant D, Hagblom R, Döhla J, Katajisto P, Brodin D, Fagerström-Billai F, Viceconte N, Eriksson M. Accumulation of Progerin Affects the Symmetry of Cell Division and Is Associated with Impaired Wnt Signaling and the Mislocalization of Nuclear Envelope Proteins. J Invest Dermatol 2019; 139:2272-2280.e12. [PMID: 31128203 DOI: 10.1016/j.jid.2019.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is the result of a defective form of the lamin A protein called progerin. While progerin is known to disrupt the properties of the nuclear lamina, the underlying mechanisms responsible for the pathophysiology of HGPS remain less clear. Previous studies in our laboratory have shown that progerin expression in murine epidermal basal cells results in impaired stratification and halted development of the skin. Stratification and differentiation of the epidermis is regulated by asymmetric stem cell division. Here, we show that expression of progerin impairs the ability of stem cells to maintain tissue homeostasis as a result of altered cell division. Quantification of basal skin cells showed an increase in symmetric cell division that correlated with progerin accumulation in HGPS mice. Investigation of the mechanisms underlying this phenomenon revealed a putative role of Wnt/β-catenin signaling. Further analysis suggested an alteration in the nuclear translocation of β-catenin involving the inner and outer nuclear membrane proteins, emerin and nesprin-2. Taken together, our results suggest a direct involvement of progerin in the transmission of Wnt signaling and normal stem cell division. These insights into the molecular mechanisms of progerin may help develop new treatment strategies for HGPS.
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Affiliation(s)
- Agustín Sola-Carvajal
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.
| | - Gwladys Revêchon
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Hafdis T Helgadottir
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Daniel Whisenant
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Robin Hagblom
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Julia Döhla
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden; Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Pekka Katajisto
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden; Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - David Brodin
- Bioinformatics and Expression Core Facility, Karolinska Institutet, Huddinge, Sweden
| | | | - Nikenza Viceconte
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Maria Eriksson
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.
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24
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Ranade D, Pradhan R, Jayakrishnan M, Hegde S, Sengupta K. Lamin A/C and Emerin depletion impacts chromatin organization and dynamics in the interphase nucleus. BMC Mol Cell Biol 2019; 20:11. [PMID: 31117946 PMCID: PMC6532135 DOI: 10.1186/s12860-019-0192-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/16/2019] [Indexed: 12/26/2022] Open
Abstract
Background Nuclear lamins are type V intermediate filament proteins that maintain nuclear structure and function. Furthermore, Emerin - an interactor of Lamin A/C, facilitates crosstalk between the cytoskeleton and the nucleus as it also interacts with actin and Nuclear Myosin 1 (NM1). Results Here we show that the depletion of Lamin A/C or Emerin, alters the localization of the nuclear motor protein - Nuclear Myosin 1 (NM1) that manifests as an increase in NM1 foci in the nucleus and are rescued to basal levels upon the combined knockdown of Lamin A/C and Emerin. Furthermore, Lamin A/C-Emerin co-depletion destabilizes cytoskeletal organization as it increases actin stress fibers. This further impinges on nuclear organization, as it enhances chromatin mobility more toward the nuclear interior in Lamin A/C-Emerin co-depleted cells. This enhanced chromatin mobility was restored to basal levels either upon inhibition of Nuclear Myosin 1 (NM1) activity or actin depolymerization. In addition, the combined loss of Lamin A/C and Emerin alters the otherwise highly conserved spatial positions of chromosome territories. Furthermore, knockdown of Lamin A/C or Lamin A/C-Emerin combined, deregulates expression levels of a candidate subset of genes. Amongst these genes, both KLK10 (Chr.19, Lamina Associated Domain (LAD+)) and MADH2 (Chr.18, LAD-) were significantly repressed, while BCL2L12 (Chr.19, LAD-) is de-repressed. These genes differentially reposition with respect to the nuclear envelope. Conclusions Taken together, these studies underscore a remarkable interplay between Lamin A/C and Emerin in modulating cytoskeletal organization of actin and NM1 that impinges on chromatin dynamics and function in the interphase nucleus. Electronic supplementary material The online version of this article (10.1186/s12860-019-0192-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devika Ranade
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Roopali Pradhan
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Muhunden Jayakrishnan
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Sushmitha Hegde
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Kundan Sengupta
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India.
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25
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Hutchinson-Gilford Progeria Syndrome-Current Status and Prospects for Gene Therapy Treatment. Cells 2019; 8:cells8020088. [PMID: 30691039 PMCID: PMC6406247 DOI: 10.3390/cells8020088] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 12/13/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is one of the most severe disorders among laminopathies—a heterogeneous group of genetic diseases with a molecular background based on mutations in the LMNA gene and genes coding for interacting proteins. HGPS is characterized by the presence of aging-associated symptoms, including lack of subcutaneous fat, alopecia, swollen veins, growth retardation, age spots, joint contractures, osteoporosis, cardiovascular pathology, and death due to heart attacks and strokes in childhood. LMNA codes for two major, alternatively spliced transcripts, give rise to lamin A and lamin C proteins. Mutations in the LMNA gene alone, depending on the nature and location, may result in the expression of abnormal protein or loss of protein expression and cause at least 11 disease phenotypes, differing in severity and affected tissue. LMNA gene-related HGPS is caused by a single mutation in the LMNA gene in exon 11. The mutation c.1824C > T results in activation of the cryptic donor splice site, which leads to the synthesis of progerin protein lacking 50 amino acids. The accumulation of progerin is the reason for appearance of the phenotype. In this review, we discuss current knowledge on the molecular mechanisms underlying the development of HGPS and provide a critical analysis of current research trends in this field. We also discuss the mouse models available so far, the current status of treatment of the disease, and future prospects for the development of efficient therapies, including gene therapy for HGPS.
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26
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Serebryannyy LA, Misteli T. HiPLA: High-throughput imaging proximity ligation assay. Methods 2018; 157:80-87. [PMID: 30419336 DOI: 10.1016/j.ymeth.2018.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/29/2018] [Accepted: 11/06/2018] [Indexed: 01/16/2023] Open
Abstract
Protein-protein interactions are essential for cellular structure and function. To delineate how the intricate assembly of protein interactions contribute to cellular processes in health and disease, new methodologies that are both highly sensitive and can be applied at large scale are needed. Here, we develop HiPLA (high-throughput imaging proximity ligation assay), a method that employs the well-established antibody-based proximity ligation assay in a high-throughput imaging screening format as a novel means to systematically visualize protein interactomes. Using HiPLA with a library of antibodies targeting nuclear proteins, we probe the interaction of 60 proteins and associated post-translational modifications (PTMs) with the nuclear lamina in a model of the premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS). We identify a subset of proteins that differentially interact with the nuclear lamina in HGPS. Using HiPLA in combination with quantitative indirect immunofluorescence, we find that the majority of differential interactions are accompanied by corresponding changes in expression of the interacting protein. Taken together, HiPLA offers a novel approach to probe cellular protein-protein interaction at a large scale and reveals mechanistic insights into the assembly of protein complexes.
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Affiliation(s)
- Leonid A Serebryannyy
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA.
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27
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Briand N, Cahyani I, Madsen-Østerbye J, Paulsen J, Rønningen T, Sørensen AL, Collas P. Lamin A, Chromatin and FPLD2: Not Just a Peripheral Ménage-à-Trois. Front Cell Dev Biol 2018; 6:73. [PMID: 30057899 PMCID: PMC6053905 DOI: 10.3389/fcell.2018.00073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/21/2018] [Indexed: 11/13/2022] Open
Abstract
At the nuclear periphery, the genome is anchored to A- and B-type nuclear lamins in the form of heterochromatic lamina-associated domains. A-type lamins also associate with chromatin in the nuclear interior, away from the peripheral nuclear lamina. This nucleoplasmic lamin A environment tends to be euchromatic, suggesting distinct roles of lamin A in the regulation of gene expression in peripheral and more central regions of the nucleus. The hot-spot lamin A R482W mutation causing familial partial lipodystrophy of Dunnigan-type (FPLD2), affects lamin A association with chromatin at the nuclear periphery and in the nuclear interior, and is associated with 3-dimensional (3D) rearrangements of chromatin. Here, we highlight features of nuclear lamin association with the genome at the nuclear periphery and in the nuclear interior. We address recent data showing a rewiring of such interactions in cells from FPLD2 patients, and in adipose progenitor and induced pluripotent stem cell models of FPLD2. We discuss associated epigenetic and genome conformation changes elicited by the lamin A R482W mutation at the gene level. The findings argue that the mutation adversely impacts both global and local genome architecture throughout the nucleus space. The results, together with emerging new computational modeling tools, mark the start of a new era in our understanding of the 3D genomics of laminopathies.
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Affiliation(s)
- Nolwenn Briand
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Norwegian Center for Stem Cell Research, Oslo University Hospital, Oslo, Norway
| | - Inswasti Cahyani
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Julia Madsen-Østerbye
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jonas Paulsen
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Torunn Rønningen
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anita L Sørensen
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Norwegian Center for Stem Cell Research, Oslo University Hospital, Oslo, Norway
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28
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Burla R, La Torre M, Merigliano C, Vernì F, Saggio I. Genomic instability and DNA replication defects in progeroid syndromes. Nucleus 2018; 9:368-379. [PMID: 29936894 PMCID: PMC7000143 DOI: 10.1080/19491034.2018.1476793] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Progeroid syndromes induced by mutations in lamin A or in its interactors – named progeroid laminopathies – are model systems for the dissection of the molecular pathways causing physiological and premature aging. A large amount of data, based mainly on the Hutchinson Gilford Progeria syndrome (HGPS), one of the best characterized progeroid laminopathy, has highlighted the role of lamins in multiple DNA activities, including replication, repair, chromatin organization and telomere function. On the other hand, the phenotypes generated by mutations affecting genes directly acting on DNA function, as mutations in the helicases WRN and BLM or in the polymerase polδ, share many of the traits of progeroid laminopathies. These evidences support the hypothesis of a concerted implication of DNA function and lamins in aging. We focus here on these aspects to contribute to the comprehension of the driving forces acting in progeroid syndromes and premature aging.
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Affiliation(s)
- Romina Burla
- a Dipartimento di Biologia e Biotecnologie "C. Darwin" , Sapienza Università di Roma , Roma , Italy.,b Istituto di Biologia e Patologia Molecolari del CNR , Rome , Italy
| | - Mattia La Torre
- a Dipartimento di Biologia e Biotecnologie "C. Darwin" , Sapienza Università di Roma , Roma , Italy.,b Istituto di Biologia e Patologia Molecolari del CNR , Rome , Italy
| | - Chiara Merigliano
- a Dipartimento di Biologia e Biotecnologie "C. Darwin" , Sapienza Università di Roma , Roma , Italy
| | - Fiammetta Vernì
- a Dipartimento di Biologia e Biotecnologie "C. Darwin" , Sapienza Università di Roma , Roma , Italy
| | - Isabella Saggio
- a Dipartimento di Biologia e Biotecnologie "C. Darwin" , Sapienza Università di Roma , Roma , Italy.,b Istituto di Biologia e Patologia Molecolari del CNR , Rome , Italy.,c Istituto Pasteur Fondazione Cenci Bolognetti , Rome , Italy
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29
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Harhouri K, Navarro C, Depetris D, Mattei MG, Nissan X, Cau P, De Sandre-Giovannoli A, Lévy N. MG132-induced progerin clearance is mediated by autophagy activation and splicing regulation. EMBO Mol Med 2018; 9:1294-1313. [PMID: 28674081 PMCID: PMC5582415 DOI: 10.15252/emmm.201607315] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hutchinson–Gilford progeria syndrome (HGPS) is a lethal premature and accelerated aging disease caused by a de novo point mutation in LMNA encoding A‐type lamins. Progerin, a truncated and toxic prelamin A issued from aberrant splicing, accumulates in HGPS cells' nuclei and is a hallmark of the disease. Small amounts of progerin are also produced during normal aging. We show that progerin is sequestered into abnormally shaped promyelocytic nuclear bodies, identified as novel biomarkers in late passage HGPS cell lines. We found that the proteasome inhibitor MG132 induces progerin degradation through macroautophagy and strongly reduces progerin production through downregulation of SRSF‐1 and SRSF‐5 accumulation, controlling prelamin A mRNA aberrant splicing. MG132 treatment improves cellular HGPS phenotypes. MG132 injection in skeletal muscle of LmnaG609G/G609G mice locally reduces SRSF‐1 expression and progerin levels. Altogether, we demonstrate progerin reduction based on MG132 dual action and shed light on a promising class of molecules toward a potential therapy for children with HGPS.
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Affiliation(s)
- Karim Harhouri
- Aix Marseille Univ, INSERM, GMGF (Génétique Médicale et Génomique Fonctionnelle), Marseille, France
| | - Claire Navarro
- Aix Marseille Univ, INSERM, GMGF (Génétique Médicale et Génomique Fonctionnelle), Marseille, France
| | - Danielle Depetris
- Aix Marseille Univ, INSERM, GMGF (Génétique Médicale et Génomique Fonctionnelle), Marseille, France
| | - Marie-Geneviève Mattei
- Aix Marseille Univ, INSERM, GMGF (Génétique Médicale et Génomique Fonctionnelle), Marseille, France
| | - Xavier Nissan
- CECS, I-STEM, Institut des cellules Souches pour le Traitement et l'Etude des maladies Monogéniques, AFM, Evry, France
| | - Pierre Cau
- Aix Marseille Univ, INSERM, GMGF (Génétique Médicale et Génomique Fonctionnelle), Marseille, France.,AP-HM, Hôpital la Timone, Service de Biologie Cellulaire, Marseille, France
| | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ, INSERM, GMGF (Génétique Médicale et Génomique Fonctionnelle), Marseille, France.,AP-HM, Hôpital la Timone, Département de Génétique Médicale, Marseille, France
| | - Nicolas Lévy
- Aix Marseille Univ, INSERM, GMGF (Génétique Médicale et Génomique Fonctionnelle), Marseille, France .,AP-HM, Hôpital la Timone, Département de Génétique Médicale, Marseille, France
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30
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Cho S, Abbas A, Irianto J, Ivanovska IL, Xia Y, Tewari M, Discher DE. Progerin phosphorylation in interphase is lower and less mechanosensitive than lamin-A,C in iPS-derived mesenchymal stem cells. Nucleus 2018; 9:230-245. [PMID: 29619860 PMCID: PMC5973135 DOI: 10.1080/19491034.2018.1460185] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Interphase phosphorylation of lamin-A,C depends dynamically on a cell's microenvironment, including the stiffness of extracellular matrix. However, phosphorylation dynamics is poorly understood for diseased forms such as progerin, a permanently farnesylated mutant of LMNA that accelerates aging of stiff and mechanically stressed tissues. Here, fine-excision alignment mass spectrometry (FEA-MS) is developed to quantify progerin and its phosphorylation levels in patient iPS cells differentiated to mesenchymal stem cells (MSCs). The stoichiometry of total A-type lamins (including progerin) versus B-type lamins measured for Progeria iPS-MSCs prove similar to that of normal MSCs, with total A-type lamins more abundant than B-type lamins. However, progerin behaves more like farnesylated B-type lamins in mechanically-induced segregation from nuclear blebs. Phosphorylation of progerin at multiple sites in iPS-MSCs cultured on rigid plastic is also lower than that of normal lamin-A and C. Reduction of nuclear tension upon i) cell rounding/detachment from plastic, ii) culture on soft gels, and iii) inhibition of actomyosin stress increases phosphorylation and degradation of lamin-C > lamin-A > progerin. Such mechano-sensitivity diminishes, however, with passage as progerin and DNA damage accumulate. Lastly, transcription-regulating retinoids exert equal effects on both diseased and normal A-type lamins, suggesting a differential mechano-responsiveness might best explain the stiff tissue defects in Progeria.
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Affiliation(s)
- Sangkyun Cho
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Amal Abbas
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Jerome Irianto
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Irena L. Ivanovska
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuntao Xia
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Manu Tewari
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Dennis E. Discher
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, USA,CONTACT Dennis E. Discher , University of Pennsylvania, 129 Towne Bldg, Philadelphia, PA 19104
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31
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Biotinylation by antibody recognition-a method for proximity labeling. Nat Methods 2017; 15:127-133. [PMID: 29256494 PMCID: PMC5790613 DOI: 10.1038/nmeth.4533] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 10/30/2017] [Indexed: 01/12/2023]
Abstract
Identification of protein-protein interactions is a major goal of biological research. Despite technical advances over the last two decades, important but still largely unsolved challenges include the high-throughput detection of interactions directly from primary tissue and the identification of interactors of insoluble proteins that form higher-order structures. We have developed a novel, proximity-based labeling approach that uses antibodies to guide biotin deposition onto adjacent proteins in fixed cells and primary tissues. We showed our method to be specific and sensitive by labeling a mitochondrial matrix protein. Next, we used this method to profile the dynamic interactome of lamin A/C in multiple cell and tissue types under various treatment conditions. The ability to detect proximal proteins and putative interactors in intact tissues, and to quantify changes caused by different conditions or in the presence of disease mutations, can provide a new window into cell biology and disease pathogenesis.
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32
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Serebryannyy L, Misteli T. Protein sequestration at the nuclear periphery as a potential regulatory mechanism in premature aging. J Cell Biol 2017; 217:21-37. [PMID: 29051264 PMCID: PMC5748986 DOI: 10.1083/jcb.201706061] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/10/2017] [Accepted: 08/17/2017] [Indexed: 12/19/2022] Open
Abstract
Serebryannyy and Misteli provide a perspective on how protein sequestration at the inner nuclear membrane and nuclear lamina might influence aging. Despite the extensive description of numerous molecular changes associated with aging, insights into the driver mechanisms of this fundamental biological process are limited. Based on observations in the premature aging syndrome Hutchinson–Gilford progeria, we explore the possibility that protein regulation at the inner nuclear membrane and the nuclear lamina contributes to the aging process. In support, sequestration of nucleoplasmic proteins to the periphery impacts cell stemness, the response to cytotoxicity, proliferation, changes in chromatin state, and telomere stability. These observations point to the nuclear periphery as a central regulator of the aging phenotype.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD
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33
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Ferri G, Storti B, Bizzarri R. Nucleocytoplasmic transport in cells with progerin-induced defective nuclear lamina. Biophys Chem 2017; 229:77-83. [PMID: 28712764 DOI: 10.1016/j.bpc.2017.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 10/19/2022]
Abstract
Recent data indicate that nuclear lamina (NL) plays a relevant role in many fundamental cellular functions. The peculiar role of NL in cells is dramatically demonstrated by the Hutchinson-Gilford progeria syndrome (HGPS), an inherited laminopathy that causes premature, rapid aging shortly after birth. In HGPS, a mutant form of Lamin A (progeria) leads to a dysmorphic NL structure, but how this perturbation is transduced into cellular changes is still largely unknown. Owing to the close structural relationship between NL and the Nuclear Pore Complex (NPC), in this work we test whether HGPS affects passive and active nucleo-cytoplasmic shuttling of cargoes by means of an established model based of fluorescence recovery after photobleaching. Our findings clearly demonstrate that dysmorphic NL is decoupled from the dynamic characteristics of passive and active transport towards and from the nucleus, as well as from the binding affinity of transport protein mediators.
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Affiliation(s)
- Gianmarco Ferri
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy; Center for Nanotechnology Innovation @ NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Barbara Storti
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Ranieri Bizzarri
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy.
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34
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Kubben N, Zhang W, Wang L, Voss TC, Yang J, Qu J, Liu GH, Misteli T. Repression of the Antioxidant NRF2 Pathway in Premature Aging. Cell 2016; 165:1361-1374. [PMID: 27259148 DOI: 10.1016/j.cell.2016.05.017] [Citation(s) in RCA: 335] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 02/04/2016] [Accepted: 04/25/2016] [Indexed: 12/23/2022]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare, invariably fatal premature aging disorder. The disease is caused by constitutive production of progerin, a mutant form of the nuclear architectural protein lamin A, leading, through unknown mechanisms, to diverse morphological, epigenetic, and genomic damage and to mesenchymal stem cell (MSC) attrition in vivo. Using a high-throughput siRNA screen, we identify the NRF2 antioxidant pathway as a driver mechanism in HGPS. Progerin sequesters NRF2 and thereby causes its subnuclear mislocalization, resulting in impaired NRF2 transcriptional activity and consequently increased chronic oxidative stress. Suppressed NRF2 activity or increased oxidative stress is sufficient to recapitulate HGPS aging defects, whereas reactivation of NRF2 activity in HGPS patient cells reverses progerin-associated nuclear aging defects and restores in vivo viability of MSCs in an animal model. These findings identify repression of the NRF2-mediated antioxidative response as a key contributor to the premature aging phenotype.
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Affiliation(s)
- Nard Kubben
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Weiqi Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; FSU-CAS Innovation Institute, Foshan University, Foshan, Guangdong 528000, China
| | - Lixia Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ty C Voss
- High-Throughput Imaging Facility, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiping Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Hui Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; FSU-CAS Innovation Institute, Foshan University, Foshan, Guangdong 528000, China; Beijing Institute for Brain Disorders, Beijing 100069, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Lee SJ, Jung YS, Yoon MH, Kang SM, Oh AY, Lee JH, Jun SY, Woo TG, Chun HY, Kim SK, Chung KJ, Lee HY, Lee K, Jin G, Na MK, Ha NC, Bárcena C, Freije JMP, López-Otín C, Song GY, Park BJ. Interruption of progerin-lamin A/C binding ameliorates Hutchinson-Gilford progeria syndrome phenotype. J Clin Invest 2016; 126:3879-3893. [PMID: 27617860 DOI: 10.1172/jci84164] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 08/04/2016] [Indexed: 11/17/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare autosomal dominant genetic disease that is caused by a silent mutation of the LMNA gene encoding lamins A and C (lamin A/C). The G608G mutation generates a more accessible splicing donor site than does WT and produces an alternatively spliced product of LMNA called progerin, which is also expressed in normal aged cells. In this study, we determined that progerin binds directly to lamin A/C and induces profound nuclear aberrations. Given this observation, we performed a random screening of a chemical library and identified 3 compounds (JH1, JH4, and JH13) that efficiently block progerin-lamin A/C binding. These 3 chemicals, particularly JH4, alleviated nuclear deformation and reversed senescence markers characteristic of HGPS cells, including growth arrest and senescence-associated β-gal (SA-β-gal) activity. We then used microarray-based analysis to demonstrate that JH4 is able to rescue defects of cell-cycle progression in both HGPS and aged cells. Furthermore, administration of JH4 to LmnaG609G/G609G-mutant mice, which phenocopy human HGPS, resulted in a marked improvement of several progeria phenotypes and an extended lifespan. Together, these findings indicate that specific inhibitors with the ability to block pathological progerin-lamin A/C binding may represent a promising strategy for improving lifespan and health in both HGPS and normal aging.
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Machowska M, Piekarowicz K, Rzepecki R. Regulation of lamin properties and functions: does phosphorylation do it all? Open Biol 2016; 5:rsob.150094. [PMID: 26581574 PMCID: PMC4680568 DOI: 10.1098/rsob.150094] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The main functions of lamins are their mechanical and structural roles as major building blocks of the karyoskeleton. They are also involved in chromatin structure regulation, gene expression, intracellular signalling pathway modulation and development. All essential lamin functions seem to depend on their capacity for assembly or disassembly after the receipt of specific signals, and after specific, selective and precisely regulated interactions through their various domains. Reversible phosphorylation of lamins is crucial for their functions, so it is important to understand how lamin polymerization and interactions are modulated, and which sequences may undergo such modifications. This review combines experimental data with results of our in silico analyses focused on lamin phosphorylation in model organisms to show the presence of evolutionarily conserved sequences and to indicate specific in vivo phosphorylations that affect particular functions.
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Affiliation(s)
- Magdalena Machowska
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wrocław, ul. Fryderyka Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Katarzyna Piekarowicz
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wrocław, ul. Fryderyka Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Ryszard Rzepecki
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wrocław, ul. Fryderyka Joliot-Curie 14a, Wrocław 50-383, Poland
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37
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Bermeo S, Vidal C, Zhou H, Duque G. Lamin A/C Acts as an Essential Factor in Mesenchymal Stem Cell Differentiation Through the Regulation of the Dynamics of the Wnt/β-Catenin Pathway. J Cell Biochem 2016; 116:2344-53. [PMID: 25846419 DOI: 10.1002/jcb.25185] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 04/01/2015] [Indexed: 11/07/2022]
Abstract
Changes in the expression of lamin A/C, a fibrilar protein of the nuclear envelope, are associated with the cellular features of age-related bone loss. Reduced expression of lamin A/C inhibits osteoblastogenesis while facilitating adipogenic differentiation of mesenchymal stem cells (MSC) in vitro and in vivo. In this study we investigated the regulatory role that lamin A/C plays on the essential elements of the Wnt/β-catenin pathway, which are pivotal in MSC differentiation. Initially, we assessed the effect of lamin A/C gene (LMNA) overexpression on MSC differentiation while compared it to lamin A/C depleted MSC. Osteogenesis and gene expression of osteogenic factors were higher in LMNA-transfected MSC as compared to control. Conversely, adipogenesis and expression of adipogenic factors were significantly lower in LMNA transfected cells. Nuclear β-catenin was significantly higher (∼two fold) in MSC expressing higher levels of LMNA as compared to control with nuclear β-catenin levels being significantly lower (∼ -42%) in siRNA-treated MSC. Luciferase activity for β-catenin-mediated transcriptional activation was significantly higher in cells overexpressing LMNA. These data indicate that MSC overexpressing LMNA have higher osteogenic and lower adipogenic differentiation potential. In conclusion, our studies demonstrate that lamin A/C plays a significant role in the differentiation of both osteoblasts and adipocytes by regulating some of the elements of Wnt/β-catenin signaling during early MSC differentiation.
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Affiliation(s)
- Sandra Bermeo
- Musculoskeletal Ageing Research Program, Sydney Medical School Nepean, The University of Sydney, Penrith, New South Wales, Australia
| | - Christopher Vidal
- Musculoskeletal Ageing Research Program, Sydney Medical School Nepean, The University of Sydney, Penrith, New South Wales, Australia
| | - Hong Zhou
- ANZAC Research Institute, The University of Sydney, Concord, New South Wales, Australia
| | - Gustavo Duque
- Musculoskeletal Ageing Research Program, Sydney Medical School Nepean, The University of Sydney, Penrith, New South Wales, Australia
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Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is an extremely rare premature aging disease presenting many features resembling the normal aging process. HGPS patients die before the age of 20 years due to cardiovascular problems and heart failure. HGPS is linked to mutations in the LMNA gene encoding the intermediate filament protein lamin A. Lamin A is a major component of the nuclear lamina, a scaffold structure at the nuclear envelope that defines mechanochemical properties of the nucleus and is involved in chromatin organization and epigenetic regulation. Lamin A is also present in the nuclear interior where it fulfills lamina-independent functions in cell signaling and gene regulation. The most common LMNA mutation linked to HGPS leads to mis-splicing of the LMNA mRNA and produces a mutant lamin A protein called progerin that tightly associates with the inner nuclear membrane and affects the dynamic properties of lamins. Progerin expression impairs many important cellular processes providing insight into potential disease mechanisms. These include changes in mechanosignaling, altered chromatin organization and impaired genome stability, and changes in signaling pathways, leading to impaired regulation of adult stem cells, defective extracellular matrix production and premature cell senescence. In this review, we discuss these pathways and their potential contribution to the disease pathologies as well as therapeutic approaches used in preclinical and clinical tests.
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Affiliation(s)
- Sandra Vidak
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Vienna Biocenter (VBC), Medical University Vienna, Dr. Bohr-Gasse 9/3, 1030, Vienna, Austria
| | - Roland Foisner
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Vienna Biocenter (VBC), Medical University Vienna, Dr. Bohr-Gasse 9/3, 1030, Vienna, Austria.
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Serrano JB, da Cruz E Silva OAB, Rebelo S. Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. MEMBRANES 2016; 6:membranes6010008. [PMID: 26784240 PMCID: PMC4812414 DOI: 10.3390/membranes6010008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 12/26/2022]
Abstract
Lamina-associated polypeptide 1 (LAP1) is a type II transmembrane protein of the inner nuclear membrane encoded by the human gene TOR1AIP1. LAP1 is involved in maintaining the nuclear envelope structure and appears be involved in the positioning of lamins and chromatin. To date, LAP1’s precise function has not been fully elucidated but analysis of its interacting proteins will permit unraveling putative associations to specific cellular pathways and cellular processes. By assessing public databases it was possible to identify the LAP1 interactome, and this was curated. In total, 41 interactions were identified. Several functionally relevant proteins, such as TRF2, TERF2IP, RIF1, ATM, MAD2L1 and MAD2L1BP were identified and these support the putative functions proposed for LAP1. Furthermore, by making use of the Ingenuity Pathways Analysis tool and submitting the LAP1 interactors, the top two canonical pathways were “Telomerase signalling” and “Telomere Extension by Telomerase” and the top functions “Cell Morphology”, “Cellular Assembly and Organization” and “DNA Replication, Recombination, and Repair”. Once again, putative LAP1 functions are reinforced but novel functions are emerging.
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Affiliation(s)
- Joana B Serrano
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Odete A B da Cruz E Silva
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Sandra Rebelo
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
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40
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Abstract
The nuclear envelope (NE) is a critical cellular structure whose constituents and roles in a myriad of cellular processes seem ever expanding. To determine the underlying mechanisms by which the NE constituents participate in various cellular events, it is necessary to understand the nature of their protein-protein associations. BioID (proximity-dependent biotin identification) is a recently established method to generate a history of protein-protein associations as they occur over time in living cells. BioID is based on fusion of a bait protein to a promiscuous biotin ligase. Expression of the BioID fusion protein in a relevant cellular environment enables biotinylation of vicinal and interacting proteins of the bait protein, permitting isolation and identification by conventional biotin-affinity capture and mass-spec analysis. In this way, BioID provides unique capabilities to identify protein-protein associations at the NE. In this chapter we provide a detailed protocol for the application of BioID to the study of NE proteins.
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Affiliation(s)
- Dae In Kim
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA
| | - Samuel C Jensen
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA
| | - Kyle J Roux
- Sanford Research, Sanford Children's Health Research Center, 2301 E. 60th Street N., Sioux Falls, SD, 57104, USA.
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, 57105, USA.
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41
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Abstract
A- and B-type lamins support the nuclear envelope, contribute to heterochromatin organization, and regulate a myriad of nuclear processes. The mechanisms by which lamins function in different cell types and the mechanisms by which lamin mutations cause over a dozen human diseases (laminopathies) remain unclear. The identification of proteins associated with lamins is likely to provide fundamental insight into these mechanisms. BioID (proximity-dependent biotin identification) is a unique and powerful method for identifying protein-protein and proximity-based interactions in living cells. BioID utilizes a mutant biotin ligase from bacteria that is fused to a protein of interest (bait). When expressed in living cells and stimulated with excess biotin, this BioID-fusion protein promiscuously biotinylates directly interacting and vicinal endogenous proteins. Following biotin-affinity capture, the biotinylated proteins can be identified using mass spectrometry. BioID thus enables screening for physiologically relevant protein associations that occur over time in living cells. BioID is applicable to insoluble proteins such as lamins that are often refractory to study by other methods and can identify weak and/or transient interactions. We discuss the use of BioID to elucidate novel lamin-interacting proteins and its applications in a broad range of biological systems, and provide detailed protocols to guide new applications.
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Affiliation(s)
- Aaron A Mehus
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA
| | - Ruthellen H Anderson
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA
| | - Kyle J Roux
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA.
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42
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Chojnowski A, Ong PF, Wong ESM, Lim JSY, Mutalif RA, Navasankari R, Dutta B, Yang H, Liow YY, Sze SK, Boudier T, Wright GD, Colman A, Burke B, Stewart CL, Dreesen O. Progerin reduces LAP2α-telomere association in Hutchinson-Gilford progeria. eLife 2015; 4. [PMID: 26312502 PMCID: PMC4565980 DOI: 10.7554/elife.07759] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/23/2015] [Indexed: 12/12/2022] Open
Abstract
Hutchinson-Gilford progeria (HGPS) is a premature ageing syndrome caused by a mutation in LMNA, resulting in a truncated form of lamin A called progerin. Progerin triggers loss of the heterochromatic marker H3K27me3, and premature senescence, which is prevented by telomerase. However, the mechanism how progerin causes disease remains unclear. Here, we describe an inducible cellular system to model HGPS and find that LAP2α (lamina-associated polypeptide-α) interacts with lamin A, while its interaction with progerin is significantly reduced. Super-resolution microscopy revealed that over 50% of telomeres localize to the lamina and that LAP2α association with telomeres is impaired in HGPS. This impaired interaction is central to HGPS since increasing LAP2α levels rescues progerin-induced proliferation defects and loss of H3K27me3, whereas lowering LAP2 levels exacerbates progerin-induced defects. These findings provide novel insights into the pathophysiology underlying HGPS, and how the nuclear lamina regulates proliferation and chromatin organization. DOI:http://dx.doi.org/10.7554/eLife.07759.001 Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic disease in which individuals age prematurely. Newborns appear normal at birth, but start ageing rapidly when they are around a year old. Symptoms of the disease include stunted growth and joint stiffness, and individuals often die of heart failure during their teens. A mutated version of a protein called lamin A causes HGPS; this mutant is known as progerin. In cells that produce progerin, the ‘telomeres’ that protect the ends of chromosomes (the structures that contain most of the cell's DNA) from damage, are unusually short. Every time a cell divides, the telomeres get shorter. If they get too short, the DNA is damaged and the cell stops dividing and enters a state known as senescence. HGPS affects some of the tissues in the body more severely than others, and these tissues tend to produce high levels of progerin. By gradually raising the levels of progerin in human cells, Chojnowski et al. found that DNA damage and cell senescence only occur when the amount of progerin in a cell exceeds a particular threshold. Moreover, the expression of telomerase—a complex that can elongate telomeres—prevented progerin-induced DNA damage and premature senescence. To find out how progerin affects cells, Chojnowski et al. compared how lamin A and progerin interact with other proteins. This revealed that progerin interacts with a protein called LAP2α more weakly than lamin A. LAP2α normally associates with telomeres, but using super-high resolution microscopy, Chojnowski et al. observed that this association is less likely to occur in the cells of people with HGPS. Importantly, increasing the amount of LAP2α in progerin-expressing cells prevented DNA damage and senescence and enabled these cells to continue dividing. Chojnowski et al. propose that in HGPS, the weak interaction between LAP2α and progerin disrupts how LAP2α interacts with telomeres, which prevents cells from dividing. Understanding this process may help to design new ways of treating HGPS, and may also help us to understand other diseases that are caused by mutations in lamin proteins. DOI:http://dx.doi.org/10.7554/eLife.07759.002
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Affiliation(s)
- Alexandre Chojnowski
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - Peh Fern Ong
- Cellular Ageing, Institute of Medical Biology, Singapore, Singapore
| | - Esther S M Wong
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - John S Y Lim
- Microscopy Unit, Institute of Medical Biology, Singapore, Singapore
| | - Rafidah A Mutalif
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - Raju Navasankari
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - Bamaprasad Dutta
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Henry Yang
- Bioinformatics Core, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yi Y Liow
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - Siu K Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Thomas Boudier
- Bioinformatics Institute, IPAL UMI 2955, Singapore, Singapore
| | - Graham D Wright
- Microscopy Unit, Institute of Medical Biology, Singapore, Singapore
| | - Alan Colman
- Stem Cell Disease Models, Institute of Medical Biology, Singapore, Singapore
| | - Brian Burke
- Nuclear Dynamics and Architecture, Institute of Medical Biology, Singapore, Singapore
| | - Colin L Stewart
- Developmental and Regenerative Biology, Institute of Medical Biology, Singapore, Singapore
| | - Oliver Dreesen
- Cellular Ageing, Institute of Medical Biology, Singapore, Singapore
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43
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Maizels Y, Gerlitz G. Shaping of interphase chromosomes by the microtubule network. FEBS J 2015; 282:3500-24. [PMID: 26040675 DOI: 10.1111/febs.13334] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/11/2015] [Accepted: 06/01/2015] [Indexed: 12/31/2022]
Abstract
It is well established that microtubule dynamics play a major role in chromosome condensation and localization during mitosis. During interphase, however, it is assumed that the metazoan nuclear envelope presents a physical barrier, which inhibits interaction between the microtubules located in the cytoplasm and the chromatin fibers located in the nucleus. In recent years, it has become apparent that microtubule dynamics alter chromatin structure and function during interphase as well. Microtubule motor proteins transport several transcription factors and exogenous DNA (such as plasmid DNA) from the cytoplasm to the nucleus. Various soluble microtubule components are able to translocate into the nucleus, where they bind various chromatin elements leading to transcriptional alterations. In addition, microtubules may apply force on the nuclear envelope, which is transmitted into the nucleus, leading to changes in chromatin structure. Thus, microtubule dynamics during interphase may affect chromatin spatial organization, as well as transcription, replication and repair.
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Affiliation(s)
- Yael Maizels
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Israel
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44
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Depreux FF, Puckelwartz MJ, Augustynowicz A, Wolfgeher D, Labno CM, Pierre-Louis D, Cicka D, Kron SJ, Holaska J, McNally EM. Disruption of the lamin A and matrin-3 interaction by myopathic LMNA mutations. Hum Mol Genet 2015; 24:4284-95. [PMID: 25948554 DOI: 10.1093/hmg/ddv160] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/27/2015] [Indexed: 12/25/2022] Open
Abstract
The nuclear face of the nuclear membrane is enriched with the intermediate filament protein lamin A. Mutations in LMNA, the gene encoding lamin A, lead to a diverse set of inherited conditions including myopathies that affect both the heart and skeletal muscle. To gain insight about lamin A protein interactions, binding proteins associated with the tail of lamin A were characterized. Of 130 nuclear proteins found associated with the lamin A tail, 17 (13%) were previously described lamin A binding partners. One protein not previously linked to lamin A, matrin-3, was selected for further study, because like LMNA mutations, matrin-3 has also been implicated in inherited myopathy. Matrin-3 binds RNA and DNA and is a nucleoplasmic protein originally identified from the insoluble nuclear fraction, referred to as the nuclear matrix. Anti-matrin-3 antibodies were found to co-immunoprecipitate lamin A, and the lamin-A binding domain was mapped to the carboxy-terminal half of matrin-3. Three-dimensional mapping of the lamin A-matrin-3 interface showed that the LMNA truncating mutation Δ303, which lacks the matrin-3 binding domain, was associated with an increased distance between lamin A and matrin-3. LMNA mutant cells are known to have altered biophysical properties and the matrin-3-lamin A interface is positioned to contribute to these defects.
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Affiliation(s)
| | - Megan J Puckelwartz
- Department of Medicine, Center for Genetic Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - Don Wolfgeher
- Department of Molecular of Genetics and Cell Biology, Proteomics Core Facility
| | - Christine M Labno
- Integrated Microscopy Facility, Office of Shared Research Facilities
| | | | | | | | | | - Elizabeth M McNally
- Department of Medicine, Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA and Center for Genetic Medicine, Northwestern University, Chicago, IL, 60611, USA
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45
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Warren DT, Tajsic T, Porter LJ, Minaisah RM, Cobb A, Jacob A, Rajgor D, Zhang QP, Shanahan CM. Nesprin-2-dependent ERK1/2 compartmentalisation regulates the DNA damage response in vascular smooth muscle cell ageing. Cell Death Differ 2015; 22:1540-50. [PMID: 25744025 PMCID: PMC4532777 DOI: 10.1038/cdd.2015.12] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/19/2014] [Accepted: 01/21/2015] [Indexed: 11/30/2022] Open
Abstract
Prelamin A accumulation and persistent DNA damage response (DDR) are hallmarks of vascular smooth muscle cell (VSMC) ageing and dysfunction. Although prelamin A is proposed to interfere with DNA repair, our understanding of the crosstalk between prelamin A and the repair process remains limited. The extracellular signal-regulated kinases 1 and 2 (ERK1/2) have emerged as key players in the DDR and are known to enhance ataxia telangiectasia-mutated protein (ATM) activity at DNA lesions, and in this study, we identified a novel relationship between prelamin A accumulation and ERK1/2 nuclear compartmentalisation during VSMC ageing. We show both prelamin A accumulation and increased DNA damage occur concomitantly, before VSMC replicative senescence, and induce the localisation of ERK1/2 to promyelocytic leukaemia protein nuclear bodies (PML NBs) at the sites of DNA damage via nesprin-2 and lamin A interactions. Importantly, VSMCs treated with DNA damaging agents also displayed prelamin A accumulation and ERK compartmentalisation at PML NBs, suggesting that prelamin A and nesprin-2 are novel components of the DDR. In support of this, disruption of ERK compartmentalisation at PML NBs, by either depletion of nesprin-2 or lamins A/C, resulted in the loss of ATM from DNA lesions. However, ATM signalling and DNA repair remained intact after lamins A/C depletion, whereas nesprin-2 disruption ablated downstream Chk2 activation and induced genomic instability. We conclude that lamins A/C and PML act as scaffolds to organise DNA-repair foci and compartmentalise nesprin-2/ERK signalling. However, nesprin-2/ERK signalling fidelity, but not their compartmentalisation at PML NBs, is essential for efficient DDR in VSMCs.
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Affiliation(s)
- D T Warren
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - T Tajsic
- Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - L J Porter
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - R M Minaisah
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - A Cobb
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - A Jacob
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - D Rajgor
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - Q P Zhang
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - C M Shanahan
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
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46
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Poleshko A, Mansfield KM, Burlingame CC, Andrake MD, Shah NR, Katz RA. The human protein PRR14 tethers heterochromatin to the nuclear lamina during interphase and mitotic exit. Cell Rep 2015; 5:292-301. [PMID: 24209742 DOI: 10.1016/j.celrep.2013.09.024] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/21/2013] [Accepted: 09/16/2013] [Indexed: 11/25/2022] Open
Abstract
The nuclear lamina is a protein meshwork that lies under the inner nuclear membrane of metazoan cells. One function of the nuclear lamina is to organize heterochromatin at the inner nuclear periphery. However, very little is known about how heterochromatin attaches to the nuclear lamina and how such attachments are restored at mitotic exit. Here, we show that a previously unstudied human protein, PRR14, functions to tether heterochromatin to the nuclear periphery during interphase, through associations with heterochromatin protein 1 (HP1) and the nuclear lamina. During early mitosis, PRR14 is released from the nuclear lamina and chromatin and remains soluble. Strikingly, at the onset of anaphase, PRR14 is incorporated rapidly into chromatin through HP1 binding. Finally, in telophase, PRR14 relocalizes to the reforming nuclear lamina. This stepwise reassembly of PRR14 suggests a function in the selection of HP1-bound heterochromatin for reattachment to the nuclear lamina as cells exit mitosis.
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47
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Schmidt T, Skerra A. The Strep-tag system for one-step affinity purification of proteins from mammalian cell culture. Methods Mol Biol 2015; 1286:83-95. [PMID: 25749948 DOI: 10.1007/978-1-4939-2447-9_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Strep-tag-or its improved version Strep-tagII-is an eight amino acid sequence that can be easily fused or conjugated to any protein or peptide of interest and that was engineered for high affinity toward streptavidin, which otherwise is widely known as a tight biotin-binding reagent. Especially in combination with immobilized Strep-Tactin, a mutant streptavidin specifically optimized toward the Strep-tagII, this system enables the facile one-step affinity purification of various biomolecules, including oligomeric and even membrane proteins. The Strep-tagII/Strep-Tactin interaction shows exquisite specificity, thus allowing efficient separation from host cell proteins, and it can be reversed simply by addition of biotin (or a suitable derivative thereof, such as desthiobiotin). Therefore, this system has become very popular for the highly efficient affinity chromatography under biochemically mild conditions. Here, we describe the purification of Strep-tagged proteins from mammalian cell lysates and cell culture supernatants.
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Affiliation(s)
- Thomas Schmidt
- IBA GmbH, Rudolf-Wissell-Str. 28, 37079, Göttingen, Germany,
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48
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Ribeiro AJ, Khanna P, Sukumar A, Dong C, Dahl KN. Nuclear stiffening inhibits migration of invasive melanoma cells. Cell Mol Bioeng 2014; 7:544-551. [PMID: 25544862 PMCID: PMC4276563 DOI: 10.1007/s12195-014-0358-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
During metastasis, melanoma cells must be sufficiently deformable to squeeze through extracellular barriers with small pore sizes. We visualize and quantify deformability of single cells using micropipette aspiration and examine the migration potential of a population of melanoma cells using a flow migration apparatus. We artificially stiffen the nucleus with recombinant overexpression of Δ50 lamin A, which is found in patients with Hutchison Gilford progeria syndrome and in aged individuals. Melanoma cells, both WM35 and Lu1205, both show reduced nuclear deformability and reduced cell invasion with the expression of Δ50 lamin A. These studies suggest that cellular aging including expression of Δ50 lamin A and nuclear stiffening may reduce the potential for metastatic cancer migration. Thus, the pathway of cancer metastasis may be kept in check by mechanical factors in addition to known chemical pathway regulation.
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Affiliation(s)
| | - Payal Khanna
- Department of Bioengineering, The Pennsylvania State University, University Park, PA 16802
| | - Aishwarya Sukumar
- Department of Biomedical Engineering, Carnegie Melon University, Pittsburgh, PA 15213
| | - Cheng Dong
- Department of Bioengineering, The Pennsylvania State University, University Park, PA 16802
| | - Kris Noel Dahl
- Department of Biomedical Engineering, Carnegie Melon University, Pittsburgh, PA 15213
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49
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Reichert C, Gölz L, Götz W, Wolf M, Deschner J, Jäger A. Dental and craniofacial characteristics in a patient with Hutchinson-Gilford progeria syndrome. J Orofac Orthop 2014; 75:251-63. [PMID: 25001855 DOI: 10.1007/s00056-014-0216-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 01/31/2013] [Indexed: 11/28/2022]
Abstract
The Hutchinson-Gilford progeria syndrome (HGPS) is an exceptionally rare medical disorder caused by mutations in the lamin A/C gene. Affected patients display typical features of premature aging. Beside general medical disorders, these patients have several specific features related to the craniofacial phenotype and the oral cavity. In this article, the dental and craniofacial characteristics of a 9-year-old girl with HGPS are presented. It is the first report addressing orthodontic tooth movement and microbiological features in a HGPS patient. We describe and discuss pathologic findings and provide a detailed histology of the teeth which had to be extracted during initial treatment.
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Affiliation(s)
- Christoph Reichert
- Department of Orthodontics, Dental Hospital, University of Bonn, Welschnonnenstr. 17, 53111, Bonn, Germany,
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50
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Dittmer TA, Sahni N, Kubben N, Hill DE, Vidal M, Burgess RC, Roukos V, Misteli T. Systematic identification of pathological lamin A interactors. Mol Biol Cell 2014; 25:1493-510. [PMID: 24623722 PMCID: PMC4004598 DOI: 10.1091/mbc.e14-02-0733] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Laminopathies are a collection of phenotypically diverse diseases that include muscular dystrophies, cardiomyopathies, lipodystrophies, and premature aging syndromes. Laminopathies are caused by >300 distinct mutations in the LMNA gene, which encodes the nuclear intermediate filament proteins lamin A and C, two major architectural elements of the mammalian cell nucleus. The genotype-phenotype relationship and the basis for the pronounced tissue specificity of laminopathies are poorly understood. Here we seek to identify on a global scale lamin A-binding partners whose interaction is affected by disease-relevant LMNA mutations. In a screen of a human genome-wide ORFeome library, we identified and validated 337 lamin A-binding proteins. Testing them against 89 known lamin A disease mutations identified 50 disease-associated interactors. Association of progerin, the lamin A isoform responsible for the premature aging disorder Hutchinson-Gilford progeria syndrome, with its partners was largely mediated by farnesylation. Mapping of the interaction sites on lamin A identified the immunoglobulin G (IgG)-like domain as an interaction hotspot and demonstrated that lamin A variants, which destabilize the Ig-like domain, affect protein-protein interactions more globally than mutations of surface residues. Analysis of a set of LMNA mutations in a single residue, which result in three phenotypically distinct diseases, identified disease-specific interactors. The results represent a systematic map of disease-relevant lamin A interactors and suggest loss of tissue-specific lamin A interactions as a mechanism for the tissue-specific appearance of laminopathic phenotypes.
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Affiliation(s)
- Travis A Dittmer
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 Department of Genetics, Harvard Medical School, Boston, MA 02215
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