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Wang J, Chao B, Piesner J, Kelly F, Petrie SK, Xiao X, Li BX. CG-SLENP: A Chemical Genetics Strategy To Selectively Label Existing Proteins and Newly Synthesized Proteins. JACS AU 2024; 4:3146-3156. [PMID: 39211582 PMCID: PMC11350722 DOI: 10.1021/jacsau.4c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 09/04/2024]
Abstract
Protein synthesis and subsequent delivery to the target locations in cells are essential for their proper functions. Methods to label and distinguish newly synthesized proteins from existing ones are critical to assess their differential properties, but such methods are lacking. We describe the first chemical genetics-based approach for selective labeling of existing and newly synthesized proteins that we termed as CG-SLENP. Using HaloTag in-frame fusion with lamin A (LA), we demonstrate that the two pools of proteins can be selectively labeled using CG-SLENP in living cells. We further employ our recently developed selective small molecule ligand LBL1 for LA to probe the potential differences between newly synthesized and existing LA. Our results show that LBL1 can differentially modulate these two pools of LA. These results indicate that the assembly states of newly synthesized LA are distinct from existing LA in living cells. The CG-SLENP method is potentially generalizable to study any cellular proteins.
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Affiliation(s)
- Jian Wang
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Bo Chao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Jake Piesner
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Felice Kelly
- Advanced
Light Microscopy Shared Resource, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Stefanie Kaech Petrie
- Department
of Neurology, Knight Cancer Institute, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Xiangshu Xiao
- Department
of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Bingbing X. Li
- Department
of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, United States
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2
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Mostafazadeh N, Peng Z. Microstructure-based nuclear lamina constitutive model. Cytoskeleton (Hoboken) 2024; 81:297-309. [PMID: 38345187 DOI: 10.1002/cm.21835] [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: 09/29/2023] [Revised: 12/15/2023] [Accepted: 01/24/2024] [Indexed: 08/20/2024]
Abstract
The nuclear lamina is widely recognized as the most crucial component in providing mechanical stability to the nucleus. However, it is still a significant challenge to model the mechanics of this multilayered protein network. We developed a constitutive model of the nuclear lamina network based on its microstructure, which accounts for the deformation phases at the dimer level, as well as the orientational arrangement and density of lamin filaments. Instead of relying on homology modeling in the previous studies, we conducted molecular simulations to predict the force-extension response of a highly accurate lamin dimer structure obtained through X-ray diffraction crystallography experimentation. Furthermore, we devised a semiflexible worm-like chain extension-force model of lamin dimer as a substitute, incorporating phases of initial stretching, uncoiling of the dimer coiled-coil, and transition of secondary structures. Subsequently, we developed a 2D network continuum model for the nuclear lamina by using our extension-force lamin dimer model and derived stress resultants. By comparing with experimentally measured lamina modulus, we found that the lamina network has sharp initial strain-hardening behavior. This also enabled us to carry out finite element simulations of the entire nucleus with an accurate microstructure-based nuclear lamina model. Finally, we conducted simulations of transendothelial transmigration of a nucleus and investigated the impact of varying network density and uncoiling constants on the critical force required for successful transmigration. The model allows us to incorporate the microstructure characteristics of the nuclear lamina into the nucleus model, thereby gaining insights into how laminopathies and mutations affect nuclear mechanics.
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Affiliation(s)
- Nima Mostafazadeh
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
| | - Zhangli Peng
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, Illinois, USA
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3
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Krüger P, Hartinger R, Djabali K. Navigating Lipodystrophy: Insights from Laminopathies and Beyond. Int J Mol Sci 2024; 25:8020. [PMID: 39125589 PMCID: PMC11311807 DOI: 10.3390/ijms25158020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 08/12/2024] Open
Abstract
Recent research into laminopathic lipodystrophies-rare genetic disorders caused by mutations in the LMNA gene-has greatly expanded our knowledge of their complex pathology and metabolic implications. These disorders, including Hutchinson-Gilford progeria syndrome (HGPS), Mandibuloacral Dysplasia (MAD), and Familial Partial Lipodystrophy (FPLD), serve as crucial models for studying accelerated aging and metabolic dysfunction, enhancing our understanding of the cellular and molecular mechanisms involved. Research on laminopathies has highlighted how LMNA mutations disrupt adipose tissue function and metabolic regulation, leading to altered fat distribution and metabolic pathway dysfunctions. Such insights improve our understanding of the pathophysiological interactions between genetic anomalies and metabolic processes. This review merges current knowledge on the phenotypic classifications of these diseases and their associated metabolic complications, such as insulin resistance, hypertriglyceridemia, hepatic steatosis, and metabolic syndrome, all of which elevate the risk of cardiovascular disease, stroke, and diabetes. Additionally, a range of published therapeutic strategies, including gene editing, antisense oligonucleotides, and novel pharmacological interventions aimed at addressing defective adipocyte differentiation and lipid metabolism, will be explored. These therapies target the core dysfunctional lamin A protein, aiming to mitigate symptoms and provide a foundation for addressing similar metabolic and genetic disorders.
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Affiliation(s)
| | | | - Karima Djabali
- Epigenetics of Aging, Department of Dermatology and Allergy, TUM School of Medicine, Munich Institute of Biomedical Engineering (MIBE), Technical University of Munich (TUM), 85748 Garching, Germany; (P.K.); (R.H.)
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4
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Kim PH, Kim JR, Tu Y, Jung H, Jeong JYB, Tran AP, Presnell A, Young SG, Fong LG. Progerin forms an abnormal meshwork and has a dominant-negative effect on the nuclear lamina. Proc Natl Acad Sci U S A 2024; 121:e2406946121. [PMID: 38917015 PMCID: PMC11228511 DOI: 10.1073/pnas.2406946121] [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: 04/15/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Progerin, the protein that causes Hutchinson-Gilford progeria syndrome, triggers nuclear membrane (NM) ruptures and blebs, but the mechanisms are unclear. We suspected that the expression of progerin changes the overall structure of the nuclear lamina. High-resolution microscopy of smooth muscle cells (SMCs) revealed that lamin A and lamin B1 form independent meshworks with uniformly spaced openings (~0.085 µm2). The expression of progerin in SMCs resulted in the formation of an irregular meshwork with clusters of large openings (up to 1.4 µm2). The expression of progerin acted in a dominant-negative fashion to disrupt the morphology of the endogenous lamin B1 meshwork, triggering irregularities and large openings that closely resembled the irregularities and openings in the progerin meshwork. These abnormal meshworks were strongly associated with NM ruptures and blebs. Of note, the progerin meshwork was markedly abnormal in nuclear blebs that were deficient in lamin B1 (~50% of all blebs). That observation suggested that higher levels of lamin B1 expression might normalize the progerin meshwork and prevent NM ruptures and blebs. Indeed, increased lamin B1 expression reversed the morphological abnormalities in the progerin meshwork and markedly reduced the frequency of NM ruptures and blebs. Thus, progerin expression disrupts the overall structure of the nuclear lamina, but that effect-along with NM ruptures and blebs-can be abrogated by increased lamin B1 expression.
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Affiliation(s)
- Paul H Kim
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Department of Bioengineering, University of California, Los Angeles, CA 90095
| | - Joonyoung R Kim
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Yiping Tu
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Hyesoo Jung
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - J Y Brian Jeong
- Advanced Light Microscopy and Spectroscopy Laboratory, California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - Anh P Tran
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Ashley Presnell
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Stephen G Young
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Loren G Fong
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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5
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Jeong S, Ha NC. Deciphering vimentin assembly: Bridging theoretical models and experimental approaches. Mol Cells 2024; 47:100080. [PMID: 38871297 PMCID: PMC11267000 DOI: 10.1016/j.mocell.2024.100080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/20/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024] Open
Abstract
The intricate assembly process of vimentin intermediate filaments (IFs), key components of the eukaryotic cytoskeleton, has yet to be elucidated. In this work, we investigated the transition from soluble tetrameric vimentin units to mature 11-nm tubular filaments, addressing a significant gap in the understanding of IF assembly. Through a combination of theoretical modeling and analysis of experimental data, we propose a novel assembly sequence, emphasizing the role of helical turns and gap filling by soluble tetramers. Our findings shed light on the unique structural dynamics of vimentin and suggest broader implications for the general principles of IF formation.
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Affiliation(s)
- Soyeon Jeong
- Department of Agricultural Biotechnology, Center for Food and Bioconversions, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconversions, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea.
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6
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Mohar NP, Cox EM, Adelizzi E, Moore SA, Mathews KD, Darbro BW, Wallrath LL. The Influence of a Genetic Variant in CCDC78 on LMNA-Associated Skeletal Muscle Disease. Int J Mol Sci 2024; 25:4930. [PMID: 38732148 PMCID: PMC11084688 DOI: 10.3390/ijms25094930] [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: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Mutations in the LMNA gene-encoding A-type lamins can cause Limb-Girdle muscular dystrophy Type 1B (LGMD1B). This disease presents with weakness and wasting of the proximal skeletal muscles and has a variable age of onset and disease severity. This variability has been attributed to genetic background differences among individuals; however, such variants have not been well characterized. To identify such variants, we investigated a multigeneration family in which affected individuals are diagnosed with LGMD1B. The primary genetic cause of LGMD1B in this family is a dominant mutation that activates a cryptic splice site, leading to a five-nucleotide deletion in the mature mRNA. This results in a frame shift and a premature stop in translation. Skeletal muscle biopsies from the family members showed dystrophic features of variable severity, with the muscle fibers of some family members possessing cores, regions of sarcomeric disruption, and a paucity of mitochondria, not commonly associated with LGMD1B. Using whole genome sequencing (WGS), we identified 21 DNA sequence variants that segregate with the family members possessing more profound dystrophic features and muscle cores. These include a relatively common variant in coiled-coil domain containing protein 78 (CCDC78). This variant was given priority because another mutation in CCDC78 causes autosomal dominant centronuclear myopathy-4, which causes cores in addition to centrally positioned nuclei. Therefore, we analyzed muscle biopsies from family members and discovered that those with both the LMNA mutation and the CCDC78 variant contain muscle cores that accumulated both CCDC78 and RyR1. Muscle cores containing mislocalized CCDC78 and RyR1 were absent in the less profoundly affected family members possessing only the LMNA mutation. Taken together, our findings suggest that a relatively common variant in CCDC78 can impart profound muscle pathology in combination with a LMNA mutation and accounts for variability in skeletal muscle disease phenotypes.
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Affiliation(s)
- Nathaniel P. Mohar
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Efrem M. Cox
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA (S.A.M.)
- Department of Neurosurgery, UNLV School of Medicine, Las Vegas, NV 89106, USA
| | - Emily Adelizzi
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Steven A. Moore
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA (S.A.M.)
| | - Katherine D. Mathews
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Benjamin W. Darbro
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Lori L. Wallrath
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (N.P.M.); (E.A.)
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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7
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Sobo JM, Alagna NS, Sun SX, Wilson KL, Reddy KL. Lamins: The backbone of the nucleocytoskeleton interface. Curr Opin Cell Biol 2024; 86:102313. [PMID: 38262116 DOI: 10.1016/j.ceb.2023.102313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024]
Abstract
The nuclear lamina (NL) is a crucial component of the inner nuclear membrane (INM) and consists of lamin filaments and associated proteins. Lamins are type V intermediate filament proteins essential for maintaining the integrity and mechanical properties of the nucleus. In human cells, 'B-type' lamins (lamin B1 and lamin B2) are ubiquitously expressed, while 'A-type' lamins (lamin A, lamin C, and minor isoforms) are expressed in a tissue- and development-specific manner. Lamins homopolymerize to form filaments that localize primarily near the INM, but A-type lamins also localize to and function in the nucleoplasm. Lamins play central roles in the assembly, structure, positioning, and mechanics of the nucleus, modulating cell signaling and influencing development, differentiation, and other activities. This review highlights recent findings on the structure and regulation of lamin filaments, providing insights into their multifaceted functions, including their role as "mechanosensors", delving into the emerging significance of lamin filaments as vital links between cytoskeletal and nuclear structures, chromatin organization, and the genome.
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Affiliation(s)
- Joan M Sobo
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Nicholas S Alagna
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sean X Sun
- Department of Mechanical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherine L Wilson
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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8
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Hadpech S, Peerapen P, Thongboonkerd V. The upregulation of lamin A/C as a compensatory mechanism during tight junction disruption in renal tubular cells mediated by calcium oxalate crystals. Curr Res Toxicol 2023; 6:100145. [PMID: 38193033 PMCID: PMC10772403 DOI: 10.1016/j.crtox.2023.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 11/12/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Calcium oxalate monohydrate (COM), the most important crystal causing kidney stone disease, upregulates lamin A/C but downregulates zonula occludens-1 (ZO-1) in renal tubular cells. While roles for F-actin and α-tubulin and their association with ZO-1 are known to regulate COM-mediated tight junction (TJ) disruption, roles of lamin A/C and its interplay with ZO-1 in COM kidney stone model remain unclear and are thus the objectives of this study. Lamin A/C was knocked down in MDCK cells by silencing RNA specific for LMNA (siLMNA). Both wild-type (WT) and siLMNA cells were treated with COM for 48-h compared with the untreated (control) cells. Western blotting and immunofluorescence staining revealed upregulated lamin A/C and downregulated ZO-1 in the COM-treated WT cells. siLMNA successfully reduced lamin A/C expression in both control and COM-treated cells. Nonetheless, siLMNA did not reverse the effect of COM on the decreases in ZO-1 and transepithelial resistance, but further reduced their levels in both control and COM-treated cells. Protein-protein interaction analysis demonstrated that two cytoskeletal proteins (actin and tubulin) served as the linkers to connect lamin A/C with ZO-1 and occludin (both of which are the TJ proteins). Altogether, these data implicate that lamin A/C and ZO-1 are indirectly associated to control TJ function, and ZO-1 expression is regulated by lamin A/C. Moreover, COM-induced upregulation of lamin A/C most likely serves as a compensatory mechanism to cope with the downregulation of ZO-1 during COM-mediated TJ disruption.
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Affiliation(s)
- Sudarat Hadpech
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Paleerath Peerapen
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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9
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Wallace M, Fedorchak GR, Agrawal R, Gilbert RM, Patel J, Park S, Paszek M, Lammerding J. The lamin A/C Ig-fold undergoes cell density-dependent changes that alter epitope binding. Nucleus 2023; 14:2180206. [PMID: 36809122 PMCID: PMC9980629 DOI: 10.1080/19491034.2023.2180206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Lamins A/C are nuclear intermediate filament proteins that are involved in diverse cellular mechanical and biochemical functions. Here, we report that recognition of Lamins A/C by a commonly used antibody (JOL-2) that binds the Lamin A/C Ig-fold and other antibodies targeting similar epitopes is highly dependent on cell density, even though Lamin A/Clevels do not change. We propose that the effect is caused by partial unfolding or masking of the C'E and/or EF loops of the Ig-fold in response to cell spreading. Surprisingly, JOL-2 antibody labeling was insensitive to disruption of cytoskeletal filaments or the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. Furthermore, neither nuclear stiffness nor nucleo-cytoskeletal force transmission changed with cell density. These findings are important for the interpretation of immunofluorescence data for Lamin A/C and also raise the intriguing prospect that the conformational changes may play a role in Lamin A/C mediated cellular function.
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Affiliation(s)
- Melanie Wallace
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Gregory R. Fedorchak
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Richa Agrawal
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Rachel M. Gilbert
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Jineet Patel
- Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Sangwoo Park
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, USA
| | - Matthew Paszek
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, USA,Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Jan Lammerding
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA,CONTACT Jan Lammerding Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY14853, USA
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10
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Worman HJ, Michaelis S. Prelamin A and ZMPSTE24 in premature and physiological aging. Nucleus 2023; 14:2270345. [PMID: 37885131 PMCID: PMC10730219 DOI: 10.1080/19491034.2023.2270345] [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: 08/29/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
As human longevity increases, understanding the molecular mechanisms that drive aging becomes ever more critical to promote health and prevent age-related disorders. Premature aging disorders or progeroid syndromes can provide critical insights into aspects of physiological aging. A major cause of progeroid syndromes which result from mutations in the genes LMNA and ZMPSTE24 is disruption of the final posttranslational processing step in the production of the nuclear scaffold protein lamin A. LMNA encodes the lamin A precursor, prelamin A and ZMPSTE24 encodes the prelamin A processing enzyme, the zinc metalloprotease ZMPSTE24. Progeroid syndromes resulting from mutations in these genes include the clinically related disorders Hutchinson-Gilford progeria syndrome (HGPS), mandibuloacral dysplasia-type B, and restrictive dermopathy. These diseases have features that overlap with one another and with some aspects of physiological aging, including bone defects resembling osteoporosis and atherosclerosis (the latter primarily in HGPS). The progeroid syndromes have ignited keen interest in the relationship between defective prelamin A processing and its accumulation in normal physiological aging. In this review, we examine the hypothesis that diminished processing of prelamin A by ZMPSTE24 is a driver of physiological aging. We review features a new mouse (LmnaL648R/L648R) that produces solely unprocessed prelamin A and provides an ideal model for examining the effects of its accumulation during aging. We also discuss existing data on the accumulation of prelamin A or its variants in human physiological aging, which call out for further validation and more rigorous experimental approaches to determine if prelamin A contributes to normal aging.
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Affiliation(s)
- Howard J. Worman
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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11
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Buxboim A, Kronenberg-Tenga R, Salajkova S, Avidan N, Shahak H, Thurston A, Medalia O. Scaffold, mechanics and functions of nuclear lamins. FEBS Lett 2023; 597:2791-2805. [PMID: 37813648 DOI: 10.1002/1873-3468.14750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Nuclear lamins are type-V intermediate filaments that are involved in many nuclear processes. In mammals, A- and B-type lamins assemble into separate physical meshwork underneath the inner nuclear membrane, the nuclear lamina, with some residual fraction localized within the nucleoplasm. Lamins are the major part of the nucleoskeleton, providing mechanical strength and flexibility to protect the genome and allow nuclear deformability, while also contributing to gene regulation via interactions with chromatin. While lamins are the evolutionary ancestors of all intermediate filament family proteins, their ultimate filamentous assembly is markedly different from their cytoplasmic counterparts. Interestingly, hundreds of genetic mutations in the lamina proteins have been causally linked with a broad range of human pathologies, termed laminopathies. These include muscular, neurological and metabolic disorders, as well as premature aging diseases. Recent technological advances have contributed to resolving the filamentous structure of lamins and the corresponding lamina organization. In this review, we revisit the multiscale lamin organization and discuss its implications on nuclear mechanics and chromatin organization within lamina-associated domains.
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Affiliation(s)
- Amnon Buxboim
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Sarka Salajkova
- Department of Biochemistry, University of Zurich, Switzerland
| | - Nili Avidan
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Hen Shahak
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Alice Thurston
- Department of Biochemistry, University of Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Switzerland
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12
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Ahn J, Jo I, Jeong S, Lee J, Ha NC. Lamin Filament Assembly Derived from the Atomic Structure of the Antiparallel Four-Helix Bundle. Mol Cells 2023; 46:309-318. [PMID: 37170772 PMCID: PMC10183791 DOI: 10.14348/molcells.2023.2144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 05/13/2023] Open
Abstract
The nucleoskeletal protein lamin is primarily responsible for the mechanical stability of the nucleus. The lamin assembly process requires the A11, A22, and ACN binding modes of the coiled-coil dimers. Although X-ray crystallography and chemical cross-linking analysis of lamin A/C have provided snapshots of A11 and ACN binding modes, the assembly mechanism of the entire filament remains to be explained. Here, we report a crystal structure of a coil 2 fragment, revealing the A22 interaction at the atomic resolution. The structure showed detailed structural features, indicating that two coiled-coil dimers of the coil 2 subdomain are separated and then re-organized into the antiparallel-four-helix bundle. Furthermore, our findings suggest that the ACN binding mode between coil 1a and the C-terminal part of coil 2 when the A11 tetramers are arranged by the A22 interactions. We propose a full assembly model of lamin A/C with the curvature around the linkers, reconciling the discrepancy between the in situ and in vitro observations. Our model accounts for the balanced elasticity and stiffness of the nuclear envelopes, which is essential in protecting the cellular nucleus from external pressure.
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Affiliation(s)
- Jinsook Ahn
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
- Present address: Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
- Present address: Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Soyeon Jeong
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
| | - Jinwook Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
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13
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Walker SG, Langland CJ, Viles J, Hecker LA, Wallrath LL. Drosophila Models Reveal Properties of Mutant Lamins That Give Rise to Distinct Diseases. Cells 2023; 12:cells12081142. [PMID: 37190051 DOI: 10.3390/cells12081142] [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: 01/26/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Mutations in the LMNA gene cause a collection of diseases known as laminopathies, including muscular dystrophies, lipodystrophies, and early-onset aging syndromes. The LMNA gene encodes A-type lamins, lamins A/C, intermediate filaments that form a meshwork underlying the inner nuclear membrane. Lamins have a conserved domain structure consisting of a head, coiled-coil rod, and C-terminal tail domain possessing an Ig-like fold. This study identified differences between two mutant lamins that cause distinct clinical diseases. One of the LMNA mutations encodes lamin A/C p.R527P and the other codes lamin A/C p.R482W, which are typically associated with muscular dystrophy and lipodystrophy, respectively. To determine how these mutations differentially affect muscle, we generated the equivalent mutations in the Drosophila Lamin C (LamC) gene, an orthologue of human LMNA. The muscle-specific expression of the R527P equivalent showed cytoplasmic aggregation of LamC, a reduced larval muscle size, decreased larval motility, and cardiac defects resulting in a reduced adult lifespan. By contrast, the muscle-specific expression of the R482W equivalent caused an abnormal nuclear shape without a change in larval muscle size, larval motility, and adult lifespan compared to controls. Collectively, these studies identified fundamental differences in the properties of mutant lamins that cause clinically distinct phenotypes, providing insights into disease mechanisms.
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Affiliation(s)
- Sydney G Walker
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christopher J Langland
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jill Viles
- Independent Researcher, Gowrie, IA 50543, USA
| | - Laura A Hecker
- Department of Biology, Clarke University, Dubuque, IA 52001, USA
| | - Lori L Wallrath
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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14
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Jain N, Lord JM, Vogel V. Mechanoimmunology: Are inflammatory epigenetic states of macrophages tuned by biophysical factors? APL Bioeng 2022; 6:031502. [PMID: 36051106 PMCID: PMC9427154 DOI: 10.1063/5.0087699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
Many inflammatory diseases that are responsible for a majority of deaths are still uncurable, in part as the underpinning pathomechanisms and how to combat them is still poorly understood. Tissue-resident macrophages play pivotal roles in the maintenance of tissue homeostasis, but if they gradually convert to proinflammatory phenotypes, or if blood-born proinflammatory macrophages persist long-term after activation, they contribute to chronic inflammation and fibrosis. While biochemical factors and how they regulate the inflammatory transcriptional response of macrophages have been at the forefront of research to identify targets for therapeutic interventions, evidence is increasing that physical factors also tune the macrophage phenotype. Recently, several mechanisms have emerged as to how physical factors impact the mechanobiology of macrophages, from the nuclear translocation of transcription factors to epigenetic modifications, perhaps even DNA methylation. Insight into the mechanobiology of macrophages and associated epigenetic modifications will deliver novel therapeutic options going forward, particularly in the context of increased inflammation with advancing age and age-related diseases. We review here how biophysical factors can co-regulate pro-inflammatory gene expression and epigenetic modifications and identify knowledge gaps that require urgent attention if this therapeutic potential is to be realized.
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Affiliation(s)
- Nikhil Jain
- Authors to whom correspondence should be addressed: and
| | | | - Viola Vogel
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zurich, Zurich, Switzerland
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15
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Shaw NM, Rios-Monterrosa JL, Fedorchak GR, Ketterer MR, Coombs GS, Lammerding J, Wallrath LL. Effects of mutant lamins on nucleo-cytoskeletal coupling in Drosophila models of LMNA muscular dystrophy. Front Cell Dev Biol 2022; 10:934586. [PMID: 36120560 PMCID: PMC9471154 DOI: 10.3389/fcell.2022.934586] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
The nuclei of multinucleated skeletal muscles experience substantial external force during development and muscle contraction. Protection from such forces is partly provided by lamins, intermediate filaments that form a scaffold lining the inner nuclear membrane. Lamins play a myriad of roles, including maintenance of nuclear shape and stability, mediation of nuclear mechanoresponses, and nucleo-cytoskeletal coupling. Herein, we investigate how disease-causing mutant lamins alter myonuclear properties in response to mechanical force. This was accomplished via a novel application of a micropipette harpooning assay applied to larval body wall muscles of Drosophila models of lamin-associated muscular dystrophy. The assay enables the measurement of both nuclear deformability and intracellular force transmission between the cytoskeleton and nuclear interior in intact muscle fibers. Our studies revealed that specific mutant lamins increase nuclear deformability while other mutant lamins cause nucleo-cytoskeletal coupling defects, which were associated with loss of microtubular nuclear caging. We found that microtubule caging of the nucleus depended on Msp300, a KASH domain protein that is a component of the linker of nucleoskeleton and cytoskeleton (LINC) complex. Taken together, these findings identified residues in lamins required for connecting the nucleus to the cytoskeleton and suggest that not all muscle disease-causing mutant lamins produce similar defects in subcellular mechanics.
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Affiliation(s)
- Nicholas M. Shaw
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Jose L. Rios-Monterrosa
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Gregory R. Fedorchak
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Margaret R. Ketterer
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Gary S. Coombs
- Biology Department, Waldorf University, Forest City, IA, United States
| | - Jan Lammerding
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Lori L. Wallrath
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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16
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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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17
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Ahn J, Jeong S, Kang SM, Jo I, Park BJ, Ha NC. Crystal structure of progeria mutant S143F lamin A/C reveals increased hydrophobicity driving nuclear deformation. Commun Biol 2022; 5:267. [PMID: 35338226 PMCID: PMC8956589 DOI: 10.1038/s42003-022-03212-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/25/2022] [Indexed: 12/29/2022] Open
Abstract
Lamins are intermediate filaments that form a 3-D meshwork in the periphery of the nuclear envelope. The recent crystal structure of a long fragment of human lamin A/C visualized the tetrameric assembly unit of the central rod domain as a polymerization intermediate. A genetic mutation of S143F caused a phenotype characterized by both progeria and muscular dystrophy. In this study, we determined the crystal structure of the lamin A/C fragment harboring the S143F mutation. The obtained structure revealed the X-shaped interaction between the tetrameric units in the crystals, potentiated by the hydrophobic interactions of the mutated Phe143 residues. Subsequent studies indicated that the X-shaped interaction between the filaments plays a crucial role in disrupting the normal lamin meshwork. Our findings suggest the assembly mechanism of the 3-D meshwork and further provide a molecular framework for understanding the aging process by nuclear deformation.
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Affiliation(s)
- Jinsook Ahn
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soyeon Jeong
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - So-Mi Kang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea.
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18
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de Leeuw R, Kronenberg-Tenga R, Eibauer M, Medalia O. Filament assembly of the C. elegans lamin in the absence of helix 1A. Nucleus 2022; 13:49-57. [PMID: 35130129 PMCID: PMC8824219 DOI: 10.1080/19491034.2022.2032917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Lamins are the major constituent of the nuclear lamina, a protein meshwork underlying the inner nuclear membrane. Nuclear lamins are type V intermediate filaments that assemble into ~3.5 nm thick filaments. To date, only the conditions for the in vitro assembly of Caenorhabditis elegans lamin (Ce-lamin) are known. Here, we investigated the assembly of Ce-lamin filaments by cryo-electron microscopy and tomography. We show that Ce-lamin is composed of ~3.5 nm protofilaments that further interact in vitro and are often seen as 6–8 nm thick filaments. We show that the assembly of lamin filaments is undisturbed by the removal of flexible domains, that is, the intrinsically unstructured head and tail domains. In contrast, much of the coiled-coil domains are scaffold elements that are essential for filament assembly. Moreover, our results suggest that Ce-lamin helix 1A has a minor scaffolding role but is important to the lateral assembly regulation of lamin protofilaments.
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Affiliation(s)
- Rebecca de Leeuw
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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19
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Coombs GS, Rios-Monterrosa JL, Lai S, Dai Q, Goll AC, Ketterer MR, Valdes MF, Uche N, Benjamin IJ, Wallrath LL. Modulation of muscle redox and protein aggregation rescues lethality caused by mutant lamins. Redox Biol 2021; 48:102196. [PMID: 34872044 PMCID: PMC8646998 DOI: 10.1016/j.redox.2021.102196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/19/2021] [Indexed: 12/28/2022] Open
Abstract
Mutations in the human LMNA gene cause a collection of diseases called laminopathies, which includes muscular dystrophy and dilated cardiomyopathy. The LMNA gene encodes lamins, filamentous proteins that form a meshwork on the inner side of the nuclear envelope. How mutant lamins cause muscle disease is not well understood, and treatment options are currently limited. To understand the pathological functions of mutant lamins so that therapies can be developed, we generated new Drosophila models and human iPS cell-derived cardiomyocytes. In the Drosophila models, muscle-specific expression of the mutant lamins caused nuclear envelope defects, cytoplasmic protein aggregation, activation of the Nrf2/Keap1 redox pathway, and reductive stress. These defects reduced larval motility and caused death at the pupal stage. Patient-derived cardiomyocytes expressing mutant lamins showed nuclear envelope deformations. The Drosophila models allowed for genetic and pharmacological manipulations at the organismal level. Genetic interventions to increase autophagy, decrease Nrf2/Keap1 signaling, or lower reducing equivalents partially suppressed the lethality caused by mutant lamins. Moreover, treatment of flies with pamoic acid, a compound that inhibits the NADPH-producing malic enzyme, partially suppressed lethality. Taken together, these studies have identified multiple new factors as potential therapeutic targets for LMNA-associated muscular dystrophy.
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Affiliation(s)
- Gary S Coombs
- Biology Department, Waldorf University, Forest City, IA, USA
| | | | - Shuping Lai
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Qiang Dai
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ashley C Goll
- Department of Biochemistry & Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Margaret R Ketterer
- Department of Biochemistry & Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Maria F Valdes
- Biology Department, Waldorf University, Forest City, IA, USA
| | - Nnamdi Uche
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WO, USA
| | - Ivor J Benjamin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lori L Wallrath
- Department of Biochemistry & Molecular Biology, University of Iowa, Iowa City, IA, USA.
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20
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Hinz BE, Walker SG, Xiong A, Gogal RA, Schnieders MJ, Wallrath LL. In Silico and In Vivo Analysis of Amino Acid Substitutions That Cause Laminopathies. Int J Mol Sci 2021; 22:ijms222011226. [PMID: 34681887 PMCID: PMC8536974 DOI: 10.3390/ijms222011226] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023] Open
Abstract
Mutations in the LMNA gene cause diseases called laminopathies. LMNA encodes lamins A and C, intermediate filaments with multiple roles at the nuclear envelope. LMNA mutations are frequently single base changes that cause diverse disease phenotypes affecting muscles, nerves, and fat. Disease-associated amino acid substitutions were mapped in silico onto three-dimensional structures of lamin A/C, revealing no apparent genotype–phenotype connections. In silico analyses revealed that seven of nine predicted partner protein binding pockets in the Ig-like fold domain correspond to sites of disease-associated amino acid substitutions. Different amino acid substitutions at the same position within lamin A/C cause distinct diseases, raising the question of whether the nature of the amino acid replacement or genetic background differences contribute to disease phenotypes. Substitutions at R249 in the rod domain cause muscular dystrophies with varying severity. To address this variability, we modeled R249Q and R249W in Drosophila Lamin C, an orthologue of LMNA. Larval body wall muscles expressing mutant Lamin C caused abnormal nuclear morphology and premature death. When expressed in indirect flight muscles, R249W caused a greater number of adults with wing posturing defects than R249Q, consistent with observations that R249W and R249Q cause distinct muscular dystrophies, with R249W more severe. In this case, the nature of the amino acid replacement appears to dictate muscle disease severity. Together, our findings illustrate the utility of Drosophila for predicting muscle disease severity and pathogenicity of variants of unknown significance.
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Affiliation(s)
- Benjamin E. Hinz
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
| | - Sydney G. Walker
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
| | - Austin Xiong
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
| | - Rose A. Gogal
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
| | - Michael J. Schnieders
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
| | - Lori L. Wallrath
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; (B.E.H.); (S.G.W.); (A.X.); (M.J.S.)
- Correspondence: ; Tel.: +1-319-335-7920
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21
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Stiekema M, Ramaekers FCS, Kapsokalyvas D, van Zandvoort MAMJ, Veltrop RJA, Broers JLV. Super-Resolution Imaging of the A- and B-Type Lamin Networks: A Comparative Study of Different Fluorescence Labeling Procedures. Int J Mol Sci 2021; 22:ijms221910194. [PMID: 34638534 PMCID: PMC8508656 DOI: 10.3390/ijms221910194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/31/2022] Open
Abstract
A- and B-type lamins are type V intermediate filament proteins. Mutations in the genes encoding these lamins cause rare diseases, collectively called laminopathies. A fraction of the cells obtained from laminopathy patients show aberrations in the localization of each lamin subtype, which may represent only the minority of the lamina disorganization. To get a better insight into more delicate and more abundant lamina abnormalities, the lamin network can be studied using super-resolution microscopy. We compared confocal scanning laser microscopy and stimulated emission depletion (STED) microscopy in combination with different fluorescence labeling approaches for the study of the lamin network. We demonstrate the suitability of an immunofluorescence staining approach when using STED microscopy, by determining the lamin layer thickness and the degree of lamin A and B1 colocalization as detected in fixed fibroblasts (co-)stained with lamin antibodies or (co-)transfected with EGFP/YFP lamin constructs. This revealed that immunofluorescence staining of cells does not lead to consequent changes in the detected lamin layer thickness, nor does it influence the degree of colocalization of lamin A and B1, when compared to the transfection approach. Studying laminopathy patient dermal fibroblasts (LMNA c.1130G>T (p.(Arg377Leu)) variant) confirmed the suitability of immunofluorescence protocols in STED microscopy, which circumvents the need for less convenient transfection steps. Furthermore, we found a significant decrease in lamin A/C and B1 colocalization in these patient fibroblasts, compared to normal human dermal fibroblasts. We conclude that super-resolution light microscopy combined with immunofluorescence protocols provides a potential tool to detect structural lamina differences between normal and laminopathy patient fibroblasts.
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Affiliation(s)
- Merel Stiekema
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Frans C. S. Ramaekers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Dimitrios Kapsokalyvas
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- Interdisciplinary Center for Clinical Research, IZKF, RWTH Aachen University, 52074 Aachen, Germany
| | - Marc A. M. J. van Zandvoort
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
- CARIM-School for Cardiovascular Diseases, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
- Institute for Molecular Cardiovascular Research IMCAR, RWTH Aachen University, 52074 Aachen, Germany
| | - Rogier J. A. Veltrop
- Institute for Molecular Cardiovascular Research IMCAR, RWTH Aachen University, 52074 Aachen, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, 6200 MD Maastricht, The Netherlands;
| | - Jos L. V. Broers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands; (M.S.); (F.C.S.R.); (D.K.); (M.A.M.J.v.Z.)
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
- CARIM-School for Cardiovascular Diseases, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
- Correspondence: ; Tel.: +31-433881366
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22
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Weber MS, Eibauer M, Sivagurunathan S, Magin TM, Goldman RD, Medalia O. Structural heterogeneity of cellular K5/K14 filaments as revealed by cryo-electron microscopy. eLife 2021; 10:70307. [PMID: 34323216 PMCID: PMC8360650 DOI: 10.7554/elife.70307] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Keratin intermediate filaments are an essential and major component of the cytoskeleton in epithelial cells. They form a stable yet dynamic filamentous network extending from the nucleus to the cell periphery, which provides resistance to mechanical stresses. Mutations in keratin genes are related to a variety of epithelial tissue diseases. Despite their importance, the molecular structure of keratin filaments remains largely unknown. In this study, we analyzed the structure of keratin 5/keratin 14 filaments within ghost mouse keratinocytes by cryo-electron microscopy and cryo-electron tomography. By averaging a large number of keratin segments, we have gained insights into the helical architecture of the filaments. Two-dimensional classification revealed profound variations in the diameter of keratin filaments and their subunit organization. Computational reconstitution of filaments of substantial length uncovered a high degree of internal heterogeneity along single filaments, which can contain regions of helical symmetry, regions with less symmetry and regions with significant diameter fluctuations. Cross-section views of filaments revealed that keratins form hollow cylinders consisting of multiple protofilaments, with an electron dense core located in the center of the filament. These findings shed light on the complex and remarkable heterogenic architecture of keratin filaments, suggesting that they are highly flexible, dynamic cytoskeletal structures.
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Affiliation(s)
- Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Thomas M Magin
- Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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23
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Ahn J, Lee J, Jeong S, Kang SM, Park BJ, Ha NC. Beta-strand-mediated dimeric formation of the Ig-like domains of human lamin A/C and B1. Biochem Biophys Res Commun 2021; 550:191-196. [PMID: 33706103 DOI: 10.1016/j.bbrc.2021.02.102] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 10/22/2022]
Abstract
Lamins are nuclear intermediate filament proteins that play an essential role in maintaining the nuclear structure by forming a 3-D meshwork. Lamins consist of the N-terminal unstructured head, the coiled-coil rod domain, and the C-terminal tail, which is mostly unstructured except for the Ig-like domain. To date, the Ig-like domain has been characterized as a monomeric structure. Here, we determined the crystal structures of human lamin A/C, including the Ig-like domain and its N- and C-terminal flanking sequences. Interestingly, the structures showed a homodimer formed by beta-strand interactions between the N- and C-terminal flanking sequences. This interaction also provides a molecular implication for the creation of a 3-D meshwork between the 3.5-nm-thick filaments. Furthermore, we determined the crystal structure of the corresponding region of lamin B1. The structure showed a similar dimeric assembly, also formed by beta-strand interactions, albeit the intersubunit distance was much shorter. Since the Ig-like domain contains many genetic hotspots causing lamin-related diseases in lamin A/C, our findings will help understand the detailed assembly of lamins in a 3-D meshwork structure and lamin-related diseases at the molecular level.
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Affiliation(s)
- Jinsook Ahn
- Department of Agricultural Biotechnology, Centre for Food Safety and Toxicology, Centre for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinwook Lee
- Department of Agricultural Biotechnology, Centre for Food Safety and Toxicology, Centre for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soyeon Jeong
- Department of Agricultural Biotechnology, Centre for Food Safety and Toxicology, Centre for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - So-Mi Kang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Centre for Food Safety and Toxicology, Centre for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea.
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Kronenberg-Tenga R, Tatli M, Eibauer M, Wu W, Shin JY, Bonne G, Worman HJ, Medalia O. A lamin A/C variant causing striated muscle disease provides insights into filament organization. J Cell Sci 2021; 134:jcs.256156. [PMID: 33536248 DOI: 10.1242/jcs.256156] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/26/2021] [Indexed: 12/31/2022] Open
Abstract
The LMNA gene encodes the A-type lamins, which polymerize into ∼3.5-nm-thick filaments and, together with B-type lamins and associated proteins, form the nuclear lamina. Mutations in LMNA cause a wide variety of pathologies. In this study, we analyzed the nuclear lamina of embryonic fibroblasts from Lmna H222P/H222P mice, which develop cardiomyopathy and muscular dystrophy. Although the organization of the lamina appeared unaltered, there were changes in chromatin and B-type lamin expression. An increase in nuclear size and consequently a relative reduction in heterochromatin near the lamina allowed for a higher resolution structural analysis of lamin filaments using cryo-electron tomography. This was most apparent when visualizing lamin filaments in situ and using a nuclear extraction protocol. Averaging of individual segments of filaments in Lmna H222P/H222P mouse fibroblasts resolved two polymers that constitute the mature filaments. Our findings provide better views of the organization of lamin filaments and the effect of a striated muscle disease-causing mutation on nuclear structure.
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Affiliation(s)
- Rafael Kronenberg-Tenga
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Meltem Tatli
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wei Wu
- Department of Medicine and Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Ji-Yeon Shin
- Department of Medicine and Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Gisèle Bonne
- Sorbonne Université, INSERM, Centre de Recherche en Myologie, Institut de Myologie, F-75651 Paris CEDEX 13, France
| | - Howard J Worman
- Department of Medicine and Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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25
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Protean Regulation of Leukocyte Function by Nuclear Lamins. Trends Immunol 2021; 42:323-335. [PMID: 33653660 DOI: 10.1016/j.it.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 02/08/2023]
Abstract
The leukocyte nucleus must be sufficiently elastic to squeeze through tissue barriers during migration, but not so collapsible as to risk damaging chromatin. The proper balance is struck in part by the composition of the nuclear lamina, a flexible meshwork composed mainly of intermediate filaments woven from type A and type B lamin proteins, that is located subjacent to the inner nuclear membrane. There is now increasing evidence that, in addition to influencing nuclear shape and stiffness and cell migration, lamins and lamin-interacting proteins may also interact functionally with chromatin to influence leukocyte gene expression, differentiation, and effector function, including T cell differentiation, B cell somatic hypermutation, and the formation of neutrophil extracellular traps (NETosis).
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26
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Burla R, La Torre M, Maccaroni K, Verni F, Giunta S, Saggio I. Interplay of the nuclear envelope with chromatin in physiology and pathology. Nucleus 2020; 11:205-218. [PMID: 32835589 PMCID: PMC7529417 DOI: 10.1080/19491034.2020.1806661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
The nuclear envelope compartmentalizes chromatin in eukaryotic cells. The main nuclear envelope components are lamins that associate with a panoply of factors, including the LEM domain proteins. The nuclear envelope of mammalian cells opens up during cell division. It is reassembled and associated with chromatin at the end of mitosis when telomeres tether to the nuclear periphery. Lamins, LEM domain proteins, and DNA binding factors, as BAF, contribute to the reorganization of chromatin. In this context, an emerging role is that of the ESCRT complex, a machinery operating in multiple membrane assembly pathways, including nuclear envelope reformation. Research in this area is unraveling how, mechanistically, ESCRTs link to nuclear envelope associated factors as LEM domain proteins. Importantly, ESCRTs work also during interphase for repairing nuclear envelope ruptures. Altogether the advances in this field are giving new clues for the interpretation of diseases implicating nuclear envelope fragility, as laminopathies and cancer. ABBREVIATIONS na, not analyzed; ko, knockout; kd, knockdown; NE, nuclear envelope; LEM, LAP2-emerin-MAN1 (LEM)-domain containing proteins; LINC, linker of nucleoskeleton and cytoskeleton complexes; Cyt, cytoplasm; Chr, chromatin; MB, midbody; End, endosomes; Tel, telomeres; INM, inner nuclear membrane; NP, nucleoplasm; NPC, Nuclear Pore Complex; ER, Endoplasmic Reticulum; SPB, spindle pole body.
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Affiliation(s)
- Romina Burla
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
| | - Mattia La Torre
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Klizia Maccaroni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Fiammetta Verni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Simona Giunta
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- Rockefeller University, New York, NY, USA
| | - Isabella Saggio
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
- Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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27
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Automated Nuclear Lamina Network Recognition and Quantitative Analysis in Structured Illumination Super-Resolution Microscope Images Using a Gaussian Mixture Model and Morphological Processing. PHOTONICS 2020. [DOI: 10.3390/photonics7040119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Studying the architecture of nuclear lamina networks is significantly important in biomedicine owing not only to their influence on the genome, but also because they are associated with several diseases. To save labor and time, an automated method for nuclear lamina network recognition and quantitative analysis is proposed for use with lattice structured illumination super-resolution microscope images in this study. This method is based on a Gaussian mixture model and morphological processing. It includes steps for target region generation, bias field correction, image segmentation, network connection, meshwork generation, and meshwork analysis. The effectiveness of the proposed method was confirmed by recognizing and quantitatively analyzing nuclear lamina networks in five images that are presented to show the method’s performance. The experimental results show that our algorithm achieved high accuracy in nuclear lamina network recognition and quantitative analysis, and the median face areas size of lamina networks from U2OS osteosarcoma cells are 0.3184 μm2.
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28
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Structural and Mechanical Aberrations of the Nuclear Lamina in Disease. Cells 2020; 9:cells9081884. [PMID: 32796718 PMCID: PMC7464082 DOI: 10.3390/cells9081884] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/02/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
The nuclear lamins are the major components of the nuclear lamina in the nuclear envelope. Lamins are involved in numerous functions, including a role in providing structural support to the cell and the mechanosensing of the cell. Mutations in the genes encoding for lamins lead to the rare diseases termed laminopathies. However, not only laminopathies show alterations in the nuclear lamina. Deregulation of lamin expression is reported in multiple cancers and several viral infections lead to a disrupted nuclear lamina. The structural and mechanical effects of alterations in the nuclear lamina can partly explain the phenotypes seen in disease, such as muscular weakness in certain laminopathies and transmigration of cancer cells. However, a lot of answers to questions about the relation between changes in the nuclear lamina and disease development remain elusive. Here, we review the current understandings of the contribution of the nuclear lamina in the structural support and mechanosensing of healthy and diseased cells.
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Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions. Cells 2020; 9:cells9071633. [PMID: 32645958 PMCID: PMC7407374 DOI: 10.3390/cells9071633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022] Open
Abstract
The molecular architecture and assembly mechanism of intermediate filaments have been enigmatic for decades. Among those, lamin filaments are of particular interest due to their universal role in cell nucleus and numerous disease-related mutations. Filament assembly is driven by specific interactions of the elementary dimers, which consist of the central coiled-coil rod domain flanked by non-helical head and tail domains. We aimed to investigate the longitudinal 'head-to-tail' interaction of lamin dimers (the so-called ACN interaction), which is crucial for filament assembly. To this end, we prepared a series of recombinant fragments of human lamin A centred around the N- and C-termini of the rod. The fragments were stabilized by fusions to heterologous capping motifs which provide for a correct formation of parallel, in-register coiled-coil dimers. As a result, we established crystal structures of two N-terminal fragments one of which highlights the propensity of the coiled-coil to open up, and one C-terminal rod fragment. Additional studies highlighted the capacity of such N- and C-terminal fragments to form specific complexes in solution, which were further characterized using chemical cross-linking. These data yielded a molecular model of the ACN complex which features a 6.5 nm overlap of the rod ends.
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Cappelletti C, Tramacere I, Cavalcante P, Schena E, Politano L, Carboni N, Gambineri A, D’Amico A, Ruggiero L, Ricci G, Siciliano G, Boriani G, Mongini TE, Vercelli L, Biagini E, Ziacchi M, D’Apice MR, Lattanzi G, Mantegazza R, Maggi L, Bernasconi P. Cytokine Profile in Striated Muscle Laminopathies: New Promising Biomarkers for Disease Prediction. Cells 2020; 9:cells9061532. [PMID: 32585971 PMCID: PMC7348753 DOI: 10.3390/cells9061532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 12/28/2022] Open
Abstract
Laminopathies are a wide and heterogeneous group of rare human diseases caused by mutations of the LMNA gene or related nuclear envelope genes. The variety of clinical phenotypes and the wide spectrum of histopathological changes among patients carrying an identical mutation in the LMNA gene make the prognostic process rather difficult, and classical genetic screens appear to have limited predictive value for disease development. The aim of this study was to evaluate whether a comprehensive profile of circulating cytokines may be a useful tool to differentiate and stratify disease subgroups, support clinical follow-ups and contribute to new therapeutic approaches. Serum levels of 51 pro- and anti-inflammatory molecules, including cytokines, chemokines and growth factors, were quantified by a Luminex multiple immune-assay in 53 patients with muscular laminopathy (Musc-LMNA), 10 with non-muscular laminopathy, 22 with other muscular disorders and in 35 healthy controls. Interleukin-17 (IL-17), granulocyte colony-stimulating factor (G-CSF) and transforming growth factor beta (TGF-β2) levels significantly discriminated Musc-LMNA from controls; interleukin-1β (IL-1β), interleukin-4 (IL-4) and interleukin-8 (IL-8) were differentially expressed in Musc-LMNA patients compared to those with non-muscular laminopathies, whereas IL-17 was significantly higher in Musc-LMNA patients with muscular and cardiac involvement. These findings support the hypothesis of a key role of the immune system in Musc-LMNA and emphasize the potential use of cytokines as biomarkers for these disorders.
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Affiliation(s)
- Cristina Cappelletti
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (P.C.); (R.M.); (L.M.); (P.B.)
- Correspondence: ; Tel.: +39-02-23944503/4511
| | - Irene Tramacere
- Department of Research and Clinical Development, Fondazione IRCCS Istituto Neurologico “Carlo Besta”, 20133 Milan, Italy;
| | - Paola Cavalcante
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (P.C.); (R.M.); (L.M.); (P.B.)
| | - Elisa Schena
- CNR Institute of Molecular Genetics, Unit of Bologna, 40136 Bologna, Italy; (E.S.); (G.L.)
- Endocrinology Unit, Department of Medical & Surgical Sciences, Alma Mater Studiorum University of Bologna, S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Luisa Politano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, University of Campania, Luigi Vanvitelli, 80138 Naples, Italy;
| | - Nicola Carboni
- Neurology Department, Hospital San Francesco of Nuoro, 08100 Nuoro, Italy;
| | - Alessandra Gambineri
- Endocrinology Unit, Department of Clinical and Medical Science, S. Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy;
| | - Adele D’Amico
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children’s Hospital, 00165 Rome, Italy;
| | - Lucia Ruggiero
- Department of Neurosciences and Reproductive and Odontostomatologic Sciences, University Federico II, 80137 Naples, Italy;
| | - Giulia Ricci
- Department of Clinical and Experimental Medicine, Neurological Clinic, 56126 Pisa, Italy; (G.R.); (G.S.)
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Neurological Clinic, 56126 Pisa, Italy; (G.R.); (G.S.)
| | - Giuseppe Boriani
- Cardiology Division, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Policlinico di Modena, 41121 Modena, Italy;
| | - Tiziana Enrica Mongini
- Department of Neurosciences “Rita Levi Montalcini”, University of Turin, 10124 Turin, Italy; (T.E.M.); (L.V.)
| | - Liliana Vercelli
- Department of Neurosciences “Rita Levi Montalcini”, University of Turin, 10124 Turin, Italy; (T.E.M.); (L.V.)
| | - Elena Biagini
- Azienda Ospedaliero Universitaria - Policlinico di St. Orsola, Cardiology Unit, Cardio-Thoracic-Vascular Department, 40138 Bologna, Italy; (E.B.); (M.Z.)
| | - Matteo Ziacchi
- Azienda Ospedaliero Universitaria - Policlinico di St. Orsola, Cardiology Unit, Cardio-Thoracic-Vascular Department, 40138 Bologna, Italy; (E.B.); (M.Z.)
| | - Maria Rosaria D’Apice
- Medical Genetics Unit, Policlinico Tor Vergata University Hospital, 00133 Rome, Italy;
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics, Unit of Bologna, 40136 Bologna, Italy; (E.S.); (G.L.)
- IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Renato Mantegazza
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (P.C.); (R.M.); (L.M.); (P.B.)
| | - Lorenzo Maggi
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (P.C.); (R.M.); (L.M.); (P.B.)
| | - Pia Bernasconi
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (P.C.); (R.M.); (L.M.); (P.B.)
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Alcorta-Sevillano N, Macías I, Rodríguez CI, Infante A. Crucial Role of Lamin A/C in the Migration and Differentiation of MSCs in Bone. Cells 2020; 9:cells9061330. [PMID: 32466483 PMCID: PMC7348862 DOI: 10.3390/cells9061330] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
Lamin A/C, intermediate filament proteins from the nuclear lamina encoded by the LMNA gene, play a central role in mediating the mechanosignaling of cytoskeletal forces into nucleus. In fact, this mechanotransduction process is essential to ensure the proper functioning of other tasks also mediated by lamin A/C: the structural support of the nucleus and the regulation of gene expression. In this way, lamin A/C is fundamental for the migration and differentiation of mesenchymal stem cells (MSCs), the progenitors of osteoblasts, thus affecting bone homeostasis. Bone formation is a complex process regulated by chemical and mechanical cues, coming from the surrounding extracellular matrix. MSCs respond to signals modulating the expression levels of lamin A/C, and therefore, adapting their nuclear shape and stiffness. To promote cell migration, MSCs need soft nuclei with low lamin A content. Conversely, during osteogenic differentiation, lamin A/C levels are known to be increased. Several LMNA mutations present a negative impact in the migration and osteogenesis of MSCs, affecting bone tissue homeostasis and leading to pathological conditions. This review aims to describe these concepts by discussing the latest state-of-the-art in this exciting area, focusing on the relationship between lamin A/C in MSCs' function and bone tissue from both, health and pathological points of view.
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32
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Kittisopikul M, Virtanen L, Taimen P, Goldman RD. Quantitative Analysis of Nuclear Lamins Imaged by Super-Resolution Light Microscopy. Cells 2019; 8:E361. [PMID: 31003483 PMCID: PMC6524165 DOI: 10.3390/cells8040361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/13/2019] [Accepted: 04/14/2019] [Indexed: 11/20/2022] Open
Abstract
The nuclear lamina consists of a dense fibrous meshwork of nuclear lamins, Type V intermediate filaments, and is ~14 nm thick according to recent cryo-electron tomography studies. Recent advances in light microscopy have extended the resolution to a scale allowing for the fine structure of the lamina to be imaged in the context of the whole nucleus. We review quantitative approaches to analyze the imaging data of the nuclear lamina as acquired by structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM), as well as the requisite cell preparation techniques. In particular, we discuss the application of steerable filters and graph-based methods to segment the structure of the four mammalian lamin isoforms (A, C, B1, and B2) and extract quantitative information.
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Affiliation(s)
- Mark Kittisopikul
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Laura Virtanen
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, 20520 Turku, Finland.
| | - Pekka Taimen
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, 20520 Turku, Finland.
- Department of Pathology, Turku University Hospital, 20520 Turku, Finland.
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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33
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Grafe M, Batsios P, Meyer I, Lisin D, Baumann O, Goldberg MW, Gräf R. Supramolecular Structures of the Dictyostelium Lamin NE81. Cells 2019; 8:cells8020162. [PMID: 30781468 PMCID: PMC6406624 DOI: 10.3390/cells8020162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/12/2019] [Accepted: 02/15/2019] [Indexed: 12/27/2022] Open
Abstract
Nuclear lamins are nucleus-specific intermediate filaments (IF) found at the inner nuclear membrane (INM) of the nuclear envelope (NE). Together with nuclear envelope transmembrane proteins, they form the nuclear lamina and are crucial for gene regulation and mechanical robustness of the nucleus and the whole cell. Recently, we characterized Dictyostelium NE81 as an evolutionarily conserved lamin-like protein, both on the sequence and functional level. Here, we show on the structural level that the Dictyostelium NE81 is also capable of assembling into filaments, just as metazoan lamin filament assemblies. Using field-emission scanning electron microscopy, we show that NE81 expressed in Xenopous oocytes forms filamentous structures with an overall appearance highly reminiscent of Xenopus lamin B2. The in vitro assembly properties of recombinant His-tagged NE81 purified from Dictyostelium extracts are very similar to those of metazoan lamins. Super-resolution stimulated emission depletion (STED) and expansion microscopy (ExM), as well as transmission electron microscopy of negatively stained purified NE81, demonstrated its capability of forming filamentous structures under low-ionic-strength conditions. These results recommend Dictyostelium as a non-mammalian model organism with a well-characterized nuclear envelope involving all relevant protein components known in animal cells.
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Affiliation(s)
- Marianne Grafe
- Department of Cell Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Petros Batsios
- Department of Cell Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Irene Meyer
- Department of Cell Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Daria Lisin
- Department of Cell Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Otto Baumann
- Department of Animal Physiology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Martin W Goldberg
- Department of Biosciences, Durham University, Science Laboratories, South Road, Durham DH1 3LE, UK.
| | - Ralph Gräf
- Department of Cell Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
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The Cutting Edge: The Role of mTOR Signaling in Laminopathies. Int J Mol Sci 2019; 20:ijms20040847. [PMID: 30781376 PMCID: PMC6412338 DOI: 10.3390/ijms20040847] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/29/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) is a ubiquitous serine/threonine kinase that regulates anabolic and catabolic processes, in response to environmental inputs. The existence of mTOR in numerous cell compartments explains its specific ability to sense stress, execute growth signals, and regulate autophagy. mTOR signaling deregulation is closely related to aging and age-related disorders, among which progeroid laminopathies represent genetically characterized clinical entities with well-defined phenotypes. These diseases are caused by LMNA mutations and feature altered bone turnover, metabolic dysregulation, and mild to severe segmental progeria. Different LMNA mutations cause muscular, adipose tissue and nerve pathologies in the absence of major systemic involvement. This review explores recent advances on mTOR involvement in progeroid and tissue-specific laminopathies. Indeed, hyper-activation of protein kinase B (AKT)/mTOR signaling has been demonstrated in muscular laminopathies, and rescue of mTOR-regulated pathways increases lifespan in animal models of Emery-Dreifuss muscular dystrophy. Further, rapamycin, the best known mTOR inhibitor, has been used to elicit autophagy and degradation of mutated lamin A or progerin in progeroid cells. This review focuses on mTOR-dependent pathogenetic events identified in Emery-Dreifuss muscular dystrophy, LMNA-related cardiomyopathies, Hutchinson-Gilford Progeria, mandibuloacral dysplasia, and type 2 familial partial lipodystrophy. Pharmacological application of mTOR inhibitors in view of therapeutic strategies is also discussed.
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NISHIMURA Y, KASAHARA K, INAGAKI M. Intermediate filaments and IF-associated proteins: from cell architecture to cell proliferation. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2019; 95:479-493. [PMID: 31611503 PMCID: PMC6819152 DOI: 10.2183/pjab.95.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/08/2019] [Indexed: 05/05/2023]
Abstract
Intermediate filaments (IFs), in coordination with microfilaments and microtubules, form the structural framework of the cytoskeleton and nucleus, thereby providing mechanical support against cellular stresses and anchoring intracellular organelles in place. The assembly and disassembly of IFs are mainly regulated by the phosphorylation of IF proteins. These phosphorylation states can be tracked using antibodies raised against phosphopeptides in the target proteins. IFs exert their functions through interactions with not only structural proteins, but also non-structural proteins involved in cell signaling, such as stress responses, apoptosis, and cell proliferation. This review highlights findings related to how IFs regulate cell division through phosphorylation cascades and how trichoplein, a centriolar protein originally identified as a keratin-associated protein, regulates the cell cycle through primary cilium formation.
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Affiliation(s)
- Yuhei NISHIMURA
- Departments of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Kousuke KASAHARA
- Department of Physiology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Masaki INAGAKI
- Department of Physiology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
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Abstract
Intermediate filaments (IFs) are one of the three major elements of the cytoskeleton. Their stability, intrinsic mechanical properties, and cell type-specific expression patterns distinguish them from actin and microtubules. By providing mechanical support, IFs protect cells from external forces and participate in cell adhesion and tissue integrity. IFs form an extensive and elaborate network that connects the cell cortex to intracellular organelles. They act as a molecular scaffold that controls intracellular organization. However, IFs have been revealed as much more than just rigid structures. Their dynamics is regulated by multiple signaling cascades and appears to contribute to signaling events in response to cell stress and to dynamic cellular functions such as mitosis, apoptosis, and migration.
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Affiliation(s)
- Sandrine Etienne-Manneville
- Institut Pasteur Paris, CNRS UMR 3691, Cell Polarity, Migration and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Paris Cedex 15, France;
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Pałka M, Tomczak A, Grabowska K, Machowska M, Piekarowicz K, Rzepecka D, Rzepecki R. Laminopathies: what can humans learn from fruit flies. Cell Mol Biol Lett 2018; 23:32. [PMID: 30002683 PMCID: PMC6034310 DOI: 10.1186/s11658-018-0093-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/05/2018] [Indexed: 01/01/2023] Open
Abstract
Lamin proteins are type V intermediate filament proteins (IFs) located inside the cell nucleus. They are evolutionarily conserved and have similar domain organization and properties to cytoplasmic IFs. Lamins provide a skeletal network for chromatin, the nuclear envelope, nuclear pore complexes and the entire nucleus. They are also responsible for proper connections between the karyoskeleton and structural elements in the cytoplasm: actin and the microtubule and cytoplasmic IF networks. Lamins affect transcription and splicing either directly or indirectly. Translocation of active genes into the close proximity of nuclear lamina is thought to result in their transcriptional silencing. Mutations in genes coding for lamins and interacting proteins in humans result in various genetic disorders, called laminopathies. Human genes coding for A-type lamin (LMNA) are the most frequently mutated. The resulting phenotypes include muscle, cardiac, neuronal, lipodystrophic and metabolic pathologies, early aging phenotypes, and combined complex phenotypes. The Drosophila melanogaster genome codes for lamin B-type (lamin Dm), lamin A-type (lamin C), and for LEM-domain proteins, BAF, LINC-complex proteins and all typical nuclear proteins. The fruit fly system is simpler than the vertebrate one since in flies there is only single lamin B-type and single lamin A-type protein, as opposed to the complex system of B- and A-type lamins in Danio, Xenopus and Mus musculus. This offers a unique opportunity to study laminopathies. Applying genetic tools based on Gal4 and in vitro nuclear assembly system to the fruit fly model may successfully advance knowledge of laminopathies. Here, we review studies of the laminopathies in the fly model system.
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Affiliation(s)
- Marta Pałka
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Aleksandra Tomczak
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Katarzyna Grabowska
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Magdalena Machowska
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Katarzyna Piekarowicz
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Dorota Rzepecka
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Ryszard Rzepecki
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland
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Exploring an optimal wavelet-based filter for cryo-ET imaging. Sci Rep 2018; 8:2582. [PMID: 29416100 PMCID: PMC5803242 DOI: 10.1038/s41598-018-20945-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/22/2018] [Indexed: 01/22/2023] Open
Abstract
Cryo-electron tomography (cryo-ET) is one of the most advanced technologies for the in situ visualization of molecular machines by producing three-dimensional (3D) biological structures. However, cryo-ET imaging has two serious disadvantages—low dose and low image contrast—which result in high-resolution information being obscured by noise and image quality being degraded, and this causes errors in biological interpretation. The purpose of this research is to explore an optimal wavelet denoising technique to reduce noise in cryo-ET images. We perform tests using simulation data and design a filter using the optimum selected wavelet parameters (three-level decomposition, level-1 zeroed out, subband-dependent threshold, a soft-thresholding and spline-based discrete dyadic wavelet transform (DDWT)), which we call a modified wavelet shrinkage filter; this filter is suitable for noisy cryo-ET data. When testing using real cryo-ET experiment data, higher quality images and more accurate measures of a biological structure can be obtained with the modified wavelet shrinkage filter processing compared with conventional processing. Because the proposed method provides an inherent advantage when dealing with cryo-ET images, it can therefore extend the current state-of-the-art technology in assisting all aspects of cryo-ET studies: visualization, reconstruction, structural analysis, and interpretation.
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