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Gopinathan G, Xu Q, Luan X, Diekwisch TGH. CFDP1 regulates the stability of pericentric heterochromatin thereby affecting RAN GTPase activity and mitotic spindle formation. PLoS Biol 2024; 22:e3002574. [PMID: 38630655 PMCID: PMC11023358 DOI: 10.1371/journal.pbio.3002574] [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: 04/23/2023] [Accepted: 03/02/2024] [Indexed: 04/19/2024] Open
Abstract
The densely packed centromeric heterochromatin at minor and major satellites is comprised of H3K9me2/3 histones, the heterochromatin protein HP1α, and histone variants. In the present study, we sought to determine the mechanisms by which condensed heterochromatin at major and minor satellites stabilized by the chromatin factor CFDP1 affects the activity of the small GTPase Ran as a requirement for spindle formation. CFDP1 colocalized with heterochromatin at major and minor satellites and was essential for the structural stability of centromeric heterochromatin. Loss of CENPA, HP1α, and H2A.Z heterochromatin components resulted in decreased binding of the spindle nucleation facilitator RCC1 to minor and major satellite repeats. Decreased RanGTP levels as a result of diminished RCC1 binding interfered with chromatin-mediated microtubule nucleation at the onset of mitotic spindle formation. Rescuing chromatin H2A.Z levels in cells and mice lacking CFDP1 through knock-down of the histone chaperone ANP32E not only partially restored RCC1-dependent RanGTP levels but also alleviated CFDP1-knockout-related craniofacial defects and increased microtubule nucleation in CFDP1/ANP32E co-silenced cells. Together, these studies provide evidence for a direct link between condensed heterochromatin at major and minor satellites and microtubule nucleation through the chromatin protein CFDP1.
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Affiliation(s)
- Gokul Gopinathan
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Qian Xu
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Xianghong Luan
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
| | - Thomas G. H. Diekwisch
- School of Medicine and Dentistry, University of Rochester, Rochester, New York, United States of America
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Giardoglou P, Deloukas P, Dedoussis G, Beis D. Cfdp1 Is Essential for Cardiac Development and Function. Cells 2023; 12:1994. [PMID: 37566073 PMCID: PMC10417793 DOI: 10.3390/cells12151994] [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: 05/16/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the prevalent cause of mortality worldwide. A combination of environmental and genetic effectors modulates the risk of developing them. Thus, it is vital to identify candidate genes and elucidate their role in the manifestation of the disease. Large-scale human studies have revealed the implication of Craniofacial Development Protein 1 (CFDP1) in Coronary Artery Disease (CAD). CFDP1 belongs to the evolutionary conserved Bucentaur (BCNT) family, and to date, its function and mechanism of action in Cardiovascular Development are still unclear. We utilized zebrafish to investigate the role of cfdp1 in the developing heart due to the high genomic homology, similarity in heart physiology, and ease of experimental manipulations. We showed that cfdp1 was expressed during development, and we tested two morpholinos and generated a cfdp1 mutant line. The cfdp1-/- embryos developed arrhythmic hearts and exhibited defective cardiac performance, which led to a lethal phenotype. Findings from both knockdown and knockout experiments showed that abrogation of cfdp1 leads to downregulation of Wnt signaling in embryonic hearts during valve development but without affecting Notch activation in this process. The cfdp1 zebrafish mutant line provides a valuable tool for unveiling the novel mechanism of regulating cardiac physiology and function. cfdp1 is essential for cardiac development, a previously unreported phenotype most likely due to early lethality in mice. The detected phenotype of bradycardia and arrhythmias is an observation with potential clinical relevance for humans carrying heterozygous CFDP1 mutations and their risk of developing CAD.
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Affiliation(s)
- Panagiota Giardoglou
- Zebrafish Disease Model Laboratory, Center for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17676 Athens, Greece;
| | - Panos Deloukas
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London Medical School, Queen Mary University of London, London E1 4NS, UK;
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17676 Athens, Greece;
| | - Dimitris Beis
- Zebrafish Disease Model Laboratory, Center for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
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Pose-Méndez S, Schramm P, Valishetti K, Köster RW. Development, circuitry, and function of the zebrafish cerebellum. Cell Mol Life Sci 2023; 80:227. [PMID: 37490159 PMCID: PMC10368569 DOI: 10.1007/s00018-023-04879-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/30/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023]
Abstract
The cerebellum represents a brain compartment that first appeared in gnathostomes (jawed vertebrates). Besides the addition of cell numbers, its development, cytoarchitecture, circuitry, physiology, and function have been highly conserved throughout avian and mammalian species. While cerebellar research in avian and mammals is extensive, systematic investigations on this brain compartment in zebrafish as a teleostian model organism started only about two decades ago, but has provided considerable insight into cerebellar development, physiology, and function since then. Zebrafish are genetically tractable with nearly transparent small-sized embryos, in which cerebellar development occurs within a few days. Therefore, genetic investigations accompanied with non-invasive high-resolution in vivo time-lapse imaging represents a powerful combination for interrogating the behavior and function of cerebellar cells in their complex native environment.
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Affiliation(s)
- Sol Pose-Méndez
- Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106, Braunschweig, Germany.
| | - Paul Schramm
- Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Komali Valishetti
- Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Reinhard W Köster
- Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106, Braunschweig, Germany.
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Marchal C, Singh N, Batz Z, Advani J, Jaeger C, Corso-Díaz X, Swaroop A. High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci. Nat Commun 2022; 13:5827. [PMID: 36207300 PMCID: PMC9547065 DOI: 10.1038/s41467-022-33427-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Chromatin organization and enhancer-promoter contacts establish unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate genomic regulation in human retina, we mapped chromatin contacts at high resolution and integrated with super-enhancers (SEs), histone marks, binding of CTCF and select transcription factors. We show that topologically associated domains (TADs) with central SEs exhibit stronger insulation and augmented contact with retinal genes relative to TADs with edge SEs. Merging genome-wide expression quantitative trait loci (eQTLs) with topology map reveals physical links between 100 eQTLs and corresponding eGenes associated with retinal neurodegeneration. Additionally, we uncover candidate genes for susceptibility variants linked to age-related macular degeneration and glaucoma. Our study of high-resolution genomic architecture of human retina provides insights into genetic control of tissue-specific functions, suggests paradigms for missing heritability, and enables the dissection of common blinding disease phenotypes.
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Affiliation(s)
- Claire Marchal
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
- In silichrom Ltd, First Floor, Angel Court, 81 St Clements St, Oxford, OX4 1AW, UK
| | - Nivedita Singh
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Zachary Batz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Catherine Jaeger
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD, 20892, USA.
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Zhou Y, Qiu J, Liu S, Wang P, Ma D, Zhang G, Cao Y, Hu L, Wang Z, Wu J, Jiang C. CFDP1 promotes hepatocellular carcinoma progression through activating NEDD4/PTEN/PI3K/AKT signaling pathway. Cancer Med 2022; 12:425-444. [PMID: 35861040 PMCID: PMC9844661 DOI: 10.1002/cam4.4919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/06/2022] [Accepted: 05/24/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND AND AIMS It is being increasingly reported that the Cranio Facial Development Protein 1 (CFDP1) plays a significant role in the onset and progression of tumors. Nonetheless, the underlying mechanisms associated with CFDP1 that contribute to hepatocellular carcinoma (HCC) and the specific biological role of CFDP1 remain vague. METHODS The Gene Expression Omnibus (GEO) database was analyzed to obtain the gene expression profiles as well as the matching clinical data of HCC patients. The gene co-expression network was developed by means of weighted gene co-expression network analysis (WGCNA) to screen for possible biomarkers that could be used for the purpose of predicting prognosis. The Cancer Genome Atlas (TCGA) and Gene Expression Profile Interaction Analysis (GEPIA) databases were used to assess the relationship between survival and expression. In addition, we identified the underlying mechanism associated with CFDP1 by analyzing the KEGG pathway database, applying the GSEA and GeneCards analysis method. We performed a sequence of experiments (in vivo and in vitro) for the purpose of investigating the specific function of CFDP1 in liver cancer. RESULTS The obtained results revealed high expression of CFDP1 in HCC tissues and cell lines. A positive correlation between the overexpression of CFDP1 and the adverse clinicopathological features was observed. Moreover, we observed that the low recurrence-free survival and overall survival were associated with CFDP1 overexpression. In addition, GeneCards and GSEA analysis showed that CFDP1 may interact with NEDD4 and participate in PTEN regulation. Meanwhile, CFDP1 can promote the malignant development of liver cancer in vivo and in vitro. The western blotting technique was also employed so as to examine the samples, and the findings demonstrated that CFDP1 enhanced the malignancy of HCC via the NEDD4-mediated PTEN/PI3K/AKT pathway. CONCLUSION We highlighted that CFDP1 played an oncogenic role in HCC and was identified as a possible clinical prognostic factor and a potential novel therapeutic target for HCC.
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Affiliation(s)
- Yan Zhou
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
| | - Jiannan Qiu
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
| | - Siyuan Liu
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
| | - Peng Wang
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
| | - Ding Ma
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
| | - Guang Zhang
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
| | - Yin Cao
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
| | - Lili Hu
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
| | - Zhongxia Wang
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
| | - Junhua Wu
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
| | - Chunping Jiang
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
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