1
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Hameed HA, Paturej J, Erbaş A. Phase behavior and dissociation kinetics of lamins in a polymer model of progeria. J Chem Phys 2025; 162:185101. [PMID: 40337942 DOI: 10.1063/5.0265578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Accepted: 04/23/2025] [Indexed: 05/09/2025] Open
Abstract
One of the key structural proteins in the eukaryotic cell nucleus is lamin. Lamins can assemble into a two-dimensional protein meshwork at the nuclear periphery, known as the nuclear lamina, which provides rigidity and shape to the nucleus. Mutations in lamin proteins that alter the structure of the nuclear lamina underlie laminopathic diseases, including Hutchinson-Gilford Progeria Syndrome (HGPS). Experiments have shown that, compared to healthy cells, lamin supramolecular structures (e.g., protofilaments) assemble into a thicker lamina in HGPS, where they form highly stable nematic microdomains at the nuclear periphery, reminiscent of liquid crystals. This significantly alters the morphological and mechanical properties of the nucleus. In this study, we investigate the aggregation of lamin fibrous structures and their dissociation kinetics from the nuclear periphery by modeling them as coarse-grained, rod-like polymer chains confined within a rigid spherical shell. Our model reproduces the formation of multidirectional nematic domains at the nuclear surface and the reduced lamin dissociation observed in HGPS nuclei by adjusting lamin concentration, lamin-lamin (head-tail), and lamin-shell association strengths. While nematic phase formation requires relatively strong lamin-shell affinity under any non-vanishing inter-lamin attraction, the thickness of the lamina layer is primarily controlled by the head-tail association strength in the model. Furthermore, the unbinding kinetics of lamin chains from the lamina exhibit a concentration-dependent facilitated dissociation, suppressed by strong intra-lamin interactions, reminiscent of diseased nuclei. Overall, our calculations reveal the physical mechanisms by which mutations affecting native lamin interactions and concentration could lead to an abnormal nuclear lamina in laminopathic diseases.
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Affiliation(s)
- Hadiya Abdul Hameed
- UNAM-National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkiye
| | - Jarosław Paturej
- Institute of Physics, University of Silesia at Katowice, Chorzów 41-500, Poland
| | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkiye
- Institute of Physics, University of Silesia at Katowice, Chorzów 41-500, Poland
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2
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Zhao J, Zhang H, Pan C, He Q, Zheng K, Tang Y. Advances in research on the relationship between the LMNA gene and human diseases (Review). Mol Med Rep 2024; 30:236. [PMID: 39422026 PMCID: PMC11529173 DOI: 10.3892/mmr.2024.13358] [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: 06/18/2024] [Accepted: 08/29/2024] [Indexed: 10/19/2024] Open
Abstract
The LMNA gene, which is responsible for encoding lamin A/C proteins, is recognized as a primary constituent of the nuclear lamina. This protein serves crucial roles in various cellular physiological activities, including the maintenance of cellular structural stability, regulation of gene expression, mechanosensing and cellular motility. A significant association has been established between the LMNA gene and several major human diseases. Mutations, dysregulated expression of the LMNA gene, and improper processing of its encoded protein can result in a spectrum of pathological conditions. These diseases, collectively termed laminopathies, are directly attributed to LMNA gene dysfunction. The present review examines the recent advancements in research concerning the LMNA gene and its association with human diseases, while exploring its pathological roles. Particular emphasis is placed on the current status of LMNA gene research in the context of tumors. This includes an analysis of the abundance of LMNA alterations in cancer and its interplay with various signaling pathways. The aim of the present review was to provide novel perspectives for studying the development of LMNA‑related diseases and additional theoretical insights for basic and clinical translational research in this field.
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Affiliation(s)
- Jiumei Zhao
- Department of Laboratory, Chongqing Nanchuan District People's Hospital, Chongqing Medical University, Chongqing 408400, P.R. China
| | - Huijuan Zhang
- Forensic Science Centre, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Chenglong Pan
- Department of Pathology, The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Qian He
- School of Biomedical Engineering, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Kepu Zheng
- Forensic Science Centre, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Yu Tang
- Department of Pathology, The Third Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
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3
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Odell J, Lammerding J. N-terminal tags impair the ability of lamin A to provide structural support to the nucleus. J Cell Sci 2024; 137:jcs262207. [PMID: 39092499 PMCID: PMC11361635 DOI: 10.1242/jcs.262207] [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: 04/25/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Lamins are intermediate filament proteins that contribute to numerous cellular functions, including nuclear morphology and mechanical stability. The N-terminal head domain of lamin is crucial for higher order filament assembly and function, yet the effects of commonly used N-terminal tags on lamin function remain largely unexplored. Here, we systematically studied the effect of two differently sized tags on lamin A (LaA) function in a mammalian cell model engineered to allow for precise control of expression of tagged lamin proteins. Untagged, FLAG-tagged and GFP-tagged LaA completely rescued nuclear shape defects when expressed at similar levels in lamin A/C-deficient (Lmna-/-) MEFs, and all LaA constructs prevented increased nuclear envelope ruptures in these cells. N-terminal tags, however, altered the nuclear localization of LaA and impaired the ability of LaA to restore nuclear deformability and to recruit emerin to the nuclear membrane in Lmna-/- MEFs. Our finding that tags impede some LaA functions but not others might explain the partial loss of function phenotypes when tagged lamins are expressed in model organisms and should caution researchers using tagged lamins to study the nucleus.
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Affiliation(s)
- Jacob Odell
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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4
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Odell J, Lammerding J. N-terminal tags impair the ability of Lamin A to provide structural support to the nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590311. [PMID: 39211210 PMCID: PMC11361184 DOI: 10.1101/2024.04.19.590311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Lamins are intermediate filament proteins that contribute to numerous cellular functions, including nuclear morphology and mechanical stability. The N-terminal head domain of lamin is critical for higher order filament assembly and function, yet the effects of commonly used N-terminal tags on lamin function remain largely unexplored. Here, we systematically studied the effect of two differently sized tags on Lamin A (LaA) function in a mammalian cell model engineered to allow for precise control of expression of tagged lamin proteins. Untagged, FLAG-tagged, and GFP-tagged LaA completely rescued nuclear shape defects when expressed at similar levels in lamin A/C-deficient ( Lmna -/- ) MEFs, and all LaA constructs prevented increased nuclear envelope (NE) ruptures in these cells. N-terminal tags, however, altered the nuclear localization of LaA and impaired the ability of LaA to restore nuclear deformability and to recruit Emerin to the nuclear membrane in Lmna -/- MEFs. Our finding that tags impede some LaA functions but not others may explain the partial loss of function phenotypes when tagged lamins are expressed in model organisms and should caution researchers using tagged lamins to study the nucleus.
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5
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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: 3] [Impact Index Per Article: 1.5] [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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6
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Wallace M, Zahr H, Perati S, Morsink CD, Johnson LE, Gacita AM, Lai S, Wallrath LL, Benjamin IJ, McNally EM, Kirby TJ, Lammerding J. Nuclear damage in LMNA mutant iPSC-derived cardiomyocytes is associated with impaired lamin localization to the nuclear envelope. Mol Biol Cell 2023; 34:mbcE21100527. [PMID: 37585285 PMCID: PMC10846625 DOI: 10.1091/mbc.e21-10-0527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
The LMNA gene encodes the nuclear envelope proteins Lamins A and C, which comprise a major part of the nuclear lamina, provide mechanical support to the nucleus, and participate in diverse intracellular signaling. LMNA mutations give rise to a collection of diseases called laminopathies, including dilated cardiomyopathy (LMNA-DCM) and muscular dystrophies. Although nuclear deformities are a hallmark of LMNA-DCM, the role of nuclear abnormalities in the pathogenesis of LMNA-DCM remains incompletely understood. Using induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) from LMNA mutant patients and healthy controls, we show that LMNA mutant iPSC-CM nuclei have altered shape or increased size compared to healthy control iPSC-CM nuclei. The LMNA mutation exhibiting the most severe nuclear deformities, R249Q, additionally caused reduced nuclear stiffness and increased nuclear fragility. Importantly, for all cell lines, the degree of nuclear abnormalities corresponded to the degree of Lamin A/C and Lamin B1 mislocalization from the nuclear envelope. The mislocalization was likely due to altered assembly of Lamin A/C. Collectively, these results point to the importance of correct lamin assembly at the nuclear envelope in providing mechanical stability to the nucleus and suggest that defects in nuclear lamina organization may contribute to the nuclear and cellular dysfunction in LMNA-DCM.
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Affiliation(s)
- Melanie Wallace
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Ithaca, NY 14853
| | - Hind Zahr
- Weill Institute for Cell and Molecular Biology, Ithaca, NY 14853
| | - Shriya Perati
- Weill Institute for Cell and Molecular Biology, Ithaca, NY 14853
| | - Chloé D. Morsink
- Department of Physiology, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, VU Medical Center, 1081 HZ Amsterdam, The Netherlands
| | | | - Anthony M. Gacita
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern Medicine, Chicago, IL 60611
| | - Shuping Lai
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Lori L. Wallrath
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA 52242
| | - Ivor J. Benjamin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern Medicine, Chicago, IL 60611
| | - Tyler J. Kirby
- Weill Institute for Cell and Molecular Biology, Ithaca, NY 14853
- Department of Physiology, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, VU Medical Center, 1081 HZ Amsterdam, The Netherlands
| | - Jan Lammerding
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Ithaca, NY 14853
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7
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Kono Y, Adam SA, Sato Y, Reddy KL, Zheng Y, Medalia O, Goldman RD, Kimura H, Shimi T. Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS. J Cell Biol 2022; 221:e202201024. [PMID: 36301259 PMCID: PMC9617480 DOI: 10.1083/jcb.202201024] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 07/14/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022] Open
Abstract
In mammalian cell nuclei, the nuclear lamina (NL) underlies the nuclear envelope (NE) to maintain nuclear structure. The nuclear lamins, the major structural components of the NL, are involved in the protection against NE rupture induced by mechanical stress. However, the specific role of the lamins in repair of NE ruptures has not been fully determined. Our analyses using immunofluorescence and live-cell imaging revealed that the nucleoplasmic pool of lamin C rapidly accumulated at sites of NE rupture induced by laser microirradiation in mouse embryonic fibroblasts. The accumulation of lamin C at the rupture sites required both the immunoglobulin-like fold domain that binds to barrier-to-autointegration factor (BAF) and a nuclear localization signal. The accumulation of nuclear BAF and cytoplasmic cyclic GMP-AMP synthase (cGAS) at the rupture sites was in part dependent on lamin A/C. These results suggest that nucleoplasmic lamin C, BAF, and cGAS concertedly accumulate at sites of NE rupture for rapid repair.
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Affiliation(s)
- Yohei Kono
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Stephen A. Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Karen L. Reddy
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert D. Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Takeshi Shimi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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8
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Chang L, Li M, Shao S, Li C, Ai S, Xue B, Hou Y, Zhang Y, Li R, Fan X, He A, Li C, Sun Y. Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells. Protein Cell 2022; 13:258-280. [PMID: 33155082 PMCID: PMC8934373 DOI: 10.1007/s13238-020-00794-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the inter-chromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.
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Affiliation(s)
- Lei Chang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510530 China
| | - Mengfan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Shipeng Shao
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Chen Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Shanshan Ai
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yiwen Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Ruifeng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Xiaoying Fan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510530 China
| | - Aibin He
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
- Center for Statistical Science, Peking University, Beijing, 100871 China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
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9
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Sengupta D, Ali SN, Bhattacharya A, Mustafi J, Mukhopadhyay A, Sengupta K. A deep hybrid learning pipeline for accurate diagnosis of ovarian cancer based on nuclear morphology. PLoS One 2022; 17:e0261181. [PMID: 34995293 PMCID: PMC8741040 DOI: 10.1371/journal.pone.0261181] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/24/2021] [Indexed: 12/31/2022] Open
Abstract
Nuclear morphological features are potent determining factors for clinical diagnostic approaches adopted by pathologists to analyze the malignant potential of cancer cells. Considering the structural alteration of the nucleus in cancer cells, various groups have developed machine learning techniques based on variation in nuclear morphometric information like nuclear shape, size, nucleus-cytoplasm ratio and various non-parametric methods like deep learning have also been tested for analyzing immunohistochemistry images of tissue samples for diagnosing various cancers. We aim to correlate the morphometric features of the nucleus along with the distribution of nuclear lamin proteins with classical machine learning to differentiate between normal and ovarian cancer tissues. It has already been elucidated that in ovarian cancer, the extent of alteration in nuclear shape and morphology can modulate genetic changes and thus can be utilized to predict the outcome of low to a high form of serous carcinoma. In this work, we have performed exhaustive imaging of ovarian cancer versus normal tissue and developed a dual pipeline architecture that combines the matrices of morphometric parameters with deep learning techniques of auto feature extraction from pre-processed images. This novel Deep Hybrid Learning model, though derived from classical machine learning algorithms and standard CNN, showed a training and validation AUC score of 0.99 whereas the test AUC score turned out to be 1.00. The improved feature engineering enabled us to differentiate between cancerous and non-cancerous samples successfully from this pilot study.
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Affiliation(s)
- Duhita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
- Homi Bhaba National Institute, Mumbai, India
| | - Sk Nishan Ali
- Artificial Intelligence and Machine Learning Division, MUST Research Trust, Hyderabad, Telangana, India
| | - Aditya Bhattacharya
- Artificial Intelligence and Machine Learning Division, MUST Research Trust, Hyderabad, Telangana, India
| | - Joy Mustafi
- Artificial Intelligence and Machine Learning Division, MUST Research Trust, Hyderabad, Telangana, India
| | - Asima Mukhopadhyay
- Chittaranjan National Cancer Institute, Newtown, Kolkata, West Bengal, India
| | - Kaushik Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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10
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Srivastava LK, Ju Z, Ghagre A, Ehrlicher AJ. Spatial distribution of lamin A/C determines nuclear stiffness and stress-mediated deformation. J Cell Sci 2021; 134:268336. [PMID: 34028539 PMCID: PMC8186481 DOI: 10.1242/jcs.248559] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 04/14/2021] [Indexed: 01/05/2023] Open
Abstract
While diverse cellular components have been identified as mechanotransduction elements, the deformation of the nucleus itself is a critical mechanosensory mechanism, implying that nuclear stiffness is essential in determining responses to intracellular and extracellular stresses. Although the nuclear membrane protein lamin A/C is known to contribute to nuclear stiffness, bulk moduli of nuclei have not been reported for various levels of lamin A/C. Here, we measure the nuclear bulk moduli as a function of lamin A/C expression and applied osmotic stress, revealing a linear dependence within the range of 2-4 MPa. We also find that the nuclear compression is anisotropic, with the vertical axis of the nucleus being more compliant than the minor and major axes in the substrate plane. We then related the spatial distribution of lamin A/C with submicron 3D nuclear envelope deformation, revealing that local areas of the nuclear envelope with higher density of lamin A/C have correspondingly lower local deformations. These findings describe the complex dispersion of nuclear deformations as a function of lamin A/C expression and distribution, implicating a lamin A/C role in mechanotransduction. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | - Zhaoping Ju
- Department of Anatomy and Cell Biology, McGill University, Montreal H3A 0C7, Canada
| | - Ajinkya Ghagre
- Department of Bioengineering, McGill University, Montreal H3A 0E9
| | - Allen J Ehrlicher
- Department of Bioengineering, McGill University, Montreal H3A 0E9.,Department of Anatomy and Cell Biology, McGill University, Montreal H3A 0C7, Canada.,Department of Biomedical Engineering, McGill University, Montreal H3A 2B4, Canada.,Department of Mechanical Engineering, McGill University, Montreal H3A 0C3.,Centre for Structural Biology, McGill University, Montreal H3G 0B1, Canada.,Goodman Cancer Research Centre, McGill University, Montreal H3A 1A3, Canada
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11
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Abstract
The nuclear envelope is often depicted as a static barrier that regulates access between the nucleus and the cytosol. However, recent research has identified many conditions in cultured cells and in vivo in which nuclear membrane ruptures cause the loss of nuclear compartmentalization. These conditions include some that are commonly associated with human disease, such as migration of cancer cells through small spaces and expression of nuclear lamin disease mutations in both cultured cells and tissues undergoing nuclear migration. Nuclear membrane ruptures are rapidly repaired in the nucleus but persist in nuclear compartments that form around missegregated chromosomes called micronuclei. This review summarizes what is known about the mechanisms of nuclear membrane rupture and repair in both the main nucleus and micronuclei, and highlights recent work connecting the loss of nuclear integrity to genome instability and innate immune signaling. These connections link nuclear membrane rupture to complex chromosome alterations, tumorigenesis, and laminopathy etiologies.
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Affiliation(s)
- John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Emily M Hatch
- Division of Basic Sciences and Human Biology, The Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
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12
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Tenga R, Medalia O. Structure and unique mechanical aspects of nuclear lamin filaments. Curr Opin Struct Biol 2020; 64:152-159. [DOI: 10.1016/j.sbi.2020.06.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 11/15/2022]
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13
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Lamin A/C Mechanotransduction in Laminopathies. Cells 2020; 9:cells9051306. [PMID: 32456328 PMCID: PMC7291067 DOI: 10.3390/cells9051306] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Mechanotransduction translates forces into biological responses and regulates cell functionalities. It is implicated in several diseases, including laminopathies which are pathologies associated with mutations in lamins and lamin-associated proteins. These pathologies affect muscle, adipose, bone, nerve, and skin cells and range from muscular dystrophies to accelerated aging. Although the exact mechanisms governing laminopathies and gene expression are still not clear, a strong correlation has been found between cell functionality and nuclear behavior. New theories base on the direct effect of external force on the genome, which is indeed sensitive to the force transduced by the nuclear lamina. Nuclear lamina performs two essential functions in mechanotransduction pathway modulating the nuclear stiffness and governing the chromatin remodeling. Indeed, A-type lamin mutation and deregulation has been found to affect the nuclear response, altering several downstream cellular processes such as mitosis, chromatin organization, DNA replication-transcription, and nuclear structural integrity. In this review, we summarize the recent findings on the molecular composition and architecture of the nuclear lamina, its role in healthy cells and disease regulation. We focus on A-type lamins since this protein family is the most involved in mechanotransduction and laminopathies.
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Lamin A/C Assembly Defects in LMNA-Congenital Muscular Dystrophy Is Responsible for the Increased Severity of the Disease Compared with Emery-Dreifuss Muscular Dystrophy. Cells 2020; 9:cells9040844. [PMID: 32244403 PMCID: PMC7226786 DOI: 10.3390/cells9040844] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/24/2020] [Accepted: 03/27/2020] [Indexed: 01/13/2023] Open
Abstract
LMNA encodes for Lamin A/C, type V intermediate filaments that polymerize under the inner nuclear membrane to form the nuclear lamina. A small fraction of Lamin A/C, less polymerized, is also found in the nucleoplasm. Lamin A/C functions include roles in nuclear resistance to mechanical stress and gene regulation. LMNA mutations are responsible for a wide variety of pathologies, including Emery–Dreifuss (EDMD) and LMNA-related congenital muscular dystrophies (L-CMD) without clear genotype–phenotype correlations. Both diseases presented with striated muscle disorders although L-CMD symptoms appear much earlier and are more severe. Seeking for pathomechanical differences to explain the severity of L-CMD mutations, we performed an in silico analysis of the UMD-LMNA database and found that L-CMD mutations mainly affect residues involved in Lamin dimer and tetramer stability. In line with this, we found increased nucleoplasmic Lamin A/C in L-CMD patient fibroblasts and mouse myoblasts compared to the control and EDMD. L-CMD myoblasts show differentiation defects linked to their inability to upregulate muscle specific nuclear envelope (NE) proteins expression. NE proteins were mislocalized, leading to misshapen nuclei. We conclude that these defects are due to both the absence of Lamin A/C from the nuclear lamina and its maintenance in the nucleoplasm of myotubes.
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15
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Altered microtubule structure, hemichannel localization and beating activity in cardiomyocytes expressing pathologic nuclear lamin A/C. Heliyon 2020; 6:e03175. [PMID: 32021920 PMCID: PMC6992992 DOI: 10.1016/j.heliyon.2020.e03175] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
Given the clinical effect of laminopathies, understanding lamin mechanical properties will benefit the treatment of heart failure. Here we report a mechano-dynamic study of LMNA mutations in neonatal rat ventricular myocytes (NRVM) using single cell spectroscopy with Atomic Force Microscopy (AFM) and measured changes in beating force, frequency and contractile amplitude of selected mutant-expressing cells within cell clusters. Furthermore, since beat-to-beat variations can provide clues on the origin of arrhythmias, we analyzed the beating rate variability using a time-domain method which provides a Poincaré plot. Data were further correlated to cell phenotypes. Immunofluorescence and calcium imaging analysis showed that mutant lamin changed NRVMs beating force and frequency. Additionally, we noted an altered microtubule network organization with shorter filament length, and defective hemichannel membrane localization (Connexin 43). These data highlight the interconnection between nucleoskeleton, cytoskeleton and sarcolemmal structures, and the transcellular consequences of mutant lamin protein in the pathogenesis of the cardiac laminopathies.
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16
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Abstract
PURPOSE OF REVIEW The purpose of this review is to provide an update on lamin A/C (LMNA)-related cardiomyopathy and discuss the current recommendations and progress in the management of this disease. LMNA-related cardiomyopathy, an inherited autosomal dominant disease, is one of the most common causes of dilated cardiomyopathy and is characterized by steady progression toward heart failure and high risks of arrhythmias and sudden cardiac death. RECENT FINDINGS We discuss recent advances in the understanding of the molecular mechanisms of the disease including altered cell biomechanics, which may represent novel therapeutic targets to advance the current management approach, which relies on standard heart failure recommendations. Future therapeutic approaches include repurposed molecularly directed drugs, siRNA-based gene silencing, and genome editing. LMNA-related cardiomyopathy is the focus of active in vitro and in vivo research, which is expected to generate novel biomarkers and identify new therapeutic targets. LMNA-related cardiomyopathy trials are currently underway.
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17
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Steele-Stallard HB, Pinton L, Sarcar S, Ozdemir T, Maffioletti SM, Zammit PS, Tedesco FS. Modeling Skeletal Muscle Laminopathies Using Human Induced Pluripotent Stem Cells Carrying Pathogenic LMNA Mutations. Front Physiol 2018; 9:1332. [PMID: 30405424 PMCID: PMC6201196 DOI: 10.3389/fphys.2018.01332] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/04/2018] [Indexed: 01/03/2023] Open
Abstract
Laminopathies are a clinically heterogeneous group of disorders caused by mutations in LMNA. The main proteins encoded by LMNA are Lamin A and C, which together with Lamin B1 and B2, form the nuclear lamina: a mesh-like structure located underneath the inner nuclear membrane. Laminopathies show striking tissue specificity, with subtypes affecting striated muscle, peripheral nerve, and adipose tissue, while others cause multisystem disease with accelerated aging. Although several pathogenic mechanisms have been proposed, the exact pathophysiology of laminopathies remains unclear, compounded by the rarity of these disorders and lack of easily accessible cell types to study. To overcome this limitation, we used induced pluripotent stem cells (iPSCs) from patients with skeletal muscle laminopathies such as LMNA-related congenital muscular dystrophy and limb-girdle muscular dystrophy 1B, to model disease phenotypes in vitro. iPSCs can be derived from readily accessible cell types, have unlimited proliferation potential and can be differentiated into cell types that would otherwise be difficult and invasive to obtain. iPSC lines from three skeletal muscle laminopathy patients were differentiated into inducible myogenic cells and myotubes. Disease-associated phenotypes were observed in these cells, including abnormal nuclear shape and mislocalization of nuclear lamina proteins. Nuclear abnormalities were less pronounced in monolayer cultures of terminally differentiated skeletal myotubes than in proliferating myogenic cells. Notably, skeletal myogenic differentiation of LMNA-mutant iPSCs in artificial muscle constructs improved detection of myonuclear abnormalities compared to conventional monolayer cultures across multiple pathogenic genotypes, providing a high-fidelity modeling platform for skeletal muscle laminopathies. Our results lay the foundation for future iPSC-based therapy development and screening platforms for skeletal muscle laminopathies.
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Affiliation(s)
- Heather B Steele-Stallard
- Department of Cell and Developmental Biology, University College London, London, United Kingdom.,Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Luca Pinton
- Department of Cell and Developmental Biology, University College London, London, United Kingdom.,Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Shilpita Sarcar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Tanel Ozdemir
- Department of Cell and Developmental Biology, University College London, London, United Kingdom.,Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Sara M Maffioletti
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Francesco Saverio Tedesco
- Department of Cell and Developmental Biology, University College London, London, United Kingdom.,The Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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18
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Dahan I, Sorrentino S, Boujemaa-Paterski R, Medalia O. Tiopronin-Protected Gold Nanoparticles as a Potential Marker for Cryo-EM and Tomography. Structure 2018; 26:1408-1413.e3. [PMID: 30078643 DOI: 10.1016/j.str.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/03/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
Gold nanoparticles (AuNPs) and their conjugation to biological samples have numerous potential applications. When combined with cryo-electron microscopy and tomography analysis, AuNPs may provide a versatile and powerful tool to identify and precisely localize proteins even when attached to cellular components. Here, we describe a general and facile approach for the synthesis of homogeneous and stable AuNPs, which can readily be conjugated to a molecule of interest and imaged by cryo-electron tomography (cryo-ET). We demonstrate the synthesis of 2.2 ± 0.45-nm tiopronin-protected AuNPs, followed by their conjugation with recombinant proteins and peptides. Visualization of the ∼2.2-nm gold-tagged peptides by cryo-ET reveals the potential use of this strategy to label and localize accessible proteins in a cellular environment with nanometric resolution.
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Affiliation(s)
- Idit Dahan
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Simona Sorrentino
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rajaa Boujemaa-Paterski
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Université Grenoble Alpes, 38400 Grenoble, France
| | - Ohad Medalia
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, 84105 Beer-Sheva, Israel; Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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19
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Insight into the functional organization of nuclear lamins in health and disease. Curr Opin Cell Biol 2018; 54:72-79. [PMID: 29800922 DOI: 10.1016/j.ceb.2018.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/24/2018] [Accepted: 05/08/2018] [Indexed: 11/20/2022]
Abstract
Lamins are the main component of the nuclear lamina, a protein meshwork at the inner nuclear membrane which primarily provide mechanical stability to the nucleus. Lamins, type V intermediate filament proteins, are also involved in many nuclear activities. Structural analysis of nuclei revealed that lamins form 3.5nm thick filaments often interact with nuclear pore complexes. Mutations in the LMNA gene, encoding A-type lamins, have been associated with at least 15 distinct diseases collectively termed laminopathies, including muscle, metabolic and neurological disorders, and premature aging syndrome. It is unclear how laminopathic mutations lead to such a wide array of diseases, essentially affecting almost all tissues.
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20
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Laurini E, Martinelli V, Lanzicher T, Puzzi L, Borin D, Chen SN, Long CS, Lee P, Mestroni L, Taylor MRG, Sbaizero O, Pricl S. Biomechanical defects and rescue of cardiomyocytes expressing pathologic nuclear lamins. Cardiovasc Res 2018; 114:846-857. [PMID: 29432544 PMCID: PMC5909658 DOI: 10.1093/cvr/cvy040] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 01/06/2018] [Accepted: 02/07/2018] [Indexed: 02/07/2023] Open
Abstract
Aims Given the clinical impact of LMNA cardiomyopathies, understanding lamin function will fulfill a clinical need and will lead to advancement in the treatment of heart failure. A multidisciplinary approach combining cell biology, atomic force microscopy (AFM), and molecular modeling was used to analyse the biomechanical properties of human lamin A/C gene (LMNA) mutations (E161K, D192G, N195K) using an in vitro neonatal rat ventricular myocyte model. Methods and results The severity of biomechanical defects due to the three LMNA mutations correlated with the severity of the clinical phenotype. AFM and molecular modeling identified distinctive biomechanical and structural changes, with increasing severity from E161K to N195K and D192G, respectively. Additionally, the biomechanical defects were rescued with a p38 MAPK inhibitor. Conclusions AFM and molecular modeling were able to quantify distinct biomechanical and structural defects in LMNA mutations E161K, D192G, and N195K and correlate the defects with clinical phenotypic severity. Improvements in cellular biomechanical phenotype was demonstrated and may represent a mechanism of action for p38 MAPK inhibition therapy that is now being used in human clinical trials to treat laminopathies.
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Affiliation(s)
- Erik Laurini
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Valentina Martinelli
- International Center for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Thomas Lanzicher
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Luca Puzzi
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Daniele Borin
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Suet Nee Chen
- Cardiovascular Institute and Adult Medical Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Carlin S Long
- Cardiovascular Institute and Adult Medical Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patrice Lee
- Array BioPharma Inc., Boulder, CO 80301, USA
| | - Luisa Mestroni
- Cardiovascular Institute and Adult Medical Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Matthew R G Taylor
- Cardiovascular Institute and Adult Medical Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Orfeo Sbaizero
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
| | - Sabrina Pricl
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, Italy
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21
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Emerging views of the nucleus as a cellular mechanosensor. Nat Cell Biol 2018; 20:373-381. [PMID: 29467443 DOI: 10.1038/s41556-018-0038-y] [Citation(s) in RCA: 365] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/09/2018] [Indexed: 12/14/2022]
Abstract
The ability of cells to respond to mechanical forces is critical for numerous biological processes. Emerging evidence indicates that external mechanical forces trigger changes in nuclear envelope structure and composition, chromatin organization and gene expression. However, it remains unclear if these processes originate in the nucleus or are downstream of cytoplasmic signals. Here we discuss recent findings that support a direct role of the nucleus in cellular mechanosensing and highlight novel tools to study nuclear mechanotransduction.
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22
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Robijns J, Houthaeve G, Braeckmans K, De Vos WH. Loss of Nuclear Envelope Integrity in Aging and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 336:205-222. [DOI: 10.1016/bs.ircmb.2017.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Biotinylation by antibody recognition-a method for proximity labeling. Nat Methods 2017; 15:127-133. [PMID: 29256494 PMCID: PMC5790613 DOI: 10.1038/nmeth.4533] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 10/30/2017] [Indexed: 01/12/2023]
Abstract
Identification of protein-protein interactions is a major goal of biological research. Despite technical advances over the last two decades, important but still largely unsolved challenges include the high-throughput detection of interactions directly from primary tissue and the identification of interactors of insoluble proteins that form higher-order structures. We have developed a novel, proximity-based labeling approach that uses antibodies to guide biotin deposition onto adjacent proteins in fixed cells and primary tissues. We showed our method to be specific and sensitive by labeling a mitochondrial matrix protein. Next, we used this method to profile the dynamic interactome of lamin A/C in multiple cell and tissue types under various treatment conditions. The ability to detect proximal proteins and putative interactors in intact tissues, and to quantify changes caused by different conditions or in the presence of disease mutations, can provide a new window into cell biology and disease pathogenesis.
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24
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de Leeuw R, Gruenbaum Y, Medalia O. Nuclear Lamins: Thin Filaments with Major Functions. Trends Cell Biol 2017; 28:34-45. [PMID: 28893461 DOI: 10.1016/j.tcb.2017.08.004] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 10/18/2022]
Abstract
The nuclear lamina is a nuclear peripheral meshwork that is mainly composed of nuclear lamins, although a small fraction of lamins also localizes throughout the nucleoplasm. Lamins are classified as type V intermediate filament (IF) proteins. Mutations in lamin genes cause at least 15 distinct human diseases, collectively termed laminopathies, including muscle, metabolic, and neuronal diseases, and can cause accelerated aging. Most of these mutations are in the LMNA gene encoding A-type lamins. A growing number of nuclear proteins are known to bind lamins and are implicated in both nuclear and cytoskeletal organization, mechanical stability, chromatin organization, signaling, gene regulation, genome stability, and cell differentiation. Recent studies reveal the organization of the lamin filament meshwork in somatic cells where they assemble as tetramers in cross-section of the filaments.
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Affiliation(s)
- Rebecca de Leeuw
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Yosef Gruenbaum
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel.
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25
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Abstract
Nuclear lamins are components of the peripheral lamina that define the mechanical properties of nuclei and tether heterochromatin to the periphery. A-type lamins localize also to the nuclear interior, but the regulation and specific functions of this nucleoplasmic lamin pool are poorly understood. In this Commentary, we summarize known pathways that are potentially involved in the localization and dynamic behavior of intranuclear lamins, including their post-translational modifications and interactions with nucleoplasmic proteins, such as lamina-associated polypeptide 2α (LAP2α; encoded by TMPO). In addition, new data suggest that lamins in the nuclear interior have an important role in chromatin regulation and gene expression through dynamic binding to both hetero- and euchromatic genomic regions and promoter subdomains, thereby affecting epigenetic pathways and chromatin accessibility. Nucleoplasmic lamins also have a role in spatial chromatin organization and may be involved in mechanosignaling. In view of this newly emerging concept, we propose that the previously reported cellular phenotypes in lamin-linked diseases are, at least in part, rooted in an impaired regulation and/or function of the nucleoplasmic lamin A/C pool.
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Affiliation(s)
- Nana Naetar
- Center of Medical Biochemistry, Max F. Perutz Laboratories (MFPL), Medical University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, Vienna A-1030, Austria
| | - Simona Ferraioli
- Center of Medical Biochemistry, Max F. Perutz Laboratories (MFPL), Medical University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, Vienna A-1030, Austria
| | - Roland Foisner
- Center of Medical Biochemistry, Max F. Perutz Laboratories (MFPL), Medical University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, Vienna A-1030, Austria
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26
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Edens LJ, Dilsaver MR, Levy DL. PKC-mediated phosphorylation of nuclear lamins at a single serine residue regulates interphase nuclear size in Xenopus and mammalian cells. Mol Biol Cell 2017; 28:1389-1399. [PMID: 28356420 PMCID: PMC5426852 DOI: 10.1091/mbc.e16-11-0786] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 01/01/2023] Open
Abstract
How nuclear size is regulated is a fundamental cell-biological question with relevance to cancers, which often exhibit enlarged nuclei. We previously reported that conventional protein kinase C (cPKC) contributes to nuclear size reductions that occur during early Xenopus development. Here we report that PKC-mediated phosphorylation of lamin B3 (LB3) contributes to this mechanism of nuclear size regulation. By mapping PKC phosphorylation sites on LB3 and testing the effects of phosphomutants in Xenopus laevis embryos, we identify the novel site S267 as being an important determinant of nuclear size. Furthermore, FRAP studies demonstrate that phosphorylation at this site increases lamina dynamics, providing a mechanistic explanation for how PKC activity influences nuclear size. We subsequently map this X. laevis LB3 phosphorylation site to a conserved site in mammalian lamin A (LA), S268. Manipulating PKC activity in cultured mammalian cells alters nuclear size, as does expression of LA-S268 phosphomutants. Taken together, these data demonstrate that PKC-mediated lamin phosphorylation is a conserved mechanism of nuclear size regulation.
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Affiliation(s)
- Lisa J Edens
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Matthew R Dilsaver
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
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27
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A model for coordinating nuclear mechanics and membrane remodeling to support nuclear integrity. Curr Opin Cell Biol 2016; 41:9-17. [PMID: 27031045 DOI: 10.1016/j.ceb.2016.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 11/20/2022]
Abstract
A polymer network of intranuclear lamin filaments underlies the nuclear envelope and provides mechanical stability to the nucleus in metazoans. Recent work demonstrates that the expression of A-type lamins scales positively with the stiffness of the cellular environment, thereby coupling nuclear and extracellular mechanics. Using the spectrin-actin network at the erythrocyte plasma membrane as a model, we contemplate how the relative stiffness of the nuclear scaffold impinges on the growing number of interphase-specific nuclear envelope remodeling events, including recently discovered, nuclear envelope-specialized quality control mechanisms. We suggest that a stiffer lamina impedes these remodeling events, necessitating local lamina remodeling and/or concomitant scaling of the efficacy of membrane-remodeling machineries that act at the nuclear envelope.
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28
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Way M. 2015 Winner: Monika Zwerger. J Cell Sci 2016; 129:1083-4. [PMID: 27442112 DOI: 10.1242/jcs.187872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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29
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Simple Separation of Functionally Distinct Populations of Lamin-Binding Proteins. Methods Enzymol 2016. [PMID: 26778555 DOI: 10.1016/bs.mie.2015.09.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
The inner membrane of the nuclear envelope (NE) is home to hundreds of integral membrane proteins (NE transmembrane proteins, "NETs") with conserved or tissue-specific roles in genome organization and nuclear function. Nearly all characterized NETs bind A- or B-type lamins directly. However, hundreds of NETs remain uncharacterized, collectively posing an enormous gap that must be bridged to understand nuclear function and genome biology. We provide technically simple protocols for the separation and recovery of functionally distinct populations of NETs and A-type lamins. This protocol was developed for emerin, an inner nuclear membrane protein that binds lamins and barrier-to-autointegration factor (BANF1) as a component of nuclear lamina structure, and has diverse roles in nuclear assembly, signaling, and gene regulation. This protocol separates easily solubilized ("easy") populations of nuclear lamina proteins (emerin, lamin A, BAF) from "sonication-dependent" populations. Depending on cell type, the "easy" and "sonication-dependent" fractions each contain up to about half the available emerin, A-type lamins, and BAF, whereas B-type lamins and histone H3 are predominantly sonication dependent. The two populations of emerin have distinct posttranslational modifications, and only one population associates with BAF. This method may be useful for functional screening or analysis of other lamin-associated proteins, including novel NETs emerging from proteomic studies.
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30
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Davidson PM, Sliz J, Isermann P, Denais C, Lammerding J. Design of a microfluidic device to quantify dynamic intra-nuclear deformation during cell migration through confining environments. Integr Biol (Camb) 2015; 7:1534-46. [PMID: 26549481 DOI: 10.1039/c5ib00200a] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ability of cells to migrate through tissues and interstitial spaces is an essential factor during development and tissue homeostasis, immune cell mobility, and in various human diseases. Deformation of the nucleus and its associated lamina during 3-D migration is gathering increasing interest in the context of cancer metastasis, with the underlying hypothesis that a softer nucleus, resulting from reduced levels of lamin A/C, may aid tumour spreading. However, current methods to study the migration of cells in confining three dimensional (3-D) environments are limited by their imprecise control over the confinement, physiological relevance, and/or compatibility with high resolution imaging techniques. We describe the design of a polydimethylsiloxane (PDMS) microfluidic device composed of channels with precisely-defined constrictions mimicking physiological environments that enable high resolution imaging of live and fixed cells. The device promotes easy cell loading and rapid, yet long-lasting (>24 hours) chemotactic gradient formation without the need for continuous perfusion. Using this device, we obtained detailed, quantitative measurements of dynamic nuclear deformation as cells migrate through tight spaces, revealing distinct phases of nuclear translocation through the constriction, buckling of the nuclear lamina, and severe intranuclear strain. Furthermore, we found that lamin A/C-deficient cells exhibited increased and more plastic nuclear deformations compared to wild-type cells but only minimal changes in nuclear volume, implying that low lamin A/C levels facilitate migration through constrictions by increasing nuclear deformability rather than compressibility. The integration of our migration devices with high resolution time-lapse imaging provides a powerful new approach to study intracellular mechanics and dynamics in a variety of physiologically-relevant applications, ranging from cancer cell invasion to immune cell recruitment.
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Affiliation(s)
- Patricia M Davidson
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
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