1
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Zaragoza MV, Bui TA, Widyastuti HP, Mehrabi M, Cang Z, Sha Y, Grosberg A, Nie Q. LMNA-Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-Derived iPSC Differentiation Support Cell Type and Lineage-Specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency. Cells 2024; 13:1479. [PMID: 39273049 PMCID: PMC11394257 DOI: 10.3390/cells13171479] [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: 06/12/2024] [Revised: 08/14/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
LMNA-related dilated cardiomyopathy (DCM) is an autosomal-dominant genetic condition with cardiomyocyte and conduction system dysfunction often resulting in heart failure or sudden death. The condition is caused by mutation in the Lamin A/C (LMNA) gene encoding Type-A nuclear lamin proteins involved in nuclear integrity, epigenetic regulation of gene expression, and differentiation. The molecular mechanisms of the disease are not completely understood, and there are no definitive treatments to reverse progression or prevent mortality. We investigated possible mechanisms of LMNA-related DCM using induced pluripotent stem cells derived from a family with a heterozygous LMNA c.357-2A>G splice-site mutation. We differentiated one LMNA-mutant iPSC line derived from an affected female (Patient) and two non-mutant iPSC lines derived from her unaffected sister (Control) and conducted single-cell RNA sequencing for 12 samples (four from Patients and eight from Controls) across seven time points: Day 0, 2, 4, 9, 16, 19, and 30. Our bioinformatics workflow identified 125,554 cells in raw data and 110,521 (88%) high-quality cells in sequentially processed data. Unsupervised clustering, cell annotation, and trajectory inference found complex heterogeneity: ten main cell types; many possible subtypes; and lineage bifurcation for cardiac progenitors to cardiomyocytes (CMs) and epicardium-derived cells (EPDCs). Data integration and comparative analyses of Patient and Control cells found cell type and lineage-specific differentially expressed genes (DEGs) with enrichment, supporting pathway dysregulation. Top DEGs and enriched pathways included 10 ZNF genes and RNA polymerase II transcription in pluripotent cells (PP); BMP4 and TGF Beta/BMP signaling, sarcomere gene subsets and cardiogenesis, CDH2 and EMT in CMs; LMNA and epigenetic regulation, as well as DDIT4 and mTORC1 signaling in EPDCs. Top DEGs also included XIST and other X-linked genes, six imprinted genes (SNRPN, PWAR6, NDN, PEG10, MEG3, MEG8), and enriched gene sets related to metabolism, proliferation, and homeostasis. We confirmed Lamin A/C haploinsufficiency by allelic expression and Western blot. Our complex Patient-derived iPSC model for Lamin A/C haploinsufficiency in PP, CM, and EPDC provided support for dysregulation of genes and pathways, many previously associated with Lamin A/C defects, such as epigenetic gene expression, signaling, and differentiation. Our findings support disruption of epigenomic developmental programs, as proposed in other LMNA disease models. We recognized other factors influencing epigenetics and differentiation; thus, our approach needs improvement to further investigate this mechanism in an iPSC-derived model.
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Affiliation(s)
- Michael V. Zaragoza
- UCI Cardiogenomics Program, Pediatrics and Biological Chemistry, UC Irvine School of Medicine, Irvine, CA 92697, USA
- Sue & Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Thuy-Anh Bui
- UCI Cardiogenomics Program, Pediatrics and Biological Chemistry, UC Irvine School of Medicine, Irvine, CA 92697, USA
| | - Halida P. Widyastuti
- UCI Cardiogenomics Program, Pediatrics and Biological Chemistry, UC Irvine School of Medicine, Irvine, CA 92697, USA
| | - Mehrsa Mehrabi
- Biomedical Engineering and Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Zixuan Cang
- Mathematics and NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Yutong Sha
- Mathematics and NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Anna Grosberg
- Sue & Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Biomedical Engineering and Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Qing Nie
- Mathematics and NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
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2
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Kelnhofer-Millevolte LE, Arnold EA, Nguyen DH, Avgousti DC. Controlling Much? Viral Control of Host Chromatin Dynamics. Annu Rev Virol 2024; 11:171-191. [PMID: 38684115 DOI: 10.1146/annurev-virology-100422-011616] [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] [Indexed: 05/02/2024]
Abstract
Viruses are exemplary molecular biologists and have been integral to scientific discovery for generations. It is therefore no surprise that nuclear replicating viruses have evolved to systematically take over host cell function through astoundingly specific nuclear and chromatin hijacking. In this review, we focus on nuclear replicating DNA viruses-herpesviruses and adenoviruses-as key examples of viral invasion in the nucleus. We concentrate on critical features of nuclear architecture, such as chromatin and the nucleolus, to illustrate the complexity of the virus-host battle for resources in the nucleus. We conclude with a discussion of the technological advances that have enabled the discoveries we describe and upcoming steps in this burgeoning field.
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Affiliation(s)
- Laurel E Kelnhofer-Millevolte
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
- Department of Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA
| | - Edward A Arnold
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Daniel H Nguyen
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA;
| | - Daphne C Avgousti
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA;
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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3
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Qiu H, Sun Y, Wang X, Gong T, Su J, Shen J, Zhou J, Xia J, Wang H, Meng X, Fu G, Zhang D, Jiang C, Liang P. Lamin A/C deficiency-mediated ROS elevation contributes to pathogenic phenotypes of dilated cardiomyopathy in iPSC model. Nat Commun 2024; 15:7000. [PMID: 39143095 PMCID: PMC11324749 DOI: 10.1038/s41467-024-51318-5] [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: 03/14/2023] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Mutations in the nuclear envelope (NE) protein lamin A/C (encoded by LMNA), cause a severe form of dilated cardiomyopathy (DCM) with early-onset life-threatening arrhythmias. However, molecular mechanisms underlying increased arrhythmogenesis in LMNA-related DCM (LMNA-DCM) remain largely unknown. Here we show that a frameshift mutation in LMNA causes abnormal Ca2+ handling, arrhythmias and disformed NE in LMNA-DCM patient-specific iPSC-derived cardiomyocytes (iPSC-CMs). Mechanistically, lamin A interacts with sirtuin 1 (SIRT1) where mutant lamin A/C accelerates degradation of SIRT1, leading to mitochondrial dysfunction and oxidative stress. Elevated reactive oxygen species (ROS) then activates the Ca2+/calmodulin-dependent protein kinase II (CaMKII)-ryanodine receptor 2 (RYR2) pathway and aggravates the accumulation of SUN1 in mutant iPSC-CMs, contributing to arrhythmias and NE deformation, respectively. Taken together, the lamin A/C deficiency-mediated ROS disorder is revealed as central to LMNA-DCM development. Manipulation of impaired SIRT1 activity and excessive oxidative stress is a potential future therapeutic strategy for LMNA-DCM.
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Affiliation(s)
- Hangyuan Qiu
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China
- Heart Center, Department of Cardiovascular Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yaxun Sun
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China
| | - Xiaochen Wang
- Key Laboratory of combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Tingyu Gong
- Key Laboratory of combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Jun Su
- Key Laboratory of combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Jiaxi Shen
- Key Laboratory of combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Jingjun Zhou
- Key Laboratory of combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Jiafeng Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Wang
- Prenatal Diagnosis Center, Hangzhou Women's Hospital, Hangzhou, China
| | - Xiangfu Meng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, China
| | - Guosheng Fu
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China
| | - Donghui Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, China
| | - Chenyang Jiang
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China.
| | - Ping Liang
- Key Laboratory of combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China.
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Wang Z, Zhao N, Zhang S, Wang D, Wang S, Liu N. YEATS domain-containing protein GAS41 regulates nuclear shape by working in concert with BRD2 and the mediator complex in colorectal cancer. Pharmacol Res 2024; 206:107283. [PMID: 38964523 DOI: 10.1016/j.phrs.2024.107283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
The maintenance of nuclear shape is essential for cellular homeostasis and disruptions in this process have been linked to various pathological conditions, including cancer, laminopathies, and aging. Despite the significance of nuclear shape, the precise molecular mechanisms controlling it are not fully understood. In this study, we have identified the YEATS domain-containing protein 4 (GAS41) as a previously unidentified factor involved in regulating nuclear morphology. Genetic ablation of GAS41 in colorectal cancer cells resulted in significant abnormalities in nuclear shape and inhibited cancer cell proliferation both in vitro and in vivo. Restoration experiments revealed that wild-type GAS41, but not a YEATS domain mutant devoid of histone H3 lysine 27 acetylation or crotonylation (H3K27ac/cr) binding, rescued the aberrant nuclear phenotypes in GAS41-deficient cells, highlighting the importance of GAS41's binding to H3K27ac/cr in nuclear shape regulation. Further experiments showed that GAS41 interacts with H3K27ac/cr to regulate the expression of key nuclear shape regulators, including LMNB1, LMNB2, SYNE4, and LEMD2. Mechanistically, GAS41 recruited BRD2 and the Mediator complex to gene loci of these regulators, promoting their transcriptional activation. Disruption of GAS41-H3K27ac/cr binding caused BRD2, MED14 and MED23 to dissociate from gene loci, leading to nuclear shape abnormalities. Overall, our findings demonstrate that GAS41 collaborates with BRD2 and the Mediator complex to control the expression of crucial nuclear shape regulators.
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Affiliation(s)
- Zhengmin Wang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130021, China
| | - Nan Zhao
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Siwei Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Deyu Wang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Shuai Wang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Nan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130021, China.
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5
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Dutta S, Muraganadan T, Vasudevan M. Evaluation of lamin A/C mechanotransduction under different surface topography in LMNA related muscular dystrophy. Cytoskeleton (Hoboken) 2024. [PMID: 39091017 DOI: 10.1002/cm.21895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 08/04/2024]
Abstract
Most of the single point mutations of the LMNA gene are associated with distinct muscular dystrophies, marked by heterogenous phenotypes but primarily the loss and symmetric weakness of skeletal muscle tissue. The molecular mechanism and phenotype-genotype relationships in these muscular dystrophies are poorly understood. An effort has been here to delineating the adaptation of mechanical inputs into biological response by mutant cells of lamin A associated muscular dystrophy. In this study, we implement engineered smooth and pattern surfaces of particular young modulus to mimic muscle physiological range. Using fluorescence and atomic force microscopy, we present distinct architecture of the actin filament along with abnormally distorted cell and nuclear shape in mutants, which showed a tendency to deviate from wild type cells. Topographic features of pattern surface antagonize the binding of the cell with it. Correspondingly, from the analysis of genome wide expression data in wild type and mutant cells, we report differential expression of the gene products of the structural components of cell adhesion as well as LINC (linkers of nucleoskeleton and cytoskeleton) protein complexes. This study also reveals mis expressed downstream signaling processes in mutant cells, which could potentially lead to onset of the disease upon the application of engineered materials to substitute the role of conventional cues in instilling cellular behaviors in muscular dystrophies. Collectively, these data support the notion that lamin A is essential for proper cellular mechanotransduction from extracellular environment to the genome and impairment of the muscle cell differentiation in the pathogenic mechanism for lamin A associated muscular dystrophy.
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Affiliation(s)
- Subarna Dutta
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, India
- Theomics International Private Limited, Bengaluru, India
| | - T Muraganadan
- CSIR-Indian Institute of Chemical Biology, Kolkata, India
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6
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Joudeh LA, Logan Schuck P, Van NM, DiCintio AJ, Stewart JA, Waldman AS. Progerin Can Induce DNA Damage in the Absence of Global Changes in Replication or Cell Proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601729. [PMID: 39005395 PMCID: PMC11244969 DOI: 10.1101/2024.07.02.601729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by features of accelerated aging, and individuals with HGPS seldom live beyond their mid-teens. The syndrome is commonly caused by a point mutation in the LMNA gene which codes for lamin A and its splice variant lamin C, components of the nuclear lamina. The mutation causing HGPS leads to production of a truncated, farnesylated form of lamin A referred to as "progerin." Progerin is also expressed at low levels in healthy individuals and appears to play a role in normal aging. HGPS is associated with an accumulation of genomic DNA double-strand breaks (DSBs) and alterations in the nature of DSB repair. The source of DSBs in HGPS is often attributed to stalling and subsequent collapse of replication forks in conjunction with faulty recruitment of repair factors to damage sites. In this work, we used a model system involving immortalized human cell lines to investigate progerin-induced genomic damage. Using an immunofluorescence approach to visualize phosphorylated histone H2AX foci which mark sites of genomic damage, we report that cells engineered to express progerin displayed a significant elevation of endogenous damage in the absence of any change in the cell cycle profile or doubling time of cells. Genomic damage was enhanced and persistent in progerin-expressing cells treated with hydroxyurea. Overexpression of wild-type lamin A did not elicit the outcomes associated with progerin expression. Our results show that DNA damage caused by progerin can occur independently from global changes in replication or cell proliferation.
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Affiliation(s)
- Liza A. Joudeh
- Department of Biological Sciences, University of South Carolina, Columbia, SC 20208
| | - P. Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, SC 20208
| | - Nina M. Van
- Department of Biological Sciences, University of South Carolina, Columbia, SC 20208
| | - Alannah J. DiCintio
- Department of Biological Sciences, University of South Carolina, Columbia, SC 20208
| | - Jason A. Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC 20208
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101
| | - Alan S. Waldman
- Department of Biological Sciences, University of South Carolina, Columbia, SC 20208
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7
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Kwartler CS, Pinelo JEE. Use of iPSC-Derived Smooth Muscle Cells to Model Physiology and Pathology. Arterioscler Thromb Vasc Biol 2024; 44:1523-1536. [PMID: 38695171 PMCID: PMC11209779 DOI: 10.1161/atvbaha.123.319703] [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] [Indexed: 06/28/2024]
Abstract
The implementation of human induced pluripotent stem cell (hiPSC) models has introduced an additional tool for identifying molecular mechanisms of disease that complement animal models. Patient-derived or CRISPR/Cas9-edited induced pluripotent stem cells differentiated into smooth muscle cells (SMCs) have been leveraged to discover novel mechanisms, screen potential therapeutic strategies, and model in vivo development. The field has evolved over almost 15 years of research using hiPSC-SMCs and has made significant strides toward overcoming initial challenges such as the lineage specificity of SMC phenotypes. However, challenges both specific (eg, the lack of specific markers to thoroughly validate hiPSC-SMCs) and general (eg, a lack of transparency and consensus around methodology in the field) remain. In this review, we highlight the recent successes and remaining challenges of the hiPSC-SMC model.
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Affiliation(s)
- Callie S. Kwartler
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Jose Emiliano Esparza Pinelo
- Division of Medical Genetics, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030
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8
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Zaragoza MV, Bui TA, Widyastuti HP, Mehrabi M, Cang Z, Sha Y, Grosberg A, Nie Q. LMNA -Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-derived iPSC Differentiation Support Cell type and Lineage-specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598335. [PMID: 38915555 PMCID: PMC11195187 DOI: 10.1101/2024.06.12.598335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
LMNA -Related Dilated Cardiomyopathy (DCM) is an autosomal-dominant genetic condition with cardiomyocyte and conduction system dysfunction often resulting in heart failure or sudden death. The condition is caused by mutation in the Lamin A/C ( LMNA ) gene encoding Type-A nuclear lamin proteins involved in nuclear integrity, epigenetic regulation of gene expression, and differentiation. Molecular mechanisms of disease are not completely understood, and there are no definitive treatments to reverse progression or prevent mortality. We investigated possible mechanisms of LMNA -Related DCM using induced pluripotent stem cells derived from a family with a heterozygous LMNA c.357-2A>G splice-site mutation. We differentiated one LMNA mutant iPSC line derived from an affected female (Patient) and two non-mutant iPSC lines derived from her unaffected sister (Control) and conducted single-cell RNA sequencing for 12 samples (4 Patient and 8 Control) across seven time points: Day 0, 2, 4, 9, 16, 19, and 30. Our bioinformatics workflow identified 125,554 cells in raw data and 110,521 (88%) high-quality cells in sequentially processed data. Unsupervised clustering, cell annotation, and trajectory inference found complex heterogeneity: ten main cell types; many possible subtypes; and lineage bifurcation for Cardiac Progenitors to Cardiomyocytes (CM) and Epicardium-Derived Cells (EPDC). Data integration and comparative analyses of Patient and Control cells found cell type and lineage differentially expressed genes (DEG) with enrichment to support pathway dysregulation. Top DEG and enriched pathways included: 10 ZNF genes and RNA polymerase II transcription in Pluripotent cells (PP); BMP4 and TGF Beta/BMP signaling, sarcomere gene subsets and cardiogenesis, CDH2 and EMT in CM; LMNA and epigenetic regulation and DDIT4 and mTORC1 signaling in EPDC. Top DEG also included: XIST and other X-linked genes, six imprinted genes: SNRPN , PWAR6 , NDN , PEG10 , MEG3 , MEG8 , and enriched gene sets in metabolism, proliferation, and homeostasis. We confirmed Lamin A/C haploinsufficiency by allelic expression and Western blot. Our complex Patient-derived iPSC model for Lamin A/C haploinsufficiency in PP, CM, and EPDC provided support for dysregulation of genes and pathways, many previously associated with Lamin A/C defects, such as epigenetic gene expression, signaling, and differentiation. Our findings support disruption of epigenomic developmental programs as proposed in other LMNA disease models. We recognized other factors influencing epigenetics and differentiation; thus, our approach needs improvement to further investigate this mechanism in an iPSC-derived model.
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9
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Pan SW, Wang HD, Hsiao HY, Hsu PJ, Tseng YC, Liang WC, Jong YJ, Yuh CH. Creatine and L-carnitine attenuate muscular laminopathy in the LMNA mutation transgenic zebrafish. Sci Rep 2024; 14:12826. [PMID: 38834813 DOI: 10.1038/s41598-024-63711-7] [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: 10/18/2023] [Accepted: 05/31/2024] [Indexed: 06/06/2024] Open
Abstract
Lamin A/C gene (LMNA) mutations contribute to severe striated muscle laminopathies, affecting cardiac and skeletal muscles, with limited treatment options. In this study, we delve into the investigations of five distinct LMNA mutations, including three novel variants and two pathogenic variants identified in patients with muscular laminopathy. Our approach employs zebrafish models to comprehensively study these variants. Transgenic zebrafish expressing wild-type LMNA and each mutation undergo extensive morphological profiling, swimming behavior assessments, muscle endurance evaluations, heartbeat measurement, and histopathological analysis of skeletal muscles. Additionally, these models serve as platform for focused drug screening. We explore the transcriptomic landscape through qPCR and RNAseq to unveil altered gene expression profiles in muscle tissues. Larvae of LMNA(L35P), LMNA(E358K), and LMNA(R453W) transgenic fish exhibit reduced swim speed compared to LMNA(WT) measured by DanioVision. All LMNA transgenic adult fish exhibit reduced swim speed compared to LMNA(WT) in T-maze. Moreover, all LMNA transgenic adult fish, except LMNA(E358K), display weaker muscle endurance than LMNA(WT) measured by swimming tunnel. Histochemical staining reveals decreased fiber size in all LMNA mutations transgenic fish, excluding LMNA(WT) fish. Interestingly, LMNA(A539V) and LMNA(E358K) exhibited elevated heartbeats. We recognize potential limitations with transgene overexpression and conducted association calculations to explore its effects on zebrafish phenotypes. Our results suggest lamin A/C overexpression may not directly impact mutant phenotypes, such as impaired swim speed, increased heart rates, or decreased muscle fiber diameter. Utilizing LMNA zebrafish models for drug screening, we identify L-carnitine treatment rescuing muscle endurance in LMNA(L35P) and creatine treatment reversing muscle endurance in LMNA(R453W) zebrafish models. Creatine activates AMPK and mTOR pathways, improving muscle endurance and swim speed in LMNA(R453W) fish. Transcriptomic profiling reveals upstream regulators and affected genes contributing to motor dysfunction, cardiac anomalies, and ion flux dysregulation in LMNA mutant transgenic fish. These findings faithfully mimic clinical manifestations of muscular laminopathies, including dysmorphism, early mortality, decreased fiber size, and muscle dysfunction in zebrafish. Furthermore, our drug screening results suggest L-carnitine and creatine treatments as potential rescuers of muscle endurance in LMNA(L35P) and LMNA(R453W) zebrafish models. Our study offers valuable insights into the future development of potential treatments for LMNA-related muscular laminopathy.
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Affiliation(s)
- Shao-Wei Pan
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Horng-Dar Wang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - He-Yun Hsiao
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Po-Jui Hsu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- Department of Laboratory Medicine, Mackay Memorial Hospital, Taipei, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu, Taiwan
- Department of Nursing, MacKay Medical College, Taipei, Taiwan
| | - Yung-Che Tseng
- Marine Research Station, Institute of Cellular and Organism Biology, Academia Sinica, I-Lan, Taiwan
| | - Wen-Chen Liang
- Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuh-Jyh Jong
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
| | - Chiou-Hwa Yuh
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan.
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
- Ph.D. Program in Environmental and Occupational Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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10
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Aschner A, Keller A, Williams A, Whitney R, Cunningham K, Hamilton RM, Pollanen M, Donner E. Cardiac arrhythmia and epilepsy genetic variants in sudden unexpected death in epilepsy. Front Neurol 2024; 15:1386730. [PMID: 38756210 PMCID: PMC11097959 DOI: 10.3389/fneur.2024.1386730] [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] [Received: 02/15/2024] [Accepted: 03/29/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction Sudden Unexpected Death in Epilepsy (SUDEP) is the leading epilepsy-related cause of death, affecting approximately 1 per 1,000 individuals with epilepsy per year. Genetic variants that affect autonomic function, such as genes associated with cardiac arrhythmias, may predispose people with epilepsy to greater risk of both sudden cardiac death and SUDEP. Advances in next generation sequencing allow for the exploration of gene variants as potential biomarkers. Methods Genetic testing for the presence of cardiac arrhythmia and epilepsy gene variants was performed via genetic panels in 39 cases of SUDEP identified via autopsy by the Ontario Forensic Pathology Service. Variants were summarized by in-silico evidence for pathogenicity from 4 algorithms (SIFT, PolyPhen-2, PROVEAN, Mutation Taster) and allele frequencies in the general population (GnomAD). A maximum credible population allele frequency of 0.00004 was calculated based on epilepsy prevalence and SUDEP incidence to assess whether a variant was compatible with a pathogenic interpretation. Results Median age at the time of death was 33.3 years (range: 2, 60). Fifty-nine percent (n=23) were male. Gene panels detected 62 unique variants in 45 genes: 19 on the arrhythmia panel and 26 on the epilepsy panel. At least one variant was identified in 28 (72%) of decedents. Missense mutations comprised 57 (92%) of the observed variants. At least three in silico models predicted 12 (46%) cardiac arrhythmia panel missense variants and 20 (65%) epilepsy panel missense variants were pathogenic. Population allele frequencies were <0.00004 for 11 (42%) of the cardiac variants and 10 (32%) of the epilepsy variants. Together, these metrics identified 13 SUDEP variants of interest. Discussion Nearly three-quarters of decedents in this SUDEP cohort carried variants in comprehensive epilepsy or cardiac arrhythmia gene panels, with more than a third having variants in both panels. The proportion of decedents with cardiac variants aligns with recent studies of the disproportionate cardiac burden the epilepsy community faces compared to the general population and suggests a possible cardiac contribution to epilepsy mortality. These results identified 13 priority targets for future functional studies of these genes potential role in sudden death and demonstrates the necessity for further exploration of potential genetic contributions to SUDEP.
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Affiliation(s)
- Amir Aschner
- Division of Neurology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Anne Keller
- Division of Neurology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Andrew Williams
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Robyn Whitney
- McMaster Children’s Hospital, McMaster University, Hamilton, ON, Canada
| | - Kris Cunningham
- Department of Pathology and Molecular Medicine, School of Medicine, Faculty of Health Sciences, Queen’s University, Kingston, ON, Canada
| | - Robert M. Hamilton
- Division of Cardiology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Michael Pollanen
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Elizabeth Donner
- Division of Neurology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Department of Pediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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11
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Kelley A, Addie S, Carrington-Lawrence S, Ferrucci L, Jones P, Hadley E, Haim T, Harper J, Kahana S, Kelley M, Kohanski R, Masliah E, McConnell C, Morrison S, Nielsen L, Santora K, Hodes R. National Institute on Aging's 50th anniversary: Advancing aging research and the health and well-being of older adults. J Am Geriatr Soc 2024; 72:1574-1582. [PMID: 38445895 PMCID: PMC11090751 DOI: 10.1111/jgs.18837] [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: 12/21/2023] [Revised: 01/26/2024] [Accepted: 02/07/2024] [Indexed: 03/07/2024]
Abstract
The National Institute on Aging (NIA), part of the National Institutes of Health (NIH), was founded in 1974 to support and conduct research on aging and the health and well-being of older adults. Fifty years ago, the concept of studying aging generated much skepticism. Early NIA-funded research findings helped establish the great value of aging research and provided the foundation for significant science advances that have improved our understanding of the aging process, diseases and conditions associated with aging, and the effects of health inequities, as well as the need to promote healthy aging lifestyles. Today, we celebrate the many important contributions to aging research made possible by NIA, as well as opportunities to continue to make meaningful progress. NIA emphasizes that the broad aging research community must continue to increase and expand our collective efforts to recruit and train a diverse next generation of aging researchers.
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Affiliation(s)
- Amy Kelley
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Siobhan Addie
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Patricia Jones
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Evan Hadley
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Todd Haim
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Jessica Harper
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Shoshana Kahana
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Melinda Kelley
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Ronald Kohanski
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Eliezer Masliah
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Cindy McConnell
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie Morrison
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisbeth Nielsen
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth Santora
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Richard Hodes
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
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12
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Zi-Yi Z, Qin Q, Fei Z, Cun-Yu C, Lin T. Nesprin proteins: bridging nuclear envelope dynamics to muscular dysfunction. Cell Commun Signal 2024; 22:208. [PMID: 38566066 PMCID: PMC10986154 DOI: 10.1186/s12964-024-01593-y] [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: 01/28/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024] Open
Abstract
This review presents a comprehensive exploration of the pivotal role played by the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, with a particular focus on Nesprin proteins, in cellular mechanics and the pathogenesis of muscular diseases. Distinguishing itself from prior works, the analysis delves deeply into the intricate interplay of the LINC complex, emphasizing its indispensable contribution to maintaining cellular structural integrity, especially in mechanically sensitive tissues such as cardiac and striated muscles. Additionally, the significant association between mutations in Nesprin proteins and the onset of Dilated Cardiomyopathy (DCM) and Emery-Dreifuss Muscular Dystrophy (EDMD) is highlighted, underscoring their pivotal role in disease pathogenesis. Through a comprehensive examination of DCM and EDMD cases, the review elucidates the disruptions in the LINC complex, nuclear morphology alterations, and muscular developmental disorders, thus emphasizing the essential function of an intact LINC complex in preserving muscle physiological functions. Moreover, the review provides novel insights into the implications of Nesprin mutations for cellular dynamics in the pathogenesis of muscular diseases, particularly in maintaining cardiac structural and functional integrity. Furthermore, advanced therapeutic strategies, including rectifying Nesprin gene mutations, controlling Nesprin protein expression, enhancing LINC complex functionality, and augmenting cardiac muscle cell function are proposed. By shedding light on the intricate molecular mechanisms underlying nuclear-cytoskeletal interactions, the review lays the groundwork for future research and therapeutic interventions aimed at addressing genetic muscle disorders.
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Affiliation(s)
- Zhou Zi-Yi
- Department of Cardiology, Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
- School of Basic Medicine, China Three Gorges University, Yichang, 443000, Hubei, People's Republic of China
| | - Qin Qin
- Department of Cardiology, Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
- School of Basic Medicine, China Three Gorges University, Yichang, 443000, Hubei, People's Republic of China
| | - Zhou Fei
- Department of Cardiology, Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China
| | - Cao Cun-Yu
- School of Basic Medicine, China Three Gorges University, Yichang, 443000, Hubei, People's Republic of China
- College of Basic Medical Sciences, Hubei Key Laboratory of Tumor Microencironment and immunotherapy, China Three Gorges University, Yichang, 443000, Hubei, People's Republic of China
| | - Teng Lin
- Department of Cardiology, Yichang Central People's Hospital, Yichang, 443003, Hubei, People's Republic of China.
- King's College London British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine & Sciences, London, SE5 9NU, UK.
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13
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Bannasch DL, Oertle DT, Vo J, Batcher KL, Stern JA, Kaplan JL, Li RHL, Madden IE, Christen M, Leeb T, Joshi N. Naturally occurring canine laminopathy leading to a dilated and fibrosing cardiomyopathy in the Nova Scotia Duck Tolling Retriever. Sci Rep 2023; 13:19077. [PMID: 37925523 PMCID: PMC10625583 DOI: 10.1038/s41598-023-46601-2] [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: 05/04/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is characterized by decreased systolic function and dilation of one or both ventricles, often leading to heart failure or sudden death. Two 10-month-old sibling Nova Scotia Duck Tolling Retrievers (NSDTR) died acutely with evidence of dilated cardiomyopathy with myocardial fibrosis. Association analysis using two cases and 35 controls identified three candidate regions homozygous in the two cases. Whole genome sequencing identified a frameshift deletion in the LMNA gene (NC_049228.1:g.41688530del, NP_001274080:p.(Asp576ThrfsTer124)). Three retrospectively identified NSDTRs with sudden death before 2 years of age and severe myocardial fibrosis were also homozygous for the deletion. One 5 year old with sudden death and myocardial fibrosis was heterozygous for the deletion. This variant was not identified in 722 dogs of other breeds, nor was it identified to be homozygous in 784 NSDTR. LMNA codes for lamin A/C proteins, which are type V intermediate filaments that provide structural support to the nuclear membrane. In humans, LMNA variants can cause DCM with sudden death as well as diseases of striated muscles, lipodystrophy, neuropathies, and accelerated aging disorders. This frameshift deletion is predicted to affect processing of prelamin A into lamin A. Pedigree analysis in the NSDTR and functional evaluation of heterozygotes is consistent with a predominantly recessive mode of inheritance and possibly low penetrance in heterozygotes in contrast to people, where most pathogenic LMNA variants are dominantly inherited.
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Affiliation(s)
- Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
| | - Danielle T Oertle
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Julia Vo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Kevin L Batcher
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Joshua A Stern
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Joanna L Kaplan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Ronald H L Li
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Indiana E Madden
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Nikhil Joshi
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, CA, USA
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14
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Emerson FJ, Lee SS. Chromatin: the old and young of it. Front Mol Biosci 2023; 10:1270285. [PMID: 37877123 PMCID: PMC10591336 DOI: 10.3389/fmolb.2023.1270285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Aging affects nearly all aspects of our cells, from our DNA to our proteins to how our cells handle stress and communicate with each other. Age-related chromatin changes are of particular interest because chromatin can dynamically respond to the cellular and organismal environment, and many modifications at chromatin are reversible. Changes at chromatin occur during aging, and evidence from model organisms suggests that chromatin factors could play a role in modulating the aging process itself, as altering proteins that work at chromatin often affect the lifespan of yeast, worms, flies, and mice. The field of chromatin and aging is rapidly expanding, and high-resolution genomics tools make it possible to survey the chromatin environment or track chromatin factors implicated in longevity with precision that was not previously possible. In this review, we discuss the state of chromatin and aging research. We include examples from yeast, Drosophila, mice, and humans, but we particularly focus on the commonly used aging model, the worm Caenorhabditis elegans, in which there are many examples of chromatin factors that modulate longevity. We include evidence of both age-related changes to chromatin and evidence of specific chromatin factors linked to longevity in core histones, nuclear architecture, chromatin remodeling, and histone modifications.
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Affiliation(s)
| | - Siu Sylvia Lee
- Lee Lab, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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15
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Upadhyay KK, Choi EYK, Foisner R, Omary MB, Brady GF. Hepatocyte-specific loss of LAP2α protects against diet-induced hepatic steatosis, steatohepatitis, and fibrosis in male mice. Am J Physiol Gastrointest Liver Physiol 2023; 325:G184-G195. [PMID: 37366543 PMCID: PMC10396226 DOI: 10.1152/ajpgi.00214.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 05/24/2023] [Accepted: 06/18/2023] [Indexed: 06/28/2023]
Abstract
There is increasing evidence for the importance of the nuclear envelope in lipid metabolism, nonalcoholic fatty liver disease (NAFLD), and nonalcoholic steatohepatitis (NASH). Human mutations in LMNA, encoding A-type nuclear lamins, cause early-onset insulin resistance and NASH, while hepatocyte-specific deletion of Lmna predisposes to NASH with fibrosis in male mice. Given that variants in the gene encoding LAP2α, a nuclear protein that regulates lamin A/C, were previously identified in patients with NAFLD, we sought to determine the role of LAP2α in NAFLD using a mouse genetic model. Hepatocyte-specific Lap2α-knockout (Lap2α(ΔHep)) mice and littermate controls were fed normal chow or high-fat diet (HFD) for 8 wk or 6 mo. Unexpectedly, male Lap2α(ΔHep) mice showed no increase in hepatic steatosis or NASH compared with controls. Rather, Lap2α(ΔHep) mice demonstrated reduced hepatic steatosis, with decreased NASH and fibrosis after long-term HFD. Accordingly, pro-steatotic genes including Cidea, Mogat1, and Cd36 were downregulated in Lap2α(ΔHep) mice, along with concomitant decreases in expression of pro-inflammatory and pro-fibrotic genes. These data indicate that hepatocyte-specific Lap2α deletion protects against hepatic steatosis and NASH in mice and raise the possibility that LAP2α could become a potential therapeutic target in human NASH.NEW & NOTEWORTHY The nuclear envelope and lamina regulate lipid metabolism and susceptibility to nonalcoholic steatohepatitis (NASH), but the role of the nuclear lamin-binding protein LAP2α in NASH has not been explored. Our data demonstrate that hepatocyte-specific loss of LAP2α protects against diet-induced hepatic steatosis, NASH, and fibrosis in male mice, with downregulation of pro-steatotic, pro-inflammatory, and pro-fibrotic lamin-regulated genes. These findings suggest that targeting LAP2α could have future potential as a novel therapeutic avenue in NASH.
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Affiliation(s)
- Kapil K Upadhyay
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States
| | - Eun-Young K Choi
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States
| | - Roland Foisner
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus, Vienna, Austria
| | - M Bishr Omary
- Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, United States
| | - Graham F Brady
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States
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16
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Fan JR, Chang SN, Chu CT, Chen HC. AKT2-mediated nuclear deformation leads to genome instability during epithelial-mesenchymal transition. iScience 2023; 26:106992. [PMID: 37378334 PMCID: PMC10291577 DOI: 10.1016/j.isci.2023.106992] [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: 02/03/2023] [Revised: 05/04/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Nuclear deformation has been observed in some cancer cells for decades, but its underlying mechanism and biological significance remain elusive. To address these questions, we employed human lung cancer A549 cell line as a model in context with transforming growth factor β (TGFβ)-induced epithelial-mesenchymal transition. Here, we report that nuclear deformation induced by TGFβ is concomitant with increased phosphorylation of lamin A at Ser390, defective nuclear lamina and genome instability. AKT2 and Smad3 serve as the downstream effectors for TGFβ to induce nuclear deformation. AKT2 directly phosphorylates lamin A at Ser390, whereas Smad3 is required for AKT2 activation upon TGFβ stimulation. Expression of the lamin A mutant with a substitution of Ser390 to Ala or suppression of AKT2 or Smad3 prevents nuclear deformation and genome instability induced by TGFβ. These findings reveal a molecular mechanism for TGFβ-induced nuclear deformation and establish a role of nuclear deformation in genome instability during epithelial-mesenchymal transition.
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Affiliation(s)
- Jia-Rong Fan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Sung-Nian Chang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ching-Tung Chu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Hong-Chen Chen
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
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17
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Xu Y, Liu J, Song W, Wang Q, Sun X, Zhao Q, Huang Y, Li H, Peng Y, Yuan J, Ji B, Ren L. Biomimetic Convex Implant for Corneal Regeneration Through 3D Printing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205878. [PMID: 36775872 PMCID: PMC10104657 DOI: 10.1002/advs.202205878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Blindness caused by corneal damage affects millions of people worldwide, and this number continues to rise. However, rapid epithelization and a stable epithelium process are the two biggest challenges for traditional corneal materials. These processes are related to corneal curvature, which is an important factor in determination of the corneal healing process and epithelial behavior during corneal damage. In this study, smooth 3D-printed convex corneal implants based on gelatin methacrylate and collagen are generated. As epithelium distribution and adhesion vary in different regions of the natural cornea, this work separates the surfaces into four regions and studies how cells sense topological cues on curvature. It is found that rabbit corneal epithelial cells (RCECs) seeded on steeper slope gradient surfaces on convex structures result in more aligned cell organization and tighter cell-substrate adhesion, which can also be verified through finite element simulation and signaling pathway analysis. In vivo transplantation of convex implants result in a better fit with adjacent tissue and stronger cell adhesion than flat implants, thereby accelerating corneal epithelialization and promoting collagen fibers and neural regeneration within 180 days. Taken together, printed convex corneal implants that facilitate corneal regeneration may offer a translational strategy for the treatment of corneal damage.
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Affiliation(s)
- Yingni Xu
- School of Materials Science and EngineeringNational Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
| | - Jia Liu
- School of Materials Science and EngineeringNational Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
| | - Wenjing Song
- School of Materials Science and EngineeringNational Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
| | - Qianchun Wang
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325001P. R. China
| | - Xiaomin Sun
- School of Materials Science and EngineeringNational Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
| | - Qi Zhao
- School of Materials Science and EngineeringNational Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
| | - Yongrui Huang
- School of Materials Science and EngineeringNational Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
| | - Haochen Li
- School of Materials Science and EngineeringNational Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
| | - Yuehai Peng
- National Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
- Guangzhou Proud Seeing Biotechnology Co., LtdGuangzhou510320P. R. China
| | - Jin Yuan
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhou510623P. R. China
| | - Baohua Ji
- Institute of Biomechanics and Applications, Department of Engineering MechanicsZhejiang UniversityHangzhou310027P. R. China
| | - Li Ren
- School of Materials Science and EngineeringNational Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Engineering of Guangdong ProvinceKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationInnovation Center for Tissue Restoration and ReconstructionSouth China University of TechnologyGuangzhou510006P. R. China
- Bioland LaboratoryGuangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangzhou510005P. R. China
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18
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Buglak DB, Bougaran P, Kulikauskas MR, Liu Z, Monaghan-Benson E, Gold AL, Marvin AP, Burciu A, Tanke NT, Oatley M, Ricketts SN, Kinghorn K, Johnson BN, Shiau CE, Rogers S, Guilluy C, Bautch VL. Nuclear SUN1 stabilizes endothelial cell junctions via microtubules to regulate blood vessel formation. eLife 2023; 12:83652. [PMID: 36989130 PMCID: PMC10059686 DOI: 10.7554/elife.83652] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Endothelial cells line all blood vessels, where they coordinate blood vessel formation and the blood-tissue barrier via regulation of cell-cell junctions. The nucleus also regulates endothelial cell behaviors, but it is unclear how the nucleus contributes to endothelial cell activities at the cell periphery. Here, we show that the nuclear-localized linker of the nucleoskeleton and cytoskeleton (LINC) complex protein SUN1 regulates vascular sprouting and endothelial cell-cell junction morphology and function. Loss of murine endothelial Sun1 impaired blood vessel formation and destabilized junctions, angiogenic sprouts formed but retracted in SUN1-depleted sprouts, and zebrafish vessels lacking Sun1b had aberrant junctions and defective cell-cell connections. At the cellular level, SUN1 stabilized endothelial cell-cell junctions, promoted junction function, and regulated contractility. Mechanistically, SUN1 depletion altered cell behaviors via the cytoskeleton without changing transcriptional profiles. Reduced peripheral microtubule density, fewer junction contacts, and increased catastrophes accompanied SUN1 loss, and microtubule depolymerization phenocopied effects on junctions. Depletion of GEF-H1, a microtubule-regulated Rho activator, or the LINC complex protein nesprin-1 rescued defective junctions of SUN1-depleted endothelial cells. Thus, endothelial SUN1 regulates peripheral cell-cell junctions from the nucleus via LINC complex-based microtubule interactions that affect peripheral microtubule dynamics and Rho-regulated contractility, and this long-range regulation is important for proper blood vessel sprouting and junction integrity.
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Affiliation(s)
- Danielle B Buglak
- Curriculum in Cell Biology and Physiology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Pauline Bougaran
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Molly R Kulikauskas
- Curriculum in Cell Biology and Physiology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Ziqing Liu
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Elizabeth Monaghan-Benson
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | - Ariel L Gold
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Allison P Marvin
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Andrew Burciu
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Natalie T Tanke
- Curriculum in Cell Biology and Physiology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Morgan Oatley
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Shea N Ricketts
- Department of Pathology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Karina Kinghorn
- Curriculum in Cell Biology and Physiology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Bryan N Johnson
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Celia E Shiau
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Stephen Rogers
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
| | - Christophe Guilluy
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | - Victoria L Bautch
- Curriculum in Cell Biology and Physiology, The University of North Carolina at Chapel HillChapel HillUnited States
- Department of Biology, The University of North Carolina at Chapel HillChapel HillUnited States
- McAllister Heart Institute, The University of North Carolina at Chapel HillChapel HillUnited States
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19
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Sadegh S, Skelton J, Anastasi E, Maier A, Adamowicz K, Möller A, Kriege NM, Kronberg J, Haller T, Kacprowski T, Wipat A, Baumbach J, Blumenthal DB. Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond. Nat Commun 2023; 14:1662. [PMID: 36966134 PMCID: PMC10039912 DOI: 10.1038/s41467-023-37349-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/13/2023] [Indexed: 03/27/2023] Open
Abstract
A long-term objective of network medicine is to replace our current, mainly phenotype-based disease definitions by subtypes of health conditions corresponding to distinct pathomechanisms. For this, molecular and health data are modeled as networks and are mined for pathomechanisms. However, many such studies rely on large-scale disease association data where diseases are annotated using the very phenotype-based disease definitions the network medicine field aims to overcome. This raises the question to which extent the biases mechanistically inadequate disease annotations introduce in disease association data distort the results of studies which use such data for pathomechanism mining. We address this question using global- and local-scale analyses of networks constructed from disease association data of various types. Our results indicate that large-scale disease association data should be used with care for pathomechanism mining and that analyses of such data should be accompanied by close-up analyses of molecular data for well-characterized patient cohorts.
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Affiliation(s)
- Sepideh Sadegh
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - James Skelton
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Elisa Anastasi
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Klaudia Adamowicz
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Anna Möller
- Biomedical Network Science Lab, Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nils M Kriege
- Faculty of Computer Science, University of Vienna, Vienna, Austria
- Research Network Data Science, University of Vienna, Vienna, Austria
| | - Jaanika Kronberg
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Toomas Haller
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - David B Blumenthal
- Biomedical Network Science Lab, Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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20
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Cross-ancestry genome-wide analysis of atrial fibrillation unveils disease biology and enables cardioembolic risk prediction. Nat Genet 2023; 55:187-197. [PMID: 36653681 PMCID: PMC9925380 DOI: 10.1038/s41588-022-01284-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 12/09/2022] [Indexed: 01/20/2023]
Abstract
Atrial fibrillation (AF) is a common cardiac arrhythmia resulting in increased risk of stroke. Despite highly heritable etiology, our understanding of the genetic architecture of AF remains incomplete. Here we performed a genome-wide association study in the Japanese population comprising 9,826 cases among 150,272 individuals and identified East Asian-specific rare variants associated with AF. A cross-ancestry meta-analysis of >1 million individuals, including 77,690 cases, identified 35 new susceptibility loci. Transcriptome-wide association analysis identified IL6R as a putative causal gene, suggesting the involvement of immune responses. Integrative analysis with ChIP-seq data and functional assessment using human induced pluripotent stem cell-derived cardiomyocytes demonstrated ERRg as having a key role in the transcriptional regulation of AF-associated genes. A polygenic risk score derived from the cross-ancestry meta-analysis predicted increased risks of cardiovascular and stroke mortalities and segregated individuals with cardioembolic stroke in undiagnosed AF patients. Our results provide new biological and clinical insights into AF genetics and suggest their potential for clinical applications.
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21
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Santini GT, Shah PP, Karnay A, Jain R. Aberrant chromatin organization at the nexus of laminopathy disease pathways. Nucleus 2022; 13:300-312. [PMID: 36503349 PMCID: PMC9746625 DOI: 10.1080/19491034.2022.2153564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/02/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Garrett T. Santini
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Parisha P. Shah
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Ashley Karnay
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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22
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Generation of a human induced pluripotent stem cell line (JSPHi003-A) from a patient with atrial fibrillation and ventricular tachycardia carrying LMNA frame shift mutation (c.1304_1307dup). Stem Cell Res 2022; 64:102909. [PMID: 36095892 DOI: 10.1016/j.scr.2022.102909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/27/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
The iPSC line was generated from the peripheral blood mononuclear cells (PBMCs) from a 53-year-old female patient carrying the LMNA gene mutation (c.1304_1307dup) diagnosed with atrial fibrillation and paroxysmal ventricular tachycardia. Through comprehensive detection, it was verified that the cell line had the LMNA gene mutation, normal karyotype, and the potential to differentiate into the three germ layers. This cell line may reveal potential therapeutic targets for atrial and ventricular arrhythmias caused by LMNA mutations.
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23
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Jones ML, Dahl KN, Lele TP, Conway DE, Shenoy V, Ghosh S, Szczesny SE. The Elephant in the Cell: Nuclear Mechanics and Mechanobiology. J Biomech Eng 2022; 144:080802. [PMID: 35147160 PMCID: PMC8990742 DOI: 10.1115/1.4053797] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/28/2022] [Indexed: 11/08/2022]
Abstract
The 2021 Summer Biomechanics, Bioengineering, and Biotransport Conference (SB3C) featured a workshop titled "The Elephant in the Room: Nuclear Mechanics and Mechanobiology." The goal of this workshop was to provide a perspective from experts in the field on the current understanding of nuclear mechanics and its role in mechanobiology. This paper reviews the major themes and questions discussed during the workshop, including historical context on the initial methods of measuring the mechanical properties of the nucleus and classifying the primary structures dictating nuclear mechanics, physical plasticity of the nucleus, the emerging role of the linker of nucleoskeleton and cytoskeleton (LINC) complex in coupling the nucleus to the cytoplasm and driving the behavior of individual cells and multicellular assemblies, and the computational models currently in use to investigate the mechanisms of gene expression and cell signaling. Ongoing questions and controversies, along with promising future directions, are also discussed.
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Affiliation(s)
| | - Kris Noel Dahl
- Department of Chemical Engineering, Carnegie Mellon University, Doherty Hall, 5000 Forbes Avenue, Pittsburgh, PA 15213; Forensics Department, Thornton Tomasetti, 120 Broadway 15th Floor, New York City, NY 10271
| | - Tanmay P. Lele
- Department of Biomedical Engineering, Texas A&M University, 101 Bizzell Street, College Station, TX 77840; Department of Chemical Engineering, Texas A&M University, 101 Bizzell Street, College Station, TX 77840; Department of Translational Medical Sciences, Texas A&M University, 101 Bizzell Street, College Station, TX 77840
| | - Daniel E. Conway
- Department of Biomedical Engineering, Virginia Commonwealth University, 601 West Main Street, P.O. Box 843068, Richmond, VA 23284
| | - Vivek Shenoy
- Materials Science and Engineering Bioengineering, University of Pennsylvania, 3231 Walnut Street, Philadelphia, PA 19104; Mechanical Engineering and Applied Mechanics, University of Pennsylvania, 3231 Walnut Street, Philadelphia, PA 19104; Center for Engineering Mechanobiology, University of Pennsylvania, 3231 Walnut Street, Philadelphia, PA 19104
| | - Soham Ghosh
- Department of Mechanical Engineering, School of Biomedical Engineering, Translational Medicine Institute, Colorado State University, 400 Isotope Drive, Fort Collins, CO 80521
| | - Spencer E. Szczesny
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802; Department of Orthopaedics and Rehabilitation, Pennsylvania State University, University Park, PA 16802
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24
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Impact of MnTBAP and Baricitinib Treatment on Hutchinson–Gilford Progeria Fibroblasts. Pharmaceuticals (Basel) 2022; 15:ph15080945. [PMID: 36015093 PMCID: PMC9415676 DOI: 10.3390/ph15080945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/26/2022] [Indexed: 02/06/2023] Open
Abstract
Hutchinson–Gilford progeria syndrome (HGPS) is a rare premature aging disease. It is caused by a mutation in the LMNA gene, which results in a 50-amino-acid truncation of prelamin A. The resultant truncated prelamin A (progerin) lacks the cleavage site for the zinc-metallopeptidase ZMPSTE24. Progerin is permanently farnesylated, carboxymethylated, and strongly anchored to the nuclear envelope. This leads to abnormalities, such as altered nuclear shape, mitochondrial dysfunction, and inflammation. HGPS patients display symptoms of physiological aging, including atherosclerosis, alopecia, lipodystrophy, and arthritis. Currently, no cure for HGPS exists. Here we focus on a drug combination consisting of the superoxide dismutase mimetic MnTBAP and JAK1/2 inhibitor baricitinib (Bar) to restore phenotypic alterations in HGPS fibroblasts. Treating HGPS fibroblasts with the MnTBAP/Bar combination improved mitochondrial functions and sustained Bar’s positive effects on reducing progerin and pro-inflammatory factor levels. Collectively, MnTBAP/Bar combination treatment ameliorates the aberrant phenotype of HGPS fibroblasts and is a potential treatment strategy for patients with HGPS.
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25
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Personalized Medicine Approach in a DCM Patient with LMNA Mutation Reveals Dysregulation of mTOR Signaling. J Pers Med 2022; 12:jpm12071149. [PMID: 35887646 PMCID: PMC9323361 DOI: 10.3390/jpm12071149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Mutations in the Lamin A/C (LMNA) gene are responsible for about 6% of all familial dilated cardiomyopathy (DCM) cases which tend to present at a young age and follow a fulminant course. Methods: We report a 47-year-old DCM patient with severely impaired left ventricular ejection fraction and NYHA functional class IV despite optimal heart failure treatment. Whole-exome sequencing revealed an LMNA E161K missense mutation as the pathogenetic cause for DCM in this patient. We generated a patient-specific LMNA-knock in (LMNA-KI) in vitro model using mES cells. Results: Beta adrenergic stimulation of cardiomyocytes derived from LMNA-KI mES cells resulted in augmented mTOR signaling and increased dysregulation of action potentials, which could be effectively prevented by the mTOR-inhibitor rapamycin. A cardiac biopsy confirmed strong activation of the mTOR-signaling pathway in the patient. An off-label treatment with oral rapamycin was initiated and resulted in an improvement in left ventricular ejection fraction (27.8% to 44.5%), NT-BNP (8120 ng/L to 2210 ng/L) and NYHA functional class. Conclusion: We have successfully generated the first in vitro model to recapitulate a patient-specific LMNA E161K mutation which leads to a severe form of DCM. The model may serve as a template for individualized and specific treatment of heart failure.
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26
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Yunisova G, Ceylaner S, Oflazer P, Deymeer F, Parman YG, Durmus H. Clinical and genetic characteristics of Emery-Dreifuss muscular dystrophy patients from Turkey: 30 years longitudinal follow-up study. Neuromuscul Disord 2022; 32:718-727. [DOI: 10.1016/j.nmd.2022.07.397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 10/17/2022]
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27
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Caruso C, Ligotti ME, Accardi G, Aiello A, Duro G, Galimberti D, Candore G. How Important Are Genes to Achieve Longevity? Int J Mol Sci 2022; 23:5635. [PMID: 35628444 PMCID: PMC9145989 DOI: 10.3390/ijms23105635] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 01/25/2023] Open
Abstract
Several studies on the genetics of longevity have been reviewed in this paper. The results show that, despite efforts and new technologies, only two genes, APOE and FOXO3A, involved in the protection of cardiovascular diseases, have been shown to be associated with longevity in nearly all studies. This happens because the genetic determinants of longevity are dynamic and depend on the environmental history of a given population. In fact, population-specific genes are thought to play a greater role in the attainment of longevity than those shared between different populations. Hence, it is not surprising that GWAS replicated associations of common variants with longevity have been few, if any, as these studies pool together different populations. An alternative way might be the study of long-life families. This type of approach is proving to be an ideal resource for uncovering protective alleles and associated biological signatures for healthy aging phenotypes and exceptional longevity.
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Affiliation(s)
- Calogero Caruso
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, 90133 Palermo, Italy; (M.E.L.); (G.A.); (A.A.); (G.C.)
| | - Mattia Emanuela Ligotti
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, 90133 Palermo, Italy; (M.E.L.); (G.A.); (A.A.); (G.C.)
- Istituto per la Ricerca e l’Innovazione Biomedica, Consiglio Nazionale delle Ricerche, 90146 Palermo, Italy;
| | - Giulia Accardi
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, 90133 Palermo, Italy; (M.E.L.); (G.A.); (A.A.); (G.C.)
| | - Anna Aiello
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, 90133 Palermo, Italy; (M.E.L.); (G.A.); (A.A.); (G.C.)
| | - Giovanni Duro
- Istituto per la Ricerca e l’Innovazione Biomedica, Consiglio Nazionale delle Ricerche, 90146 Palermo, Italy;
| | | | - Giuseppina Candore
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, 90133 Palermo, Italy; (M.E.L.); (G.A.); (A.A.); (G.C.)
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Raman R, Karpova A, Kreutz MR. One-step purification of tag free and soluble lamin B1 from an E. coli bacterial expression system. Protein Expr Purif 2022; 193:106057. [PMID: 35077781 DOI: 10.1016/j.pep.2022.106057] [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: 09/01/2021] [Revised: 12/08/2021] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
Abstract
Lamin B1 is an intermediate filament protein that is a core component of the nuclear lamina. Structural studies and biochemical characterization of lamin B1 are severely hampered by the tendency of the protein to form inclusion bodies in E. coli bacterial expression systems. Therefore, the purity and consistency of the protein varies from batch to batch. In this work, we have purified a tag-free lamin B1 protein from a soluble fraction following bacterial expression. We also checked the functional properties of the purified as well as of the subsequently lyophilised protein. The current protocol helps to purify functional lamin B1 in a single step.
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Affiliation(s)
- Rajeev Raman
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany.
| | - Anna Karpova
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany; Center for Behavioral Brain Sciences, Otto von Guericke University, 39120, Magdeburg, Germany
| | - Michael R Kreutz
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany; Center for Behavioral Brain Sciences, Otto von Guericke University, 39120, Magdeburg, Germany; Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany; German Center for Neurodegenerative Diseases (DZNE), 39120, Magdeburg, Germany
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29
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MDS/AML with del5q: An acquired "laminopathy"? Cell Stem Cell 2022; 29:498-499. [PMID: 35395184 DOI: 10.1016/j.stem.2022.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this issue of Cell Stem Cell, Reilly et al. propose loss of LMNB1, the gene encoding lamin B1, often deleted in MDS/AML, as a novel genetic basis for the abnormal nuclear shape of neutrophils (known as acquired Pelger-Huët anomaly) and a cause of HSPC fate alterations promoting malignancy.
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30
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Abstract
The multilevel organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism and the same hierarchical organization is in action for gene expression, tissue and organ architectures, and ecological systems.The still more common approach to such state of affairs is to think that causally relevant events originate from the lower level in the form of perturbations, that climb up the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such rigid bottom-up causative model is unable to offer realistic models of many biological phenomena.Complex network approach allows to uncover the nature of multilevel organization, but in order to operationally define the organization principles of biological systems, we need to go further and complement network approach with sensible measures of order and organization. These measures, while keeping their original physical meaning, must not impose theoretical premises not verifiable in biological frameworks. We will show here how relatively simple and largely hypothesis-free multidimensional statistics tools can satisfactorily meet these criteria.
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Affiliation(s)
- Mariano Bizzarri
- Istituto Superiore di Sanità AND Sapienza University, Environment and Health Department AND Department of Experimental Medicine, Rome, Italy
| | - Alessandro Giuliani
- Istituto Superiore di Sanità AND Sapienza University, Environment and Health Department AND Department of Experimental Medicine, Rome, Italy.
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Yang J, Argenziano MA, Burgos Angulo M, Bertalovitz A, Beidokhti MN, McDonald TV. Phenotypic Variability in iPSC-Induced Cardiomyocytes and Cardiac Fibroblasts Carrying Diverse LMNA Mutations. Front Physiol 2021; 12:778982. [PMID: 34975533 PMCID: PMC8716763 DOI: 10.3389/fphys.2021.778982] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
Mutations in the LMNA gene (encoding lamin A/C) are a significant cause of familial arrhythmogenic cardiomyopathy. Although the penetrance is high, there is considerable phenotypic variability in disease onset, rate of progression, arrhythmias, and severity of myopathy. To begin to address whether this variability stems from specific LMNA mutation sites and types, we generated seven patient-specific induced pluripotent stem cell (iPSC) lines with various LMNA mutations. IPSC-derived cardiomyocytes (iCMs) and cardiac fibroblasts (iCFs) were differentiated from each line for phenotypic analyses. LMNA expression and extracellular signal-regulated kinase pathway activation were perturbed to differing degrees in both iCMs and iCFs from the different lines. Enhanced apoptosis was observed in iCMs but not in iCFs. Markedly diverse irregularities of nuclear membrane morphology were present in iCFs but not iCMs, while iCMs demonstrated variable sarcomere disarray. Heterogenous electrophysiological aberrations assayed by calcium indicator imaging and multi-electrode array suggest differing substrates for arrhythmia that were accompanied by variable ion channel gene expression in the iCMs. Coculture studies suggest enhancement of the LMNA mutation effects on electrophysiological function exerted by iCFs. This study supports the utility of patient-specific iPSC experimental platform in the exploration of mechanistic and phenotypic heterogeneity of different mutations within a cardiac disease-associated gene. The addition of genetically defined coculture of cardiac-constituent non-myocytes further expands the capabilities of this approach.
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Affiliation(s)
- Jiajia Yang
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Mariana A. Argenziano
- Heart Institute, Department of Medicine (Division of Cardiovascular Sciences), Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Mariana Burgos Angulo
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Alexander Bertalovitz
- Heart Institute, Department of Medicine (Division of Cardiovascular Sciences), Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Maliheh Najari Beidokhti
- Heart Institute, Department of Medicine (Division of Cardiovascular Sciences), Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Thomas V. McDonald
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Heart Institute, Department of Medicine (Division of Cardiovascular Sciences), Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- *Correspondence: Thomas V. McDonald,
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Galal MA, Abdel Jabar M, Zhra M, Abdel Rahman AM, Aljada A. Absolute quantification of senescence mediators in cells using multiple reaction monitoring liquid chromatography-Tandem mass spectrometry. Anal Chim Acta 2021; 1184:339009. [PMID: 34625254 DOI: 10.1016/j.aca.2021.339009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The identification of unique senescence markers remains challenging. Current hallmarks of senescent cells, including increased senescence-associated β-galactosidase activity, increased levels of cell cycle regulators such as p16INK4a, p27, and p53, and altered levels of sirtuins and lamins, are detected commonly by Western blot and immunohistochemistry methods. Mass spectrometry outperforms these conventional quantification methods in terms of high throughput, specificity, and reproducibility. OBJECTIVES To develop multiple reaction monitoring-based tandem mass spectrometric senescence assay for simultaneous measuring of p16INK4a, p27, p53, p53-β, the seven proteins of the sirtuins family and the four transcript variants of lamins proteins in aging cell model and cancerous cell lines. METHODOLOGY Multiple reaction monitoring-tandem mass transitions per protein were developed for each signature peptide(s) and stable isotope-labeled internal standard. The developed assay was validated in a matrix using breast cancer MCF7 cell lines according to the US-FDA guidelines for bioanalytical assays. RESULTS The analytes chromatographic peaks were baseline separated and showed linear behavior in a wide dynamic range with r2 ≥ 0.98. The method for all proteins has passed the inter/intra-day precision and accuracy validation using three levels of quality control samples. The accuracy and the precision for most analytes were 80-120% and ≤20%, respectively. The method's sensitivity for the panels' signature peptides ranged from 1 ng μL-1 to 1 μg mL-1. Extraction recovery assessed in two quality control levels was >60% for most analytes. This LC-MS-MS validated senescence assay showed reduced lamin A, lamin A△10, lamin A△50, SIRT1, SIRT3, SIRT5, p53, and p16INK4a, as well as p53-β induction, are implicated in replicative senescence. Meanwhile, increased lamin C: lamin A ratio was evident and can diagnose breast carcinogenesis. Moreover, in breast cancer metastasis, reduced SIRT2 and p27 and elevated levels of lamin A△50, SIRT5, SIRT7, and p53-β are evident. CONCLUSION LC-MS/MS is a potent alternative tool to the currently available assays. The high throughput method established can study senescence's role in different pathophysiological processes.
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Affiliation(s)
- Mariam Ahmed Galal
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia
| | - Mai Abdel Jabar
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Riyadh, 11211, Saudi Arabia
| | - Mahmoud Zhra
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia
| | - Anas M Abdel Rahman
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia; Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Riyadh, 11211, Saudi Arabia.
| | - Ahmad Aljada
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
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Rajeev M, Ratan C, Krishnan K, Vijayan M. Hutchinson-Gilford Progeria Syndrome (Hgps) And Application Of Gene Therapy Based Crispr/Cas Technology As A Promising Innovative Treatment Approach. Recent Pat Biotechnol 2021; 15:266-285. [PMID: 34602042 DOI: 10.2174/1872208315666210928114720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hutchinson-Gilford progeria syndrome (HGPS) also known as progeria of childhood or progeria is a rare, rapid, autosomal dominant genetic disorder characterized by premature aging which occurs shortly after birth. HGPS occurs as a result of de novo point mutation in the gene recognized as LMNA gene that encodes two proteins Lamin A protein and Lamin C protein which are the structural components of the nuclear envelope. Mutations in the gene trigger abnormal splicing and induce internal deletion of 50 amino acids leading to the development of a truncated form of Lamin A protein known as Progerin. Progerin generation can be considered as the crucial step in HGPS since the protein is highly toxic to human cells, permanently farnesylated, and exhibits variation in several biochemical and structural properties within the individual. HGPS also produces complications such as skin alterations, growth failure, atherosclerosis, hair and fat loss, and bone and joint diseases. We have also revised all relevant patents relating to Hutchinson-gilford progeria syndrome and its therapy in the current article. METHOD The goal of the present review article is to provide information about Hutchinson-Gilford progeria syndrome (HGPS) and the use of CRISPR/Cas technology as a promising treatment approach in the treatment of the disease. The review also discusses about different pharmacological and non-pharmacological methods of treatment currently used for HGPS. RESULTS The main limitation associated with progeria is the lack of a definitive cure. The existing treatment modality provides only symptomatic relief. Therefore, it is high time to develop a therapeutic method that hastens premature aging in such patients. CONCLUSION CRISPR/Cas technology is a novel gene-editing tool that allows genome editing at specific loci, and is found to be a promising therapeutic approach for the treatment of genetic disorders such as HGPS where dominant-negative mutations take place.
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Affiliation(s)
- Mekha Rajeev
- Amrita School of Pharmacy, Amrita Vihwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P. O., Kochi, Kerala 682041. India
| | - Chameli Ratan
- Amrita School of Pharmacy, Amrita Vihwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P. O., Kochi, Kerala 682041. India
| | - Karthik Krishnan
- Amrita School of Pharmacy, Amrita Vihwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P. O., Kochi, Kerala 682041. India
| | - Meenu Vijayan
- Amrita School of Pharmacy, Amrita Vihwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P. O., Kochi, Kerala 682041. India
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Dong A, Cheung TH. Deciphering the chromatin organization and dynamics for muscle stem cell function. Curr Opin Cell Biol 2021; 73:124-132. [PMID: 34534837 DOI: 10.1016/j.ceb.2021.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 12/28/2022]
Abstract
The chromatin landscape represents a critical regulatory layer for precise transcriptional control. Chromosome architecture restrains the physical access to the DNA elements and is one of the determinants that specifies cell identity. Adult stem cells possess the unique ability to differentiate into a specific lineage. One of the underexplored areas in skeletal muscle biology is the molecular mechanism guiding the chromatin organization changes in muscle stem cell specification, myogenic determination, and differentiation. In this review, we focus on the regulatory network guiding the progression of muscle stem cells to differentiated progeny. We summarize recent findings regarding the mechanisms directing myogenic cell fate decision and differentiation, with a particular focus on three-dimensional chromosome architecture and long noncoding RNA-associated chromatin accessibility changes.
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Affiliation(s)
- Anqi Dong
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Tom H Cheung
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China; Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China.
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Nishikawa T, Kuwano Y, Nakata M, Rokutan K, Nishida K. Multiple G-quadruplexes in the LMNA promoter regulate LMNA variant 6 transcription and promote colon cancer cell growth. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194746. [PMID: 34419630 DOI: 10.1016/j.bbagrm.2021.194746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
Lamin A/C proteins, major components of the nuclear lamina, are encoded by the LMNA gene. These proteins have multiple cellular functions, including DNA transcription and replication, chromatin organization, regulation of the cell cycle, and apoptosis. Mutations in LMNA are associated with a variety of diseases called laminopathies. LMNA has implications in cancer; however, its mechanisms of dysregulation in cancer cells are not yet fully understood. In this study, among the LMNA transcript variants, we focused on a transcriptional variant 6 (termed LMNA-V6), which contains unique 3 exons upstream of exon 1 of LMNA. The promoter region of LMNA-V6 formed multiple G-quadruplexes and increased its transcriptional activity. Moreover, LMNA-V6 negatively regulated other LMNA mRNA variants, lamin A and lamin C, via direct interaction with their promoter. Knockdown of LMNA-V6 decreased the proliferation of colon cancer cells, whereas overexpression of the unique 3 exons of LMNA-V6 increased cell growth. Furthermore, microarray gene expression profiling showed that alteration of LMNA-V6 levels influenced the expression of p53 in colon cancer cells. Taken together, the results suggest that LMNA-V6 may be a novel functional RNA whose expression is regulated through multiple G-quadruplexes in colon cancer cells.
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Affiliation(s)
- Tatsuya Nishikawa
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan; Department of Onco-cardiology, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan.
| | - Mayu Nakata
- Student Lab, Tokushima University Faculty of Medicine, Tokushima, Japan
| | - Kazuhito Rokutan
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Kensei Nishida
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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Shemer Y, Mekies LN, Ben Jehuda R, Baskin P, Shulman R, Eisen B, Regev D, Arbustini E, Gerull B, Gherghiceanu M, Gottlieb E, Arad M, Binah O. Investigating LMNA-Related Dilated Cardiomyopathy Using Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Int J Mol Sci 2021; 22:ijms22157874. [PMID: 34360639 PMCID: PMC8346174 DOI: 10.3390/ijms22157874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/09/2023] Open
Abstract
LMNA-related dilated cardiomyopathy is an inherited heart disease caused by mutations in the LMNA gene encoding for lamin A/C. The disease is characterized by left ventricular enlargement and impaired systolic function associated with conduction defects and ventricular arrhythmias. We hypothesized that LMNA-mutated patients' induced Pluripotent Stem Cell-derived cardiomyocytes (iPSC-CMs) display electrophysiological abnormalities, thus constituting a suitable tool for deciphering the arrhythmogenic mechanisms of the disease, and possibly for developing novel therapeutic modalities. iPSC-CMs were generated from two related patients (father and son) carrying the same E342K mutation in the LMNA gene. Compared to control iPSC-CMs, LMNA-mutated iPSC-CMs exhibited the following electrophysiological abnormalities: (1) decreased spontaneous action potential beat rate and decreased pacemaker current (If) density; (2) prolonged action potential duration and increased L-type Ca2+ current (ICa,L) density; (3) delayed afterdepolarizations (DADs), arrhythmias and increased beat rate variability; (4) DADs, arrhythmias and cessation of spontaneous firing in response to β-adrenergic stimulation and rapid pacing. Additionally, compared to healthy control, LMNA-mutated iPSC-CMs displayed nuclear morphological irregularities and gene expression alterations. Notably, KB-R7943, a selective inhibitor of the reverse-mode of the Na+/Ca2+ exchanger, blocked the DADs in LMNA-mutated iPSC-CMs. Our findings demonstrate cellular electrophysiological mechanisms underlying the arrhythmias in LMNA-related dilated cardiomyopathy.
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Affiliation(s)
- Yuval Shemer
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Rappaport Research Institute, Technion—Israel Institute of Technology, Haifa 31096, Israel; (Y.S.); (L.N.M.); (R.B.J.); (P.B.); (R.S.); (B.E.); (D.R.)
| | - Lucy N. Mekies
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Rappaport Research Institute, Technion—Israel Institute of Technology, Haifa 31096, Israel; (Y.S.); (L.N.M.); (R.B.J.); (P.B.); (R.S.); (B.E.); (D.R.)
| | - Ronen Ben Jehuda
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Rappaport Research Institute, Technion—Israel Institute of Technology, Haifa 31096, Israel; (Y.S.); (L.N.M.); (R.B.J.); (P.B.); (R.S.); (B.E.); (D.R.)
- Department of Biotechnology, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Polina Baskin
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Rappaport Research Institute, Technion—Israel Institute of Technology, Haifa 31096, Israel; (Y.S.); (L.N.M.); (R.B.J.); (P.B.); (R.S.); (B.E.); (D.R.)
| | - Rita Shulman
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Rappaport Research Institute, Technion—Israel Institute of Technology, Haifa 31096, Israel; (Y.S.); (L.N.M.); (R.B.J.); (P.B.); (R.S.); (B.E.); (D.R.)
| | - Binyamin Eisen
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Rappaport Research Institute, Technion—Israel Institute of Technology, Haifa 31096, Israel; (Y.S.); (L.N.M.); (R.B.J.); (P.B.); (R.S.); (B.E.); (D.R.)
| | - Danielle Regev
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Rappaport Research Institute, Technion—Israel Institute of Technology, Haifa 31096, Israel; (Y.S.); (L.N.M.); (R.B.J.); (P.B.); (R.S.); (B.E.); (D.R.)
| | - Eloisa Arbustini
- Centre for Inherited Cardiovascular Diseases, IRCCS Foundation, Policlinico San Matteo, 27100 Pavia, Italy;
| | - Brenda Gerull
- Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, 97080 Würzburg, Germany;
| | | | - Eyal Gottlieb
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion—Israel Institute of Technology, Haifa 31096, Israel;
| | - Michael Arad
- Leviev Heart Center, Sheba Medical Center, Ramat Gan 52621, Israel;
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ofer Binah
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Rappaport Research Institute, Technion—Israel Institute of Technology, Haifa 31096, Israel; (Y.S.); (L.N.M.); (R.B.J.); (P.B.); (R.S.); (B.E.); (D.R.)
- Correspondence: ; Tel.: +972-4-8295262; Fax: +972-4-8513919
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Nuclear Organization during Hepatogenesis in Zebrafish Requires Uhrf1. Genes (Basel) 2021; 12:genes12071081. [PMID: 34356097 PMCID: PMC8304062 DOI: 10.3390/genes12071081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 01/07/2023] Open
Abstract
Acquisition of cellular fate during development is initiated and maintained by well-coordinated patterns of gene expression that are dictated by the epigenetic landscape and genome organization in the nucleus. While the epigenetic marks that mediate developmental gene expression patterns during organogenesis have been well studied, less is known about how epigenetic marks influence nuclear organization during development. This study examines the relationship between nuclear structure, chromatin accessibility, DNA methylation, and gene expression during hepatic outgrowth in zebrafish larvae. We investigate the relationship between these features using mutants that lack DNA methylation. Hepatocyte nuclear morphology was established coincident with hepatocyte differentiation at 80 h post-fertilization (hpf), and nuclear shape and size continued to change until the conclusion of outgrowth and morphogenesis at 120 hpf. Integrating ATAC-Seq analysis with DNA methylation profiling of zebrafish livers at 120 hpf showed that closed and highly methylated chromatin occupies most transposable elements and that open chromatin correlated with gene expression. DNA hypomethylation, due to mutation of genes encoding ubiquitin-like, containing PHD and RING Finger Domains 1 (uhrf1) and DNA methyltransferase (dnmt1), did not block hepatocyte differentiation, but had dramatic effects on nuclear organization. Hepatocytes in uhrf1 mutants have large, deformed nuclei with multiple nucleoli, downregulation of nucleolar genes, and a complete lack of the nuclear lamina. Loss of lamin B2 staining was phenocopied by dnmt1 mutation. Together, these data show that hepatocyte nuclear morphogenesis coincides with organ morphogenesis and outgrowth, and that DNA methylation directs chromatin organization, and, in turn, hepatocyte nuclear shape and size during liver development.
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Arnold R, Vehns E, Randl H, Djabali K. Baricitinib, a JAK-STAT Inhibitor, Reduces the Cellular Toxicity of the Farnesyltransferase Inhibitor Lonafarnib in Progeria Cells. Int J Mol Sci 2021; 22:ijms22147474. [PMID: 34299092 PMCID: PMC8307450 DOI: 10.3390/ijms22147474] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/25/2022] Open
Abstract
Hutchinson–Gilford progeria syndrome (HGPS) is an ultra-rare multisystem premature aging disorder that leads to early death (mean age of 14.7 years) due to myocardial infarction or stroke. Most cases have a de novo point mutation at position G608G within exon 11 of the LMNA gene. This mutation leads to the production of a permanently farnesylated truncated prelamin A protein called “progerin” that is toxic to the cells. Recently, farnesyltransferase inhibitor (FTI) lonafarnib has been approved by the FDA for the treatment of patients with HGPS. While lonafarnib treatment irrefutably ameliorates HGPS disease, it is however not a cure. FTI has been shown to cause several cellular side effects, including genomic instability as well as binucleated and donut-shaped nuclei. We report that, in addition to these cellular stresses, FTI caused an increased frequency of cytosolic DNA fragment formation. These extranuclear DNA fragments colocalized with cGAs and activated the cGAS-STING-STAT1 signaling axis, upregulating the expression of proinflammatory cytokines in FTI-treated human HGPS fibroblasts. Treatment with lonafarnib and baricitinib, a JAK-STAT inhibitor, not only prevented the activation of the cGAS STING-STAT1 pathway, but also improved the overall HGPS cellular homeostasis. These ameliorations included progerin levels, nuclear shape, proteostasis, cellular ATP, proliferation, and the reduction of cellular inflammation and senescence. Thus, we suggest that combining lonafarnib with baricitinib might provide an opportunity to reduce FTI cellular toxicity and ameliorate HGPS symptoms further than lonafarnib alone.
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Affiliation(s)
- Rouven Arnold
- Epigenetics of Aging, Department of Dermatology and Allergy, TUM School of Medicine, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Elena Vehns
- Epigenetics of Aging, Department of Dermatology and Allergy, TUM School of Medicine, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Hannah Randl
- Epigenetics of Aging, Department of Dermatology and Allergy, TUM School of Medicine, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Karima Djabali
- Epigenetics of Aging, Department of Dermatology and Allergy, TUM School of Medicine, Technical University of Munich (TUM), 85748 Garching, Germany
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Kychygina A, Dall'Osto M, Allen JAM, Cadoret JC, Piras V, Pickett HA, Crabbe L. Progerin impairs 3D genome organization and induces fragile telomeres by limiting the dNTP pools. Sci Rep 2021; 11:13195. [PMID: 34162976 PMCID: PMC8222272 DOI: 10.1038/s41598-021-92631-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/11/2021] [Indexed: 11/09/2022] Open
Abstract
Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity. A key player in this spatial scattering of chromosomes is the nuclear envelope (NE). The NE tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins. This organization is perturbed in cells from Hutchinson–Gilford progeria syndrome (HGPS), a genetic disorder characterized by premature aging features. Here, we show that HGPS-related lamina defects trigger an altered 3D telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state. The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late. As a consequence, we detected a higher density of replication forks traveling simultaneously on DNA fibers, which relies on limiting cellular dNTP pools to support processive DNA synthesis. Remarkably, increasing dNTP levels in HGPS cells rescued fragile telomeres, and improved the replicative capacity of the cells. Our work highlights a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.
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Affiliation(s)
- Anna Kychygina
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.,INSERM UMR1291, CNRS UMR5051, UT3, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), 31059, Toulouse, France
| | - Marina Dall'Osto
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | - Vincent Piras
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.
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Yadahalli R, Kheur S, Adwani A, Bhonde R, Raj AT, Patil S. Nuclear Blebbing Frequency in Tobacco-Induced Oral Potentially Malignant Disorders: A Pilot Study. Acta Cytol 2021; 65:403-410. [PMID: 34120116 DOI: 10.1159/000516496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/10/2021] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Tobacco contains several genotoxic agents including N-nitrosamine which has the potential to cause significant nuclear damage. Nuclear blebbing is a form of protrusion on the nuclear membrane and could potentially be caused by tobacco-induced genotoxicity and is closely associated with malignancy. Thus, the present study aimed to assess if tobacco-associated oral potentially malignant disorders including oral submucous fibrosis (OSF) and oral leukoplakia have a higher nuclear blebbing frequency than patients with normal oral mucosa with no history of tobacco use. METHODS The sample consisted of patients with OSF (n = 30) and oral leukoplakia (n = 10) and normal oral mucosa (n = 10). Exfoliated cells collected from the study groups were smeared on a clean microscopic slide and stained by May-Grunwald-Giemsa stain. A baseline frequency of nuclear blebbing was evaluated using a bright-field microscope with a ×100 objective. The number of nuclear blebbing per 1,000 epithelial cells was recorded and expressed in percentage. ANOVA, the Mann-Whitney U test, and Spearman's correlation were used to analyze the data. RESULTS The mean rank of distribution of nuclear blebbing showed significant difference between all 3 groups, with the highest frequency noted in leukoplakia, followed by oral submucous and normal oral mucosa. Within OSF, the frequency of nuclear blebbing significantly increased from early stage to advanced stage. In OSF, a statistically significant positive linear correlation was noted between duration (in years), frequency (per day) of tobacco use, clinical grading, and nuclear blebbing. DISCUSSION/CONCLUSIONS The frequency of nuclear blebbing was significantly higher in oral potentially malignant disorders than normal mucosa. Nuclear blebbing also exhibited a strong dose- and time-dependent correlation with tobacco usage and clinical staging in OSF. The nuclear blebbing frequency could be a noninvasive, economic tool to assess malignant risk in tobacco-induced oral potentially malignant disorders.
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Affiliation(s)
- Roopa Yadahalli
- Department of Oral Pathology and Microbiology, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, India
| | - Supriya Kheur
- Department of Oral Pathology and Microbiology, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, India
| | - Aanchal Adwani
- Department of Oral Pathology and Microbiology, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, India
| | - Ramesh Bhonde
- Department of Oral Pathology and Microbiology, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, India
| | - A Thirumal Raj
- Department of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai, India
| | - Shankargouda Patil
- Division of Oral Pathology College of Dentistry, Department of Maxillofacial Surgery and Diagnostic Sciences, Jazan University, Jazan, Saudi Arabia
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A targeted antisense therapeutic approach for Hutchinson-Gilford progeria syndrome. Nat Med 2021; 27:536-545. [PMID: 33707773 PMCID: PMC10158310 DOI: 10.1038/s41591-021-01274-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare accelerated aging disorder characterized by premature death from myocardial infarction or stroke. It is caused by de novo single-nucleotide mutations in the LMNA gene that activate a cryptic splice donor site, resulting in the production of a toxic form of lamin A, which is termed progerin. Here we present a potential genetic therapeutic strategy that utilizes antisense peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs) to block pathogenic splicing of mutant transcripts. Of several candidates, PPMO SRP-2001 provided the most significant decrease in progerin transcripts in patient fibroblasts. Intravenous delivery of SRP-2001 to a transgenic mouse model of HGPS produced significant reduction of progerin transcripts in the aorta, a particularly critical target tissue in HGPS. Long-term continuous treatment with SRP-2001 yielded a 61.6% increase in lifespan and rescue of vascular smooth muscle cell loss in large arteries. These results provide a rationale for proceeding to human trials.
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Muscle Enriched Lamin Interacting Protein ( Mlip) Binds Chromatin and Is Required for Myoblast Differentiation. Cells 2021; 10:cells10030615. [PMID: 33802236 PMCID: PMC7998221 DOI: 10.3390/cells10030615] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 11/20/2022] Open
Abstract
Muscle-enriched A-type lamin-interacting protein (Mlip) is a recently discovered Amniota gene that encodes proteins of unknown biological function. Here we report Mlip’s direct interaction with chromatin, and it may function as a transcriptional co-factor. Chromatin immunoprecipitations with microarray analysis demonstrated a propensity for Mlip to associate with genomic regions in close proximity to genes that control tissue-specific differentiation. Gel mobility shift assays confirmed that Mlip protein complexes with genomic DNA. Blocking Mlip expression in C2C12 myoblasts down-regulates myogenic regulatory factors (MyoD and MyoG) and subsequently significantly inhibits myogenic differentiation and the formation of myotubes. Collectively our data demonstrate that Mlip is required for C2C12 myoblast differentiation into myotubes. Mlip may exert this role as a transcriptional regulator of a myogenic program that is unique to amniotes.
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Ding B, Tang Y, Ma S, Akter M, Liu ML, Zang T, Zhang CL. Disease Modeling with Human Neurons Reveals LMNB1 Dysregulation Underlying DYT1 Dystonia. J Neurosci 2021; 41:2024-2038. [PMID: 33468570 PMCID: PMC7939088 DOI: 10.1523/jneurosci.2507-20.2020] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 02/08/2023] Open
Abstract
DYT1 dystonia is a hereditary neurologic movement disorder characterized by uncontrollable muscle contractions. It is caused by a heterozygous mutation in Torsin A (TOR1A), a gene encoding a membrane-embedded ATPase. While animal models provide insights into disease mechanisms, significant species-dependent differences exist since animals with the identical heterozygous mutation fail to show pathology. Here, we model DYT1 by using human patient-specific cholinergic motor neurons (MNs) that are generated through either direct conversion of patients' skin fibroblasts or differentiation of induced pluripotent stem cells (iPSCs). These human MNs with the heterozygous TOR1A mutation show reduced neurite length and branches, markedly thickened nuclear lamina, disrupted nuclear morphology, and impaired nucleocytoplasmic transport (NCT) of mRNAs and proteins, whereas they lack the perinuclear "blebs" that are often observed in animal models. Furthermore, we uncover that the nuclear lamina protein LMNB1 is upregulated in DYT1 cells and exhibits abnormal subcellular distribution in a cholinergic MNs-specific manner. Such dysregulation of LMNB1 can be recapitulated by either ectopic expression of the mutant TOR1A gene or shRNA-mediated downregulation of endogenous TOR1A in healthy control MNs. Interestingly, downregulation of LMNB1 can largely ameliorate all the cellular defects in DYT1 MNs. These results reveal the value of disease modeling with human patient-specific neurons and indicate that dysregulation of LMNB1, a crucial component of the nuclear lamina, may constitute a major molecular mechanism underlying DYT1 pathology.SIGNIFICANCE STATEMENT Inaccessibility to patient neurons greatly impedes our understanding of the pathologic mechanisms for dystonia. In this study, we employ reprogrammed human patient-specific motor neurons (MNs) to model DYT1, the most severe hereditary form of dystonia. Our results reveal disease-dependent deficits in nuclear morphology and nucleocytoplasmic transport (NCT). Most importantly, we further identify LMNB1 dysregulation as a major contributor to these deficits, uncovering a new pathologic mechanism for DYT1 dystonia.
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Affiliation(s)
- Baojin Ding
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70503
| | - Yu Tang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, China
| | - Shuaipeng Ma
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Masuma Akter
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70503
| | - Meng-Lu Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Tong Zang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Chun-Li Zhang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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The flavonoid morin alleviates nuclear deformation in aged cells by disrupting progerin-lamin A/C binding. J Funct Foods 2021. [DOI: 10.1016/j.jff.2020.104331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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45
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Koblan LW, Erdos MR, Wilson C, Cabral WA, Levy JM, Xiong ZM, Tavarez UL, Davison LM, Gete YG, Mao X, Newby GA, Doherty SP, Narisu N, Sheng Q, Krilow C, Lin CY, Gordon LB, Cao K, Collins FS, Brown JD, Liu DR. In vivo base editing rescues Hutchinson-Gilford progeria syndrome in mice. Nature 2021; 589:608-614. [PMID: 33408413 PMCID: PMC7872200 DOI: 10.1038/s41586-020-03086-7] [Citation(s) in RCA: 251] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS or progeria) is typically caused by a dominant-negative C•G-to-T•A mutation (c.1824 C>T; p.G608G) in LMNA, the gene that encodes nuclear lamin A. This mutation causes RNA mis-splicing that produces progerin, a toxic protein that induces rapid ageing and shortens the lifespan of children with progeria to approximately 14 years1-4. Adenine base editors (ABEs) convert targeted A•T base pairs to G•C base pairs with minimal by-products and without requiring double-strand DNA breaks or donor DNA templates5,6. Here we describe the use of an ABE to directly correct the pathogenic HGPS mutation in cultured fibroblasts derived from children with progeria and in a mouse model of HGPS. Lentiviral delivery of the ABE to fibroblasts from children with HGPS resulted in 87-91% correction of the pathogenic allele, mitigation of RNA mis-splicing, reduced levels of progerin and correction of nuclear abnormalities. Unbiased off-target DNA and RNA editing analysis did not detect off-target editing in treated patient-derived fibroblasts. In transgenic mice that are homozygous for the human LMNA c.1824 C>T allele, a single retro-orbital injection of adeno-associated virus 9 (AAV9) encoding the ABE resulted in substantial, durable correction of the pathogenic mutation (around 20-60% across various organs six months after injection), restoration of normal RNA splicing and reduction of progerin protein levels. In vivo base editing rescued the vascular pathology of the mice, preserving vascular smooth muscle cell counts and preventing adventitial fibrosis. A single injection of ABE-expressing AAV9 at postnatal day 14 improved vitality and greatly extended the median lifespan of the mice from 215 to 510 days. These findings demonstrate the potential of in vivo base editing as a possible treatment for HGPS and other genetic diseases by directly correcting their root cause.
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Affiliation(s)
- Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Wilson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Wayne A Cabral
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan M Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Zheng-Mei Xiong
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Urraca L Tavarez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lindsay M Davison
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yantenew G Gete
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Xiaojing Mao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Sean P Doherty
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chad Krilow
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Therapeutic Innovation Center, Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Kronos, Bio Inc., Cambridge, MA, USA
| | - Leslie B Gordon
- Hasbro Children's Hospital, Alpert Medical School of Brown University, Providence, RI, USA
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kan Cao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Jonathan D Brown
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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Abstract
Nuclear lamins form an elastic meshwork underlying the inner nuclear membrane and provide mechanical rigidity to the nucleus and maintain shape. Lamins also maintain chromosome positioning and play important roles in several nuclear processes like replication, DNA damage repair, transcription, and epigenetic modifications. LMNA mutations affect cardiac tissue, muscle tissues, adipose tissues to precipitate several diseases collectively termed as laminopathies. However, the rationale behind LMNA mutations and laminopathies continues to elude scientists. During interphase, several chromosomes form inter/intrachromosomal contacts inside nucleoplasm and several chromosomal loops also stretch out to make a ‘loop-cluster’ which are key players to regulate gene expressions. In this perspective, we have proposed that the lamin network in tandem with nuclear actin and myosin provide mechanical rigidity to the chromosomal contacts and facilitate loop-clusters movements. LMNA mutations thus might perturb the landscape of chromosomal contacts or loop-clusters positioning which can impair gene expression profile.
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Affiliation(s)
- Manindra Bera
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics , Kolkata, India.,Department of Cell Biology, Yale University School of Medicine , Connecticut, New Haven, USA
| | - Kaushik Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics , Kolkata, India.,Homi Bhabha National Institute , Mumbai, India
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47
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Babatz TD, Spear ED, Xu W, Sun OL, Nie L, Carpenter EP, Michaelis S. Site specificity determinants for prelamin A cleavage by the zinc metalloprotease ZMPSTE24. J Biol Chem 2020; 296:100165. [PMID: 33293369 PMCID: PMC7948416 DOI: 10.1074/jbc.ra120.015792] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/23/2020] [Accepted: 12/08/2020] [Indexed: 01/11/2023] Open
Abstract
The integral membrane zinc metalloprotease ZMPSTE24 is important for human health and longevity. ZMPSTE24 performs a key proteolytic step in maturation of prelamin A, the farnesylated precursor of the nuclear scaffold protein lamin A. Mutations in the genes encoding either prelamin A or ZMPSTE24 that prevent cleavage cause the premature aging disease Hutchinson–Gilford progeria syndrome (HGPS) and related progeroid disorders. ZMPSTE24 has a novel structure, with seven transmembrane spans that form a large water-filled membrane chamber whose catalytic site faces the chamber interior. Prelamin A is the only known mammalian substrate for ZMPSTE24; however, the basis of this specificity remains unclear. To define the sequence requirements for ZMPSTE24 cleavage, we mutagenized the eight residues flanking the prelamin A scissile bond (TRSY↓LLGN) to all other 19 amino acids, creating a library of 152 variants. We also replaced these eight residues with sequences derived from putative ZMPSTE24 cleavage sites from amphibian, bird, and fish prelamin A. Cleavage of prelamin A variants was assessed using an in vivo yeast assay that provides a sensitive measure of ZMPSTE24 processing efficiency. We found that residues on the C-terminal side of the cleavage site are most sensitive to changes. Consistent with other zinc metalloproteases, including thermolysin, ZMPSTE24 preferred hydrophobic residues at the P1’ position (Leu647), but in addition, showed a similar, albeit muted, pattern at P2’. Our findings begin to define a consensus sequence for ZMPSTE24 that helps to clarify how this physiologically important protease functions and may ultimately lead to identifying additional substrates.
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Affiliation(s)
- Timothy D Babatz
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA
| | - Eric D Spear
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA
| | - Wenxin Xu
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA
| | - Olivia L Sun
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA
| | - Laiyin Nie
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA.
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48
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Rashidi N, Pant AD, Salinas SD, Shah M, Thomas VS, Zhang G, Dorairaj S, Amini R. Iris stromal cell nuclei deform to more elongated shapes during pharmacologically-induced miosis and mydriasis. Exp Eye Res 2020; 202:108373. [PMID: 33253707 DOI: 10.1016/j.exer.2020.108373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/01/2020] [Accepted: 11/24/2020] [Indexed: 01/03/2023]
Abstract
Nuclear shape alteration in ocular tissues, which can be used as a metric for overall cell deformation, may also lead to changes in gene expression and protein synthesis that could affect the biomechanics of the tissue extracellular matrix. The biomechanics of iris tissue is of particular interest in the study of primary angle-closure glaucoma. As the first step towards understanding the mutual role of the biomechanics and deformation of the iris on the activity of its constituent stromal cells, we conducted an ex-vivo study in freshly excised porcine eyes. Iris deformation was achieved by activating the constituent smooth muscles of the iris. Pupillary responses were initiated by inducing miosis and mydriasis, and the irides were placed in a fixative, bisected, and sliced into thin sections in a nasal and temporal horizontal orientation. The tissue sections were stained with DAPI for nucleus, and z-stacks were acquired using confocal microscopy. Images were analyzed to determine the nuclear aspect ratio (NAR) using both three-dimensional (3D) reconstructions of the nuclear surfaces as well as projections of the same 3D reconstruction into flat two-dimensional (2D) shapes. We observed that regardless of the calculation method (i.e., one that employed 3D surface reconstructions versus one that employed 2D projected images) the NAR increased in both the miosis group and the mydriasis group. Three-dimensional quantifications showed that NAR increased from 2.52 ± 0.96 in control group to 2.80 ± 0.81 and 2.74 ± 0.94 in the mydriasis and miosis groups, respectively. Notwithstanding the relative convenience in calculating the NAR using the 2D projected images, the 3D reconstructions were found to generate more physiologically realistic values and, thus, can be used in the development of future computational models to study primary angle-closure glaucoma. Since the iris undergoes large deformations in response to ambient light, this study suggests that the iris stromal cells are subjected to a biomechanically active micro-environment during their in-vivo physiological function.
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Affiliation(s)
- Neda Rashidi
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA; Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anup D Pant
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA; Department of Engineering, East Carolina University, Greenville, NC, 27858, USA
| | - Samuel D Salinas
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA; Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Mickey Shah
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Vineet S Thomas
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Ge Zhang
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Syril Dorairaj
- Department of Ophthalmology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rouzbeh Amini
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA; Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA; Department of Mechanical and Industrial Engineering, Northeastern University, 334 Snell Engineering, 360 Huntington Ave., Boston, MA, 02115, USA.
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49
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Wang F, Zhang W, Yang Q, Kang Y, Fan Y, Wei J, Liu Z, Dai S, Li H, Li Z, Xu L, Chu C, Qu J, Si C, Ji W, Liu GH, Long C, Niu Y. Generation of a Hutchinson-Gilford progeria syndrome monkey model by base editing. Protein Cell 2020; 11:809-824. [PMID: 32729022 PMCID: PMC7647984 DOI: 10.1007/s13238-020-00740-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
Abstract
Many human genetic diseases, including Hutchinson-Gilford progeria syndrome (HGPS), are caused by single point mutations. HGPS is a rare disorder that causes premature aging and is usually caused by a de novo point mutation in the LMNA gene. Base editors (BEs) composed of a cytidine deaminase fused to CRISPR/Cas9 nickase are highly efficient at inducing C to T base conversions in a programmable manner and can be used to generate animal disease models with single amino-acid substitutions. Here, we generated the first HGPS monkey model by delivering a BE mRNA and guide RNA (gRNA) targeting the LMNA gene via microinjection into monkey zygotes. Five out of six newborn monkeys carried the mutation specifically at the target site. HGPS monkeys expressed the toxic form of lamin A, progerin, and recapitulated the typical HGPS phenotypes including growth retardation, bone alterations, and vascular abnormalities. Thus, this monkey model genetically and clinically mimics HGPS in humans, demonstrating that the BE system can efficiently and accurately generate patient-specific disease models in non-human primates.
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Affiliation(s)
- Fang Wang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing, 100101, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiaoyan Yang
- The Leon H Charney Division of Cardiology, New York University School of Medicine, New York, NY, 10016, USA
| | - Yu Kang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Jingkuan Wei
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Zunpeng Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaoxing Dai
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zifan Li
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Lizhu Xu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Chu Chu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chenyang Si
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Weizhi Ji
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Guang-Hui Liu
- Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
| | - Chengzu Long
- The Leon H Charney Division of Cardiology, New York University School of Medicine, New York, NY, 10016, USA.
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, 10016, USA.
- Department of Neurology, New York University School of Medicine, New York, NY, 10016, USA.
| | - Yuyu Niu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China.
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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50
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Bozhok YM, Golovko O, Nikonenko AG. nPAsym: an open-source plugin for ImageJ to quantify nuclear shape asymmetry. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 196:105562. [PMID: 32544781 DOI: 10.1016/j.cmpb.2020.105562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/07/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVES The nucleus is a complex and dynamic organelle enclosing the major part of the cell's genome. A growing body of evidence suggests that changes in the shape of this organelle can influence cell activities. The other way around, altered nuclear shape may be indicative of impaired cell function. Symmetry is an important aspect of nuclear shape not receiving the attention it merits. We address this problem by presenting a software tool allowing to quantify nuclear shape asymmetry in light microscopy images. METHODS The software named nPAsym is written in Scala and implemented as a plugin to ImageJ making possible to use it in combination with other ImageJ tools. The plugin works with 8-bit images segmented into black nuclear masks and white background. It performs a number of operations allowing to analyze multiple objects within a single image, removing some segmentation artefacts, filtering out objects incomplete and below a specified size. The feature of interest is quantified using the notion of point asymmetry. The performance of nPAsym was tested in a small-scale study comparing nuclear shapes for cells of nodular goiter, follicular thyroid adenoma and papillary thyroid carcinoma. RESULTS We present nPAsym, the ImageJ plugin, that measures nuclear shape asymmetry. It works with digital microscopic images segmented using either a raster graphics editor or built-in ImageJ functions. nPAsym is packaged in a single .jar file and does not require installation as well as configuration. It has proved effective in distinguishing between some of the nuclear shape phenotypes. CONCLUSIONS nPAsym is the user-friendly, platform-independent and open-source software tool allowing to quantify nuclear shape asymmetry in digital images captured from cytologic and histologic preparations. It has a potential to become useful for both experimental research and diagnostics.
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Affiliation(s)
- Y M Bozhok
- Department of Functional Diagnostics, V.P. Komisarenko Institute of Endocrinology and Metabolism, Vyshgorodska str. 69, 04114, Kyiv, Ukraine
| | - O Golovko
- Department of Cytology, Bogomoletz Institute of Physiology, Bogomoletz str. 4, 01024, Kyiv, Ukraine
| | - A G Nikonenko
- Department of Cytology, Bogomoletz Institute of Physiology, Bogomoletz str. 4, 01024, Kyiv, Ukraine.
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