1
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Li Z, Kegui H, Piao W, Xuejiu W, Lim KT, Jin H. PAI-1 transfected-conditioned media promotes osteogenic differentiation of hBMSCs. Cell Biol Int 2024. [PMID: 38654436 DOI: 10.1002/cbin.12166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/28/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Reconstruction of injured bone remains challenging in the clinic owing to the lack of suitable bone grafts. The utilization of PAI-1 transfected-conditioned media (P-CM) has demonstrated its ability to facilitate the differentiation process of mesenchymal stem cells (MSCs), potentially serving as a crucial mediator in tissue regeneration. This research endeavored to explore the therapeutic potential of P-CM concerning the differentiation of human bone marrow mesenchymal stem cells (hBMSCs). To assess new bone formation, a rat calvaria critical defect model was employed, while in vitro experiments involved the use of the alizarin Red-S mineral induction test. In the rat calvaria critical defect model, P-CM treatment resulted in significan new bone formation. In vitro, P-CM treated hBMSCs displayed robust osteogenesis compared to the control group, as demonstrated by the mineral induction test using alizarin Red-S. P-CM with hydroxyapatite/β-tricalcium phosphate/fibrin gel treatment significantly exhibited new bone formation, and the expression of osteogenic associated markers was enhanced in the P-CM-treated group. In conclusion, results demonstrate that P-CM treatment significantly enhanced the osteogenic differantiation efficiency and new bone formation, thus could be used as an ideal therapeutic biomolecule for constructing bone-specific implants, especially for orthopedic and dental applications.
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Affiliation(s)
- Zhang Li
- Department of Oral and Maxillofacial Surgery, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Hou Kegui
- Department of Oral and Maxillofacial Surgery, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Wang Piao
- Department of Oral and Maxillofacial Surgery, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Wang Xuejiu
- Department of Oral and Maxillofacial Surgery, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Ki-Taek Lim
- Department of Biosystems Engineering, Kangwon National University, Chuncheon, South Korea
| | - Hexiu Jin
- Department of Oral and Maxillofacial Surgery, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
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2
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Zhang L, Li X, Gao H, Li P. The Role of Circular RNA Variants Generated from the NFIX Gene in Different Diseases. Mol Pharm 2024; 21:1027-1037. [PMID: 38315004 DOI: 10.1021/acs.molpharmaceut.3c00933] [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: 02/07/2024]
Abstract
Circular RNAs (circRNAs) have been identified as important regulators in different developmental processes and disease pathogenesis. The loop structure of circRNAs makes them very stable in different conditions and microenvironments. circRNAs can affect microRNA (miRNA) and RNA binding protein (RBP) activity, encode functional proteins and regulate gene transcription. Recently, two circNFIX variants derived from the same gene, the Nuclear Factor I X (NFIX) gene, were determined as participants in the pathological processes of various diseases such as heart diseases and cancers. Both circNFIX variants are exonic circular RNAs and mainly function by sponging miRNAs. In this review, we summarize the current knowledge on circRNAs, elucidate the origins and properties of two circNFIX variants, explore the roles of two circNFIX variants in different diseases, and present clinical perspectives.
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Affiliation(s)
- Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, No. 38 DengZhou Road, Qingdao 266021, China
| | - Xin Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, No. 38 DengZhou Road, Qingdao 266021, China
| | - Huijuan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, No. 38 DengZhou Road, Qingdao 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, No. 38 DengZhou Road, Qingdao 266021, China
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3
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Solta A, Ernhofer B, Boettiger K, Megyesfalvi Z, Heeke S, Hoda MA, Lang C, Aigner C, Hirsch FR, Schelch K, Döme B. Small cells - big issues: biological implications and preclinical advancements in small cell lung cancer. Mol Cancer 2024; 23:41. [PMID: 38395864 PMCID: PMC10893629 DOI: 10.1186/s12943-024-01953-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Current treatment guidelines refer to small cell lung cancer (SCLC), one of the deadliest human malignancies, as a homogeneous disease. Accordingly, SCLC therapy comprises chemoradiation with or without immunotherapy. Meanwhile, recent studies have made significant advances in subclassifying SCLC based on the elevated expression of the transcription factors ASCL1, NEUROD1, and POU2F3, as well as on certain inflammatory characteristics. The role of the transcription regulator YAP1 in defining a unique SCLC subset remains to be established. Although preclinical analyses have described numerous subtype-specific characteristics and vulnerabilities, the so far non-existing clinical subtype distinction may be a contributor to negative clinical trial outcomes. This comprehensive review aims to provide a framework for the development of novel personalized therapeutic approaches by compiling the most recent discoveries achieved by preclinical SCLC research. We highlight the challenges faced due to limited access to patient material as well as the advances accomplished by implementing state-of-the-art models and methodologies.
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Affiliation(s)
- Anna Solta
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Büsra Ernhofer
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Kristiina Boettiger
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Zsolt Megyesfalvi
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Simon Heeke
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mir Alireza Hoda
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Christian Lang
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Division of Pulmonology, Department of Medicine II, Medical University of Vienna, Vienna, Austria
| | - Clemens Aigner
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Fred R Hirsch
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Center for Thoracic Oncology, Mount Sinai Health System, Tisch Cancer Institute, New York, NY, USA.
| | - Karin Schelch
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Balazs Döme
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.
- National Koranyi Institute of Pulmonology, Budapest, Hungary.
- Department of Translational Medicine, Lund University, Lund, Sweden.
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4
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Keeley PW, Trod S, Gamboa BN, Coffey PJ, Reese BE. Nfia Is Critical for AII Amacrine Cell Production: Selective Bipolar Cell Dependencies and Diminished ERG. J Neurosci 2023; 43:8367-8384. [PMID: 37775301 PMCID: PMC10711738 DOI: 10.1523/jneurosci.1099-23.2023] [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: 06/13/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023] Open
Abstract
The nuclear factor one (NFI) transcription factor genes Nfia, Nfib, and Nfix are all enriched in late-stage retinal progenitor cells, and their loss has been shown to retain these progenitors at the expense of later-generated retinal cell types. Whether they play any role in the specification of those later-generated fates is unknown, but the expression of one of these, Nfia, in a specific amacrine cell type may intimate such a role. Here, Nfia conditional knockout (Nfia-CKO) mice (both sexes) were assessed, finding a massive and largely selective absence of AII amacrine cells. There was, however, a partial reduction in type 2 cone bipolar cells (CBCs), being richly interconnected to AII cells. Counts of dying cells showed a significant increase in Nfia-CKO retinas at postnatal day (P)7, after AII cell numbers were already reduced but in advance of the loss of type 2 CBCs detected by P10. Those results suggest a role for Nfia in the specification of the AII amacrine cell fate and a dependency of the type 2 CBCs on them. Delaying the conditional loss of Nfia to the first postnatal week did not alter AII cell number nor differentiation, further suggesting that its role in AII cells is solely associated with their production. The physiological consequences of their loss were assessed using the ERG, finding the oscillatory potentials to be profoundly diminished. A slight reduction in the b-wave was also detected, attributed to an altered distribution of the terminals of rod bipolar cells, implicating a role of the AII amacrine cells in constraining their stratification.SIGNIFICANCE STATEMENT The transcription factor NFIA is shown to play a critical role in the specification of a single type of retinal amacrine cell, the AII cell. Using an Nfia-conditional knockout mouse to eliminate this population of retinal neurons, we demonstrate two selective bipolar cell dependencies on the AII cells; the terminals of rod bipolar cells become mis-stratified in the inner plexiform layer, and one type of cone bipolar cell undergoes enhanced cell death. The physiological consequence of this loss of the AII cells was also assessed, finding the cells to be a major contributor to the oscillatory potentials in the electroretinogram.
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Affiliation(s)
- Patrick W Keeley
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106-5060
| | - Stephanie Trod
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106-5060
| | - Bruno N Gamboa
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106-5060
| | - Pete J Coffey
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106-5060
| | - Benjamin E Reese
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106-5060
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, California 93106-5060
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5
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Choi J, Lee H. NFIB-MLL1 complex is required for the stemness and Dlx5-dependent osteogenic differentiation of C3H10T1/2 mesenchymal stem cells. J Biol Chem 2023; 299:105193. [PMID: 37633334 PMCID: PMC10519831 DOI: 10.1016/j.jbc.2023.105193] [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: 04/10/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023] Open
Abstract
Despite significant progress in our understanding of the molecular mechanism of mesenchymal stem cell (MSC) differentiation, less is known about the factors maintaining the stemness and plasticity of MSCs. Here, we show that the NFIB-MLL1 complex plays key roles in osteogenic differentiation and stemness of C3H10T1/2 MSCs. We find that depletion of either NFIB or MLL1 results in a severely hampered osteogenic potential and failed activation of key osteogenic transcription factors, such as Dlx5, Runx2, and Osx, following osteogenic stimuli. In addition, the NFIB-MLL1 complex binds directly to the promoter of Dlx5, and exogenous expression of Myc-Dlx5, but not the activation of either the BMP- or the Wnt-signaling pathway, is sufficient to restore the osteogenic potential of cells depleted of NFIB or MLL1. Moreover, chromatin immunoprecipitation (ChIP) and ChIP-sequencing analysis showed that the NFIB-MLL1 complex mediates the deposition of trimethylated histone H3K4 at both Dlx5 and Cebpa, key regulator genes that function at the early stages of osteogenic and adipogenic differentiation, respectively, in uncommitted C3H10T1/2 MSCs. Surprisingly, the depletion of either NFIB or MLL1 leads to decreased trimethylated histone H3K4 and results in elevated trimethylated histone H3K9 at those developmental genes. Furthermore, gene expression profiling and ChIP-sequencing analysis revealed lineage-specific changes in chromatin landscape and gene expression in response to osteogenic stimuli. Taken together, these data provide evidence for the hitherto unknown role of the NFIB-MLL1 complex in the maintenance and lineage-specific differentiation of C3H10T1/2 MSCs and support the epigenetic regulatory mechanism underlying the stemness and plasticity of MSCs.
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Affiliation(s)
- Janghyun Choi
- Department of Biological Sciences, College of Natural Science, Inha University, Incheon, South Korea.
| | - Hansol Lee
- Department of Biological Sciences, College of Natural Science, Inha University, Incheon, South Korea.
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6
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Landi S, Giannetti F, Benzoni P, Campostrini G, Rossi G, Piantoni C, Bertoli G, Bonfanti C, Carnevali L, Bucchi A, Baruscotti M, Careccia G, Messina G, Barbuti A. Lack of the transcription factor Nfix causes tachycardia in mice sinus node and rats neonatal cardiomyocytes. Acta Physiol (Oxf) 2023; 239:e13981. [PMID: 37186371 DOI: 10.1111/apha.13981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023]
Abstract
AIMS Nfix is a transcription factor belonging to the Nuclear Factor I (NFI) family comprising four members (Nfia, b, c, x). Nfix plays important roles in the development and function of several organs. In muscle development, Nfix controls the switch from embryonic to fetal myogenesis by promoting fast twitching fibres. In the adult muscle, following injury, lack of Nfix impairs regeneration, inducing higher content of slow-twitching fibres. Nfix is expressed also in the heart, but its function has been never investigated before. We studied Nfix role in this organ. METHODS Using Nfix-null and wild type (WT) mice we analyzed: (1) the expression pattern of Nfix during development by qPCR and (2) the functional alterations caused by its absence, by in vivo telemetry and in vitro patch clamp analysis. RESULTS AND CONCLUSIONS Nfix expression start in the heart from E12.5. Adult hearts of Nfix-null mice show a hearts morphology and sarcomeric proteins expression similar to WT. However, Nfix-null animals show tachycardia that derives form an intrinsic higher beating rate of the sinus node (SAN). Molecular and functional analysis revealed that sinoatrial cells of Nfix-null mice express a significantly larger L-type calcium current (Cacna1d + Cacna1c). Interestingly, downregulation of Nfix by sh-RNA in primary cultures of neonatal rat ventricular cardiomyocytes induced a similar increase in their spontaneous beating rate and in ICaL current. In conclusion, our data provide the first demonstration of a role of Nfix that, increasing the L-type calcium current, modulates heart rate.
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Affiliation(s)
- Sara Landi
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Federica Giannetti
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Patrizia Benzoni
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Giulia Campostrini
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Giuliana Rossi
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Chiara Piantoni
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Giorgia Bertoli
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Chiara Bonfanti
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Luca Carnevali
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Annalisa Bucchi
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Mirko Baruscotti
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Giorgia Careccia
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Graziella Messina
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Andrea Barbuti
- The Cell Physiology MiLab, Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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7
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Lenk HÇ, Løvsletten Smith R, O'Connell KS, Jukić MM, Kringen MK, Andreassen OA, Ingelman‐Sundberg M, Molden E. Impact of NFIB and CYP1A variants on clozapine serum concentration-A retrospective naturalistic cohort study on 526 patients with known smoking habits. Clin Transl Sci 2022; 16:62-72. [PMID: 36152308 PMCID: PMC9841299 DOI: 10.1111/cts.13422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/11/2022] [Accepted: 09/08/2022] [Indexed: 02/06/2023] Open
Abstract
Clinical response of clozapine is closely associated with serum concentration. Although tobacco smoking is the key environmental factor underlying interindividual variability in clozapine metabolism, recent genome-wide studies suggest that CYP1A and NFIB genetic variants may also be of significant importance, but their quantitative impact is unclear. We investigated the effects of the rs2472297 C>T (CYP1A) and rs28379954 T>C (NFIB) polymorphisms on serum concentrations in smokers and nonsmokers. The study retrospectively included 526 patients with known smoking habits (63.7% smokers) from a therapeutic drug monitoring service in Norway. Clozapine dose-adjusted concentrations (C/D) and patient proportions with subtherapeutic levels (<1070 nmol/L) were compared between CYP1A/NFIB variant allele carriers and homozygous wild-type carriers (noncarriers), in both smokers and nonsmokers. Clozapine C/D was reduced in patients carrying CYP1A-T and NFIB-C variants versus noncarriers, both among smokers (-48%; p < 0.0001) and nonsmokers (-35%; p = 0.028). Patients who smoke carrying CYP1A-T and NFIB-C variants had a 66% reduction in clozapine C/D versus nonsmoking noncarriers (p < 0.0001). The patient proportion with subtherapeutic levels was 2.9-fold higher in patients who smoke carrying NFIB-C and CYP1A-T variants versus nonsmoking noncarriers (p < 0.0001). In conclusion, CYP1A and NFIB variants have significant and additive impact on clozapine dose requirements for reaching target serum concentrations. Patients who smoke carrying the studied CYP1A and NFIB variants, comprising 2.5% of the study population, may need threefold higher doses to prevent risk of clozapine undertreatment. The results suggest that pre-emptive genotyping of NFIB and CYP1A may be utilized to guide clozapine dosing and improve clinical outcomes in patients with treatment-resistant schizophrenia.
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Affiliation(s)
- Hasan Çağın Lenk
- Center for PsychopharmacologyDiakonhjemmet HospitalOsloNorway,Section for Pharmacology and Pharmaceutical Biosciences, Department of PharmacyUniversity of OsloOsloNorway
| | - Robert Løvsletten Smith
- Center for PsychopharmacologyDiakonhjemmet HospitalOsloNorway,Division of Mental Health and Addiction, NORMENT CentreOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Kevin S. O'Connell
- Division of Mental Health and Addiction, NORMENT CentreOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Marin M. Jukić
- Section of Pharmacogenetics, Department of Physiology and PharmacologyKarolinska InstitutetStockholmSweden,Department of Physiology, Faculty of PharmacyUniversity of BelgradeBelgradeSerbia
| | - Marianne Kristiansen Kringen
- Center for PsychopharmacologyDiakonhjemmet HospitalOsloNorway,Department of Life Sciences and HealthOslo Metropolitan UniversityOsloNorway
| | - Ole A. Andreassen
- Division of Mental Health and Addiction, NORMENT CentreOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Magnus Ingelman‐Sundberg
- Section of Pharmacogenetics, Department of Physiology and PharmacologyKarolinska InstitutetStockholmSweden
| | - Espen Molden
- Center for PsychopharmacologyDiakonhjemmet HospitalOsloNorway,Section for Pharmacology and Pharmaceutical Biosciences, Department of PharmacyUniversity of OsloOsloNorway
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8
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Lenk HÇ, Klöditz K, Johansson I, Smith RL, Jukić MM, Molden E, Ingelman-Sundberg M. The Polymorphic Nuclear Factor NFIB Regulates Hepatic CYP2D6 Expression and Influences Risperidone Metabolism in Psychiatric Patients. Clin Pharmacol Ther 2022; 111:1165-1174. [PMID: 35253216 PMCID: PMC9314634 DOI: 10.1002/cpt.2571] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/21/2022] [Indexed: 12/02/2022]
Abstract
The genetic background for interindividual variability of the polymorphic CYP2D6 enzyme activity remains incompletely understood and the role of NFIB genetic polymorphism for this variability was evaluated in this translational study. We investigated the effect of NFIB expression in vitro using 3D liver spheroids, Huh7 cells, and the influence of the NFIB polymorphism on metabolism of risperidone in patients in vivo. We found that NFIB regulates several important pharmacogenes, including CYP2D6. NFIB inhibited CYP2D6 gene expression in Huh7 cells and NFIB expression in livers was predominantly nuclear and reduced at the mRNA and protein level in carriers of the NFIB rs28379954 T>C allele. Based on 604 risperidone treated patients genotyped for CYP2D6 and NFIB, we found that the rate of risperidone hydroxylation was elevated in NFIB rs28379954 T>C carriers among CYP2D6 normal metabolizers, resulting in a similar rate of drug metabolism to what is observed in CYP2D6 ultrarapid metabolizers, with no such effect observed in CYP2D6 poor metabolizers lacking functional enzyme. The results indicate that NFIB constitutes a novel nuclear factor in the regulation of cytochrome P450 genes, and that its polymorphism is a predictor for the rate of CYP2D6 dependent drug metabolism in vivo.
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Affiliation(s)
- Hasan Çağın Lenk
- Center for Psychopharmacology, Diakonhjemmet Hospital, Vinderen, Oslo, Norway.,Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Katharina Klöditz
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - Inger Johansson
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Løvsletten Smith
- Center for Psychopharmacology, Diakonhjemmet Hospital, Vinderen, Oslo, Norway.,NORMENT, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marin M Jukić
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden.,Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Vinderen, Oslo, Norway.,Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
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9
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Transcriptional Regulation of RIP2 Gene by NFIB Is Associated with Cellular Immune and Inflammatory Response to APEC Infection. Int J Mol Sci 2022; 23:ijms23073814. [PMID: 35409172 PMCID: PMC8998712 DOI: 10.3390/ijms23073814] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 02/04/2023] Open
Abstract
Avian pathogenic E. coli (APEC) can cause localized or systemic infection, resulting in large economic losses per year, and impact health of humans. Previous studies showed that RIP2 (receptor interacting serine/threonine kinase 2) and its signaling pathway played an important role in immune response against APEC infection. In this study, chicken HD11 cells were used as an in vitro model to investigate the function of chicken RIP2 and the transcription factor binding to the RIP2 core promoter region via gene overexpression, RNA interference, RT-qPCR, Western blotting, dual luciferase reporter assay, CHIP-PCR, CCK-8, and flow cytometry assay following APEC stimulation. Results showed that APEC stimulation promoted RIP2 expression and cells apoptosis, and inhibited cells viability. Knockdown of RIP2 significantly improved cell viability and suppressed the apoptosis of APEC-stimulated cells. Transcription factor NFIB (Nuclear factor I B) and GATA1 (globin transcription factor 1) binding site was identified in the core promoter region of RIP2 from −2300 bp to −1839 bp. However, only NFIB was confirmed to be bound to the core promoter of RIP2. Overexpression of NFIB exacerbated cell injuries with significant reduction in cell viability and increased cell apoptosis and inflammatory cytokines levels, whereas opposite results were observed in NFIB inhibition treatment group. Moreover, RIP2 was up-regulated by NFIB overexpression, and RIP2 silence mitigated the effect of NFIB overexpression in cell apoptosis, inflammation, and activation of NFκB signaling pathways. This study demonstrated that NFIB overexpression accelerated APEC-induced apoptosis and inflammation via up-regulation of RIP2 mediated downstream pathways in chicken HD11 cells.
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10
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Davila RA, Spiller C, Harkins D, Harvey T, Jordan PW, Gronostajski RM, Piper M, Bowles J. Deletion of NFIX results in defective progression through meiosis within the mouse testis. Biol Reprod 2022; 106:1191-1205. [PMID: 35243487 PMCID: PMC9198952 DOI: 10.1093/biolre/ioac049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/17/2022] [Accepted: 02/24/2022] [Indexed: 12/05/2022] Open
Abstract
Members of the nuclear factor I (NFI) family are key regulators of stem cell biology during development, with well-documented roles for NFIA, NFIB, and NFIX in a variety of developing tissues, including brain, muscle, and lung. Given the central role these factors play in stem cell biology, we posited that they may be pivotal for spermatogonial stem cells or further developing spermatogonia during testicular development. Surprisingly, in stark contrast to other developing organ systems where NFI members are co-expressed, these NFI family members show discrete patterns of expression within the seminiferous tubules. Sertoli cells (spermatogenic supporting cells) express NFIA, spermatocytes express NFIX, round spermatids express NFIB, and peritubular myoid cells express each of these three family members. Further analysis of NFIX expression during the cycle of the seminiferous epithelium revealed expression not in spermatogonia, as we anticipated, but in spermatocytes. These data suggested a potential role for NFIX in spermatogenesis. To investigate, we analyzed mice with constitutive deletion of Nfix (Nfix-null). Assessment of germ cells in the postnatal day 20 (P20) testes of Nfix-null mice revealed that spermatocytes initiate meiosis, but zygotene stage spermatocytes display structural defects in the synaptonemal complex, and increased instances of unrepaired DNA double-strand breaks. Many developing spermatocytes in the Nfix-null testis exhibited multinucleation. As a result of these defects, spermatogenesis is blocked at early diplotene and very few round spermatids are produced. Collectively, these novel data establish the global requirement for NFIX in correct meiotic progression during the first wave of spermatogenesis.
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Affiliation(s)
- Raul Ayala Davila
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Cassy Spiller
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Danyon Harkins
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Tracey Harvey
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Philip W Jordan
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia
| | - Josephine Bowles
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
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11
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Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nat Genet 2022; 54:328-341. [PMID: 35288709 PMCID: PMC8920898 DOI: 10.1038/s41588-022-01018-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells expressing a panoply of molecular programs. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. Here, we set out to integrate several single-cell RNA-sequencing (scRNA-seq) datasets that collectively span mouse gastrulation and organogenesis, supplemented with new profiling of ~150,000 nuclei from approximately embryonic day 8.5 (E8.5) embryos staged in one-somite increments. Overall, we define cell states at each of 19 successive stages spanning E3.5 to E13.5 and heuristically connect them to their pseudoancestors and pseudodescendants. Although constructed through automated procedures, the resulting directed acyclic graph (TOME (trajectories of mammalian embryogenesis)) is largely consistent with our contemporary understanding of mammalian development. We leverage TOME to systematically nominate transcription factors (TFs) as candidate regulators of each cell type's specification, as well as 'cell-type homologs' across vertebrate evolution.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Junyue Cao
- The Rockefeller University, New York, NY, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Christine M Disteche
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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12
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Li J, Glover JD, Zhang H, Peng M, Tan J, Mallick CB, Hou D, Yang Y, Wu S, Liu Y, Peng Q, Zheng SC, Crosse EI, Medvinsky A, Anderson RA, Brown H, Yuan Z, Zhou S, Xu Y, Kemp JP, Ho YYW, Loesch DZ, Wang L, Li Y, Tang S, Wu X, Walters RG, Lin K, Meng R, Lv J, Chernus JM, Neiswanger K, Feingold E, Evans DM, Medland SE, Martin NG, Weinberg SM, Marazita ML, Chen G, Chen Z, Zhou Y, Cheeseman M, Wang L, Jin L, Headon DJ, Wang S. Limb development genes underlie variation in human fingerprint patterns. Cell 2022; 185:95-112.e18. [PMID: 34995520 PMCID: PMC8740935 DOI: 10.1016/j.cell.2021.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022]
Abstract
Fingerprints are of long-standing practical and cultural interest, but little is known about the mechanisms that underlie their variation. Using genome-wide scans in Han Chinese cohorts, we identified 18 loci associated with fingerprint type across the digits, including a genetic basis for the long-recognized “pattern-block” correlations among the middle three digits. In particular, we identified a variant near EVI1 that alters regulatory activity and established a role for EVI1 in dermatoglyph patterning in mice. Dynamic EVI1 expression during human development supports its role in shaping the limbs and digits, rather than influencing skin patterning directly. Trans-ethnic meta-analysis identified 43 fingerprint-associated loci, with nearby genes being strongly enriched for general limb development pathways. We also found that fingerprint patterns were genetically correlated with hand proportions. Taken together, these findings support the key role of limb development genes in influencing the outcome of fingerprint patterning. GWAS identifies variants associated with fingerprint type across all digits Fingerprint-associated genes are strongly enriched for limb development functions Evi1 alters dermatoglyphs in mice by modulating limb rather than skin development Fingerprint patterns are genetically correlated with hand and finger proportions
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Affiliation(s)
- Jinxi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - James D Glover
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Haiguo Zhang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Meifang Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Chandana Basu Mallick
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK; Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Dan Hou
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Sijie Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yu Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Edie I Crosse
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu 225326, PRC
| | - Shen Zhou
- Shanghai Foreign Language School, Shanghai 200083, PRC
| | - Yanqing Xu
- Forest Ridge School of the Sacred Heart, Bellevue, WA 98006, USA
| | - John P Kemp
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia
| | - Yvonne Y W Ho
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | - Danuta Z Loesch
- Psychology Department, La Trobe University, Melbourne, VIC, Australia
| | | | | | | | - Xiaoli Wu
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ruogu Meng
- Center for Data Science in Health and Medicine, Peking University, Beijing 100191, PRC
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, PRC
| | - Jonathan M Chernus
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Katherine Neiswanger
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David M Evans
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | | | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mary L Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Clinical and Translational Science, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Gang Chen
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Yong Zhou
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PRC
| | - Michael Cheeseman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Lan Wang
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai 200438, PRC.
| | - Denis J Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, PRC.
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13
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Benner P, Vingron M. Quantifying the tissue-specific regulatory information within enhancer DNA sequences. NAR Genom Bioinform 2021; 3:lqab095. [PMID: 34729474 PMCID: PMC8557370 DOI: 10.1093/nargab/lqab095] [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: 05/07/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/04/2022] Open
Abstract
Recent efforts to measure epigenetic marks across a wide variety of different cell types and tissues provide insights into the cell type-specific regulatory landscape. We use these data to study whether there exists a correlate of epigenetic signals in the DNA sequence of enhancers and explore with computational methods to what degree such sequence patterns can be used to predict cell type-specific regulatory activity. By constructing classifiers that predict in which tissues enhancers are active, we are able to identify sequence features that might be recognized by the cell in order to regulate gene expression. While classification performances vary greatly between tissues, we show examples where our classifiers correctly predict tissue-specific regulation from sequence alone. We also show that many of the informative patterns indeed harbor transcription factor footprints.
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Affiliation(s)
- Philipp Benner
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
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14
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Eto H, Kishi Y. Brain regionalization by Polycomb-group proteins and chromatin accessibility. Bioessays 2021; 43:e2100155. [PMID: 34536032 DOI: 10.1002/bies.202100155] [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: 06/22/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/10/2022]
Abstract
During brain development, neural precursor cells (NPCs) in different brain regions produce different types of neurons, and each of these regions plays a different role in the adult brain. Therefore, precise regionalization is essential in the early stages of brain development, and irregular regionalization has been proposed as the cause of neurodevelopmental disorders. The mechanisms underlying brain regionalization have been well studied in terms of morphogen-induced expression of critical transcription factors for regionalization. NPC potential in different brain regions is defined by chromatin structures that regulate the plasticity of gene expression. Herein, we present recent findings on the importance of chromatin structure in brain regionalization, particularly with respect to its regulation by Polycomb-group proteins and chromatin accessibility.
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Affiliation(s)
- Hikaru Eto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke Kishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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15
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Han S, Okawa S, Wilkinson GA, Ghazale H, Adnani L, Dixit R, Tavares L, Faisal I, Brooks MJ, Cortay V, Zinyk D, Sivitilli A, Li S, Malik F, Ilnytskyy Y, Angarica VE, Gao J, Chinchalongporn V, Oproescu AM, Vasan L, Touahri Y, David LA, Raharjo E, Kim JW, Wu W, Rahmani W, Chan JAW, Kovalchuk I, Attisano L, Kurrasch D, Dehay C, Swaroop A, Castro DS, Biernaskie J, Del Sol A, Schuurmans C. Proneural genes define ground-state rules to regulate neurogenic patterning and cortical folding. Neuron 2021; 109:2847-2863.e11. [PMID: 34407390 DOI: 10.1016/j.neuron.2021.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/19/2021] [Accepted: 07/08/2021] [Indexed: 02/06/2023]
Abstract
Asymmetric neuronal expansion is thought to drive evolutionary transitions between lissencephalic and gyrencephalic cerebral cortices. We report that Neurog2 and Ascl1 proneural genes together sustain neurogenic continuity and lissencephaly in rodent cortices. Using transgenic reporter mice and human cerebral organoids, we found that Neurog2 and Ascl1 expression defines a continuum of four lineage-biased neural progenitor cell (NPC) pools. Double+ NPCs, at the hierarchical apex, are least lineage restricted due to Neurog2-Ascl1 cross-repression and display unique features of multipotency (more open chromatin, complex gene regulatory network, G2 pausing). Strikingly, selectively eliminating double+ NPCs by crossing Neurog2-Ascl1 split-Cre mice with diphtheria toxin-dependent "deleter" strains locally disrupts Notch signaling, perturbs neurogenic symmetry, and triggers cortical folding. In support of our discovery that double+ NPCs are Notch-ligand-expressing "niche" cells that control neurogenic periodicity and cortical folding, NEUROG2, ASCL1, and HES1 transcript distribution is modular (adjacent high/low zones) in gyrencephalic macaque cortices, prefiguring future folds.
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Affiliation(s)
- Sisu Han
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Integrated BioBank of Luxembourg, 3555, 3531 Dudelange, Luxembourg
| | - Grey Atteridge Wilkinson
- Department of Biochemistry and Molecular Biology, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Hussein Ghazale
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lata Adnani
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry and Molecular Biology, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Rajiv Dixit
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ligia Tavares
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Imrul Faisal
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew J Brooks
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-1204, USA
| | - Veronique Cortay
- Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Dawn Zinyk
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada
| | - Adam Sivitilli
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Saiqun Li
- Department of Biochemistry and Molecular Biology, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Faizan Malik
- Department of Medical Genetics, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Vladimir Espinosa Angarica
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Jinghua Gao
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vorapin Chinchalongporn
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ana-Maria Oproescu
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lakshmy Vasan
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yacine Touahri
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Luke Ajay David
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eko Raharjo
- Department of Comparative Biology and Experimental Medicine, HBI, ACHRI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-1204, USA
| | - Wei Wu
- Department of Pathology and Laboratory Medicine, Charbonneau Cancer Institute, HBI, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Waleed Rahmani
- Department of Comparative Biology and Experimental Medicine, HBI, ACHRI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jennifer Ai-Wen Chan
- Department of Pathology and Laboratory Medicine, Charbonneau Cancer Institute, HBI, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Deborah Kurrasch
- Department of Medical Genetics, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Colette Dehay
- Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-1204, USA
| | - Diogo S Castro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, HBI, ACHRI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Carol Schuurmans
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry and Molecular Biology, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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16
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Xu Y, Chen X, Yu L, Wang Y, Wang H, Wu Z, Wu S, Bao W. SLC4A11 and MFSD3 Gene Expression Changes in Deoxynivalenol Treated IPEC-J2 Cells. Front Genet 2021; 12:697883. [PMID: 34367255 PMCID: PMC8335166 DOI: 10.3389/fgene.2021.697883] [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: 04/20/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Deoxynivalenol (DON) caused serious cytotoxicity for animal cells. However, genes involved in regulating DON toxicity and the underlying molecular mechanisms remain largely unknown. This study explored the role of SLC4A11 and MFSD3 in alleviating DON toxicity and analyzed the DNA methylation changes of these two genes. Viability and cell cycle analysis showed that DON exposure decreased the IPEC-J2 viability (P < 0.01), blocked the cell cycle in the G2/M phase (P < 0.01), and increased the rate of apoptosis (P < 0.05). Expression of the SLC4A11 and MFSD3 genes was significantly downregulated upon DON exposure (P < 0.01). Overexpression of SLC4A11 and MFSD3 can enhance the cell viability (P < 0.01). DNA methylation assays indicated that promoter methylation of SLC4A11 (mC-1 and mC-23) and MFSD3 (mC-1 and mC-12) were significantly higher compared with those in the controls and correlated negatively with mRNA expression (P < 0.05). Further analysis showed that mC-1 of SLC4A11 and MFSD3 was located in transcription factor binding sites for NF-1 and Sp1. Our findings revealed the novel biological functions of porcine SLC4A11 and MFSD3 genes in regulating the cytotoxic effects induced by DON, and may contribute to the detection of biomarkers and drug targets for predicting and eliminating the potential toxicity of DON.
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Affiliation(s)
- Yafei Xu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaolei Chen
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Luchen Yu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yi Wang
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Haifei Wang
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengchang Wu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
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17
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Yeon GB, Shin WH, Yoo SH, Kim D, Jeon BM, Park WU, Bae Y, Park JY, You S, Na D, Kim DS. NFIB induces functional astrocytes from human pluripotent stem cell-derived neural precursor cells mimicking in vivo astrogliogenesis. J Cell Physiol 2021; 236:7625-7641. [PMID: 33949692 DOI: 10.1002/jcp.30405] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/18/2022]
Abstract
The ability to generate astrocytes from human pluripotent stem cells (hPSCs) offers a promising cellular model to study the development and physiology of human astrocytes. The extant methods for generating functional astrocytes required long culture periods and there remained much ambiguity on whether such paradigms follow the innate developmental program. In this report, we provided an efficient and rapid method for generating physiologically functional astrocytes from hPSCs. Overexpressing the nuclear factor IB in hPSC-derived neural precursor cells induced a highly enriched astrocyte population in 2 weeks. RNA sequencing and functional analyses demonstrated progressive transcriptomic and physiological changes in the cells, resembling in vivo astrocyte development. Further analyses substantiated previous results and established the MAPK pathway necessary for astrocyte differentiation. Hence, this differentiation paradigm provides a prospective in vitro model for human astrogliogenesis studies and the pathophysiology of neurological diseases concerning astrocytes.
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Affiliation(s)
- Gyu-Bum Yeon
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Won-Ho Shin
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, Korea
| | - Seo Hyun Yoo
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Dongyun Kim
- Department of Biotechnology, Korea University, Seoul, Korea
| | | | - Won-Ung Park
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Yeonju Bae
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Korea
| | - Jae-Yong Park
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Korea
| | - Seungkwon You
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul, Korea
| | - Dae-Sung Kim
- Department of Biotechnology, Korea University, Seoul, Korea.,Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
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18
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Curry RN, Glasgow SM. The Role of Neurodevelopmental Pathways in Brain Tumors. Front Cell Dev Biol 2021; 9:659055. [PMID: 34012965 PMCID: PMC8127784 DOI: 10.3389/fcell.2021.659055] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Disruptions to developmental cell signaling pathways and transcriptional cascades have been implicated in tumor initiation, maintenance and progression. Resurgence of aberrant neurodevelopmental programs in the context of brain tumors highlights the numerous parallels that exist between developmental and oncologic mechanisms. A deeper understanding of how dysregulated developmental factors contribute to brain tumor oncogenesis and disease progression will help to identify potential therapeutic targets for these malignancies. In this review, we summarize the current literature concerning developmental signaling cascades and neurodevelopmentally-regulated transcriptional programs. We also examine their respective contributions towards tumor initiation, maintenance, and progression in both pediatric and adult brain tumors and highlight relevant differentiation therapies and putative candidates for prospective treatments.
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Affiliation(s)
- Rachel N. Curry
- Department of Neuroscience, Baylor College of Medicine, Center for Cell and Gene Therapy, Houston, TX, United States
- Integrative Molecular and Biomedical Sciences, Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Stacey M. Glasgow
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
- Neurosciences Graduate Program, University of California, San Diego, San Diego, CA, United States
- Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, CA, United States
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19
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Abe K, Kanehira M, Ohkouchi S, Kumata S, Suzuki Y, Oishi H, Noda M, Sakurada A, Miyauchi E, Fujiwara T, Harigae H, Okada Y. Targeting stanniocalcin-1-expressing tumor cells elicits efficient antitumor effects in a mouse model of human lung cancer. Cancer Med 2021; 10:3085-3100. [PMID: 33826244 PMCID: PMC8085941 DOI: 10.1002/cam4.3852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/23/2021] [Accepted: 02/28/2021] [Indexed: 12/26/2022] Open
Abstract
Lung cancer is the most common cause of cancer‐related death in developed countries; therefore, the generation of effective targeted therapeutic regimens is essential. Recently, gene therapy approaches toward malignant cells have emerged as attractive molecular therapeutics. Previous studies have indicated that stanniocalcin‐1 (STC‐1), a hormone involved in calcium and phosphate homeostasis, positively regulates proliferation, apoptosis resistance, and glucose metabolism in lung cancer cell lines. In this study, we investigated if targeting STC‐1 in tumor cells could be a promising strategy for lung cancer gene therapy. We confirmed that STC‐1 levels in peripheral blood were higher in lung cancer patients than in healthy donors and that STC‐1 expression was observed in five out of eight lung cancer cell lines. A vector expressing a suicide gene, uracil phosphoribosyltransferase (UPRT), under the control of the STC‐1 promoter, was constructed (pPSTC‐1‐UPRT) and transfected into three STC‐1‐positive cell lines, PC‐9, A549, and H1299. When stably transfected, we observed significant cell growth inhibition using 5‐fluorouracil (5‐FU) treatment. Furthermore, growth of the STC‐1‐negative lung cancer cell line, LK‐2 was significantly arrested when combined with STC‐1‐positive cells transfected with pPSTC‐1‐UPRT. We believe that conferring cytotoxicity in STC‐1‐positive lung cancer cells using a suicide gene may be a useful therapeutic strategy for lung cancer.
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Affiliation(s)
- Kotaro Abe
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masahiko Kanehira
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Center for Life Science Research, University of Yamanashi, Chuo, Japan
| | - Shinya Ohkouchi
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Sakiko Kumata
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Yamato Suzuki
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hisashi Oishi
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masafumi Noda
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Akira Sakurada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Eisaku Miyauchi
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Yoshinori Okada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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20
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Cheng R, Gao S, Hu W, Liu Y, Cao Y. Nuclear factor I/B mediates epithelial-mesenchymal transition in human melanoma cells through ZEB1. Oncol Lett 2020; 21:81. [PMID: 33363618 PMCID: PMC7723069 DOI: 10.3892/ol.2020.12342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 09/10/2020] [Indexed: 12/13/2022] Open
Abstract
The relationship between nuclear factor I/B (NFIB) and cancer attracts growing research interest. NFIB has diverse and specific roles in tumor progression and invasion. However, the potential effects and functions of this transcription factor in melanoma remain unclear. The present study sought to determine the distinguishing properties of NFIB in melanoma cells. Immunohistochemical examination of the tissues of 15 patients with melanoma indicated that the expression of NFIB was high in melanoma specimens, compared with the benign nevus and normal skin specimens. In addition, the relationship between high NFIB expression and low overall survival rate was assessed. Functional studies demonstrated that NFIB enhanced the malignancy of melanoma, including proliferation, migration and invasion. In addition, NFIB silencing in A375 and A875 cell lines inhibited the process of epithelial-mesenchymal transition (EMT), upregulated E-cadherin and zona occludens-1, but suppressed N-cadherin and vimentin expression. These findings may suggest a new function of NFIB in promoting the migration and invasion of melanoma cells. Therefore, the present study further evaluated the association between NFIB and zinc finger protein E-box binding homeobox-1 (ZEB1) in melanoma. Mechanistic experiments revealed that NFIB exerted its roles during EMT by regulating ZEB1. Overall, the present data indicates that NFIB promotes the malignancy of melanoma, particularly EMT, by modulating the ZEB1 axis, such as ZEB2, ATM and CHK1, which may represent a potential molecular therapeutic target in melanoma.
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Affiliation(s)
- Ruimin Cheng
- Department of Dermatology, Tongji Hospital, The Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Sheng Gao
- Department of Dermatology, Tongji Hospital, The Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Wei Hu
- Department of Dermatology, Tongji Hospital, The Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yamei Liu
- Department of Dermatology, Tongji Hospital, The Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yuchun Cao
- Department of Dermatology, Tongji Hospital, The Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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21
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Cui X, Dong Y, Li M, Wang X, Jiang M, Yang W, Liu G, Sun S, Xu W. A circular RNA from NFIX facilitates oxidative stress-induced H9c2 cells apoptosis. In Vitro Cell Dev Biol Anim 2020; 56:715-722. [PMID: 33067659 DOI: 10.1007/s11626-020-00476-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Myocardial infarction is the leading cause of death worldwide, and cardiomyocyte apoptosis during myocardial infarction and reperfusion is a significant factor of poor prognosis. As important regulatory molecules, biofunctions of circRNAs in the pathogenesis of myocardial infarction remain elusive. To confirm the expression level and biological function of circNFIX in cardiomyocytes upon oxidative stress. Divergent polymerase chain reaction and Sanger sequencing were performed to verify the circular structure. The stability of circNFIX was confirmed by RNase R treatment and actinomycin D assay. In order to simulate oxidative stress during myocardial infarction, H9c2 cells were subjected to hydrogen peroxide and hypoxia stimulation. In vivo, mouse models of myocardial ischemia were established. The biological function of circNFIX in cardiomyocytes was investigated through loss- and gain-of-function assays, and cardiomyocyte apoptosis level was detected by the terminal deoxyribonucleotidyl transferase-mediated TdT-mediated dUTP nick end labeling assay and Western blot. CircNFIX is abundant, conserved, and stable in H9c2 cells. The expression of circNFIX was significantly downregulated in cardiomyocytes subjected to oxidative stress. Enforced CircNFIX promotes H9c2 cells apoptosis induced by hydrogen peroxide, in sharp contrast to circNFIX knockdown. In this study, we found that circNFIX served as a pro-apoptosis factor in cardiomyocyte apoptosis. CircNFIX possesses potential to be the biomarker and therapeutic target in myocardial infarction.
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Affiliation(s)
- Xianglun Cui
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Yanhan Dong
- Institute for Translational Medicine, Qingdao University, Deng Zhou Road 38, Qingdao, 266021, China
| | - Mingyu Li
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Xuekang Wang
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Meiqing Jiang
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Weiwei Yang
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Gege Liu
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Shuqi Sun
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China
| | - Wenhua Xu
- Department of Inspection, The Medical Faculty, Qingdao University, Qingdao, 266003, China.
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22
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Sihombing NRB, Winarni TI, van Bokhoven H, van der Burgt I, de Leeuw N, Faradz SMH. Pathogenic variant in NFIX gene affecting three sisters due to paternal mosaicism. Am J Med Genet A 2020; 182:2731-2736. [PMID: 32945093 DOI: 10.1002/ajmg.a.61835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/14/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022]
Abstract
We present a family with three girls presenting similar dysmorphic features, including overgrowth, intellectual disability, macrocephaly, prominent forehead, midface retrusion, strabismus, and scoliosis. Both parents were unaffected, suggesting the presence of an autosomal recessive syndrome. Following exome sequencing, a heterozygous nonsense variant was identified in the NFIX gene in all three siblings. The father appeared to have a low-grade (7%) mosaicism for this variant in his blood. Previously, de novo pathogenic variants in NFIX have been identified in Marshall-Smith syndrome and Malan syndrome, which share distinctive phenotypic features shared with the patients of the present family. This case emphasizes the importance of further molecular analysis especially in familial cases, to exclude the possibility of parental mosaicism.
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Affiliation(s)
- Nydia Rena Benita Sihombing
- Doctoral Program of Medical and Health Sciences, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Tri Indah Winarni
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ineke van der Burgt
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sultana M H Faradz
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
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23
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Smith RL, O'Connell K, Athanasiu L, Djurovic S, Kringen MK, Andreassen OA, Molden E. Identification of a novel polymorphism associated with reduced clozapine concentration in schizophrenia patients-a genome-wide association study adjusting for smoking habits. Transl Psychiatry 2020; 10:198. [PMID: 32555152 PMCID: PMC7303159 DOI: 10.1038/s41398-020-00888-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 11/28/2022] Open
Abstract
Clozapine (CLZ) is the superior antipsychotic drug for treatment of schizophrenia, but exhibits an extensive interpatient pharmacokinetic variability. Here, we conducted a genome-wide association study (GWAS) of CLZ serum concentration adjusting for known smoking habits, which is a major nongenetic factor reducing CLZ levels. The study included 484 patients with 10,283 steady-state serum concentrations of CLZ and N-desmethylclozapine, prescribed dosing, co-medications and known smoking habits (n = 422; 9284 serum samples) from a therapeutic drug monitoring (TDM) service. The GWAS analyses were performed with and without smoking habits as covariate, where possible hits were assessed in relation to the target CLZ concentration range applied in the TDM service (300-2500 nmol/L). The smoking-independent analysis of N-desmethylclozapine serum concentration and the CLZ-to-N-desmethylclozapine ratio replicated the previously identified locus on chromosome 4. After adjusting for smoking habits in patients confirmed as 'smokers' (61%) or 'nonsmokers' (39%), a novel variant (rs28379954; minor T>C allele frequency 4.1%; 7.6% CT carriers in the population) within the gene encoding the nuclear factor 1 B-type (NFIB) was significantly associated with reduced CLZ serum concentration (p = 1.68 × 10-8, beta = -0.376; explained variance 7.63%). There was no significant association between rs28379954 and N-desmethylclozapine concentration in the GWAS analysis (p = 5.63 × 10-5). The fraction of CLZ TDM samples below 300 nmol/L was significantly higher in carriers vs. noncarriers of the rs28379954 minor C allele [12.0% (95% CI: 9.4-14.7) vs. 6.2% (95% CI: 5.7-6.8), p < 0.001]. We identified a novel variant in the NFIB gene associated with reduced CLZ levels and increased risk of subtherapeutic serum concentrations. This warrants testing of clinical relevance of screening for this gene variant, and also experimental studies to investigate the biological mechanisms of NFIB involvement in CLZ pharmacokinetics.
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Affiliation(s)
| | - Kevin O'Connell
- CoE NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lavinia Athanasiu
- CoE NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marianne Kristiansen Kringen
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - Ole A Andreassen
- CoE NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway.
- Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway.
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24
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Nuclear factor IX promotes glioblastoma development through transcriptional activation of Ezrin. Oncogenesis 2020; 9:39. [PMID: 32291386 PMCID: PMC7156762 DOI: 10.1038/s41389-020-0223-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
Enhanced migration is pivotal for the malignant development of glioblastoma (GBM), but the underlying molecular mechanism that modulates the migration of the GBM cells remains obscure. Here we show that nuclear factor IX (NFIX) is significantly upregulated in human GBM lesions compared with normal or low-grade gliomas. NFIX deficiency impairs the migration of GBM cells and inhibits the tumor growth in the hippocampus of immunodeficient nude mice. Mechanistically, NFIX silencing suppresses the expression of Ezrin, a protein that crosslinks actin cytoskeleton and plasma membrane, which is also positively correlated with GBM malignancy. NFIX depletion induced migration inhibition of GBM cells can be rescued by the replenishment of Ezrin. Furthermore, we identify a NFIX response element (RE) between −840 and −825 bp in the promoter region of the Ezrin gene. Altogether, our findings show, for the first time that NFIX can transcriptionally upregulate the expression of Ezrin and contribute to the enhanced migration of GBM cells, suggesting that NFIX is a potential target for GBM therapy.
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25
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Zenker M, Bunt J, Schanze I, Schanze D, Piper M, Priolo M, Gerkes EH, Gronostajski RM, Richards LJ, Vogt J, Wessels MW, Hennekam RC. Variants in nuclear factor I genes influence growth and development. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:611-626. [DOI: 10.1002/ajmg.c.31747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/26/2019] [Accepted: 10/09/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Martin Zenker
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Jens Bunt
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
| | - Ina Schanze
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Denny Schanze
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Michael Piper
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
- School of Biomedical SciencesThe University of Queensland Brisbane Queensland Australia
| | - Manuela Priolo
- Operative Unit of Medical GeneticsGreat Metropolitan Hospital Bianchi‐Melacrino‐Morelli Reggio Calabria Italy
| | - Erica H. Gerkes
- Department of Genetics, University of GroningenUniversity Medical Center Groningen Groningen the Netherlands
| | - Richard M. Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life SciencesState University of New York Buffalo NY
| | - Linda J. Richards
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
- School of Biomedical SciencesThe University of Queensland Brisbane Queensland Australia
| | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health PartnersWomen's and Children's Hospitals NHS Foundation Trust Birmingham UK
| | - Marja W. Wessels
- Department of Clinical Genetics, Erasmus MCUniversity Medical Center Rotterdam Rotterdam The Netherlands
| | - Raoul C. Hennekam
- Department of PediatricsUniversity of Amsterdam Amsterdam The Netherlands
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26
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Li H, Lampe JN. Neonatal cytochrome P450 CYP3A7: A comprehensive review of its role in development, disease, and xenobiotic metabolism. Arch Biochem Biophys 2019; 673:108078. [PMID: 31445893 DOI: 10.1016/j.abb.2019.108078] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 12/14/2022]
Abstract
The human cytochrome P450 CYP3A7, once thought to be an enzyme exclusive to fetal livers, has more recently been identified in neonates and developing infants as old as 24 months post-gestational age. CYP3A7 has been demonstrated to metabolize two endogenous compounds that are known to be important in the growth and development of the fetus and neonate, namely dehydroepiandrosterone sulfate (DHEA-S) and all-trans retinoic acid (atRA). In addition, it is also known to metabolize a variety of drugs and xenobiotics, albeit generally to a lesser extent relative to CYP3A4/5. CYP3A7 is an important component in the development and protection of the fetal liver and additionally plays a role in certain disease states, such as cancer and adrenal hyperplasia. Ultimately, a full understanding of the expression, regulation, and metabolic properties of CYP3A7 is needed to provide neonates with appropriate individualized pharmacotherapy. This article summarizes the current state of knowledge of CYP3A7, including its discovery, distribution, alleles, RNA splicing, expression and regulation, metabolic properties, substrates, and inhibitors.
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Affiliation(s)
- Haixing Li
- Sino-German Joint Research Institute Nanchang University, 235 East Nanjing Road, Nanchang, 330047, Jiangxi, PR China
| | - Jed N Lampe
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd., Aurora, CO, 80045, USA.
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27
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Hickey SL, Berto S, Konopka G. Chromatin Decondensation by FOXP2 Promotes Human Neuron Maturation and Expression of Neurodevelopmental Disease Genes. Cell Rep 2019; 27:1699-1711.e9. [PMID: 31067457 PMCID: PMC6794152 DOI: 10.1016/j.celrep.2019.04.044] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 03/08/2019] [Accepted: 04/08/2019] [Indexed: 01/06/2023] Open
Abstract
Forkhead box P2 (FOXP2) is a transcription factor expressed in the human brain that peaks during fetal development, and disruption in its ability to regulate downstream target genes leads to vulnerability to neurodevelopmental disorders. However, the mechanisms by which FOXP2 exerts regulatory control over targets during neuronal maturation have not been fully elucidated. Here, we use genome-wide chromatin accessibility assays and transcriptome-wide expression analyses in differentiating human neurons to show that FOXP2 represses proliferation-promoting genes in a DNA-binding-dependent manner. In contrast, FOXP2 and its cofactors, NFIA and NFIB, activate neuronal maturation genes in a manner that does not require FOXP2 to interact with DNA directly. Moreover, comparisons with expression data from the developing human brain suggest that FOXP2 and NFIA- or NFIB-dependent chromatin alterations drive maturation of excitatory cortical neurons. Thus, FOXP2 and its NFI cofactors may be specifically important for the development of cortical circuits underlying neurodevelopmental disorders.
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Affiliation(s)
- Stephanie L Hickey
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stefano Berto
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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28
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Sumardika IW, Chen Y, Tomonobu N, Kinoshita R, Ruma IMW, Sato H, Kondo E, Inoue Y, Yamauchi A, Murata H, Yamamoto KI, Tomida S, Shien K, Yamamoto H, Soh J, Futami J, Putranto EW, Hibino T, Nishibori M, Toyooka S, Sakaguchi M. Neuroplastin-β mediates S100A8/A9-induced lung cancer disseminative progression. Mol Carcinog 2019; 58:980-995. [PMID: 30720226 DOI: 10.1002/mc.22987] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/21/2022]
Abstract
Compiling evidence indicates an unusual role of extracellular S100A8/A9 in cancer metastasis. S100A8/A9 secreted from either cancer cells or normal cells including epithelial and inflammatory cells stimulates cancer cells through S100A8/A9 sensor receptors in an autocrine or paracrine manner, leading to cancer cell metastatic progression. We previously reported a novel S100A8/A9 receptor, neuroplastin-β (NPTNβ), which plays a critical role in atopic dermatitis when it is highly activated in keratinocytes by an excess amount of extracellular S100A8/A9 in the inflammatory skin lesion. Interestingly, our expression profiling of NPTNβ showed significantly high expression levels in lung cancer cell lines in a consistent manner. We hence aimed to determine the significance of NPTNβ as an S100A8/A9 receptor in lung cancer. Our results showed that NPTNβ has strong ability to induce cancer-related cellular events, including anchorage-independent growth, motility and invasiveness, in lung cancer cells in response to extracellular S100A8/A9, eventually leading to the expression of a cancer disseminative phenotype in lung tissue in vivo. Mechanistic investigation revealed that binding of S100A8/A9 to NPTNβ mediates activation of NFIA and NFIB and following SPDEF transcription factors through orchestrated upstream signals from TRAF2 and RAS, which is linked to anchorage-independent growth, motility and invasiveness. Overall, our results indicate the importance of the S100A8/A9-NPTNβ axis in lung cancer disseminative progression and reveal a pivotal role of its newly identified downstream signaling, TRAF2/RAS-NFIA/NFIB-SPDEF, in linking to the aggressive development of lung cancers.
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Affiliation(s)
- I Wayan Sumardika
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan.,Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Youyi Chen
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Nahoko Tomonobu
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Rie Kinoshita
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - I Made Winarsa Ruma
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan.,Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Hiroki Sato
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Eisaku Kondo
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medicine and Dental Sciences, Niigata-shi, Niigata, Japan
| | - Yusuke Inoue
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, Kiryu-shi, Gunma, Japan
| | - Akira Yamauchi
- Department of Biochemistry, Kawasaki Medical School, Kurashiki-shi, Okayama, Japan
| | - Hitoshi Murata
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Ken-Ichi Yamamoto
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Shuta Tomida
- Department of Biobank, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Kita-ku, Okayama, Japan
| | - Kazuhiko Shien
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Hiromasa Yamamoto
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Junichi Soh
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Junichiro Futami
- Department of Medical and Bioengineering Science, Okayama University Graduate School of Natural Science and Technology, Kita-ku, Okayama, Japan
| | - Endy Widya Putranto
- Department of Pediatrics, Dr. Sardjito Hospital/Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Toshihiko Hibino
- Department of Dermatology, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Masahiro Nishibori
- Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Shinichi Toyooka
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
| | - Masakiyo Sakaguchi
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama-shi, Okayama, Japan
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29
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Oishi S, Harkins D, Kurniawan ND, Kasherman M, Harris L, Zalucki O, Gronostajski RM, Burne THJ, Piper M. Heterozygosity for Nuclear Factor One X in mice models features of Malan syndrome. EBioMedicine 2019; 39:388-400. [PMID: 30503862 PMCID: PMC6354567 DOI: 10.1016/j.ebiom.2018.11.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Nuclear Factor One X (NFIX) haploinsufficiency in humans results in Malan syndrome, a disorder characterized by overgrowth, macrocephaly and intellectual disability. Although clinical assessments have determined the underlying symptomology of Malan syndrome, the fundamental mechanisms contributing to the enlarged head circumference and intellectual disability in these patients remains undefined. METHODS Here, we used Nfix heterozygous mice as a model to investigate these aspects of Malan syndrome. Volumetric magnetic resonance imaging (MRI) was used to calculate the volumes of 20 brain sub regions. Diffusion tensor MRI was used to perform tractography-based analyses of the corpus callosum, hippocampal commissure, and anterior commissure, as well as structural connectome mapping of the whole brain. Immunohistochemistry examined the neocortical cellular populations. Two behavioral assays were performed, including the active place avoidance task to assess spatial navigation and learning and memory function, and the 3-chambered sociability task to examine social behaviour. FINDINGS Adult Nfix+/- mice exhibit significantly increased brain volume (megalencephaly) compared to wildtypes, with the cerebral cortex showing the highest increase. Moreover, all three forebrain commissures, in particular the anterior commissure, revealed significantly reduced fractional anisotropy, axial and radial diffusivity, and tract density intensity. Structural connectome analyses revealed aberrant connectivity between many crucial brain regions. Finally, Nfix+/- mice exhibit behavioral deficits that model intellectual disability. INTERPRETATION Collectively, these data provide a significant conceptual advance in our understanding of Malan syndrome by suggesting that megalencephaly underlies the enlarged head size of these patients, and that disrupted cortical connectivity may contribute to the intellectual disability these patients exhibit. FUND: Australian Research Council (ARC) Discovery Project Grants, ARC Fellowship, NYSTEM and Australian Postgraduate Fellowships.
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Affiliation(s)
- Sabrina Oishi
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nyoman D Kurniawan
- The Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Maria Kasherman
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; The Francis Crick Institute, 1 Midland Road, King's Cross, London, United Kingdom
| | - Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Thomas H J Burne
- The Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, Brisbane, QLD 4076, Australia
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; The Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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30
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Fraser J, Essebier A, Brown AS, Davila RA, Sengar AS, Tu Y, Ensbey KS, Day BW, Scott MP, Gronostajski RM, Wainwright BJ, Boden M, Harvey TJ, Piper M. Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar development. Brain Struct Funct 2018; 224:811-827. [PMID: 30511336 DOI: 10.1007/s00429-018-1801-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 11/24/2018] [Indexed: 01/06/2023]
Abstract
Cerebellar granule neurons are the most numerous neuronal subtype in the central nervous system. Within the developing cerebellum, these neurons are derived from a population of progenitor cells found within the external granule layer of the cerebellar anlage, namely the cerebellar granule neuron precursors (GNPs). The timely proliferation and differentiation of these precursor cells, which, in rodents occurs predominantly in the postnatal period, is tightly controlled to ensure the normal morphogenesis of the cerebellum. Despite this, our understanding of the factors mediating how GNP differentiation is controlled remains limited. Here, we reveal that the transcription factor nuclear factor I X (NFIX) plays an important role in this process. Mice lacking Nfix exhibit reduced numbers of GNPs during early postnatal development, but elevated numbers of these cells at postnatal day 15. Moreover, Nfix-/- GNPs exhibit increased proliferation when cultured in vitro, suggestive of a role for NFIX in promoting GNP differentiation. At a mechanistic level, profiling analyses using both ChIP-seq and RNA-seq identified the actin-associated factor intersectin 1 as a downstream target of NFIX during cerebellar development. In support of this, mice lacking intersectin 1 also displayed delayed GNP differentiation. Collectively, these findings highlight a key role for NFIX and intersectin 1 in the regulation of cerebellar development.
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Affiliation(s)
- James Fraser
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Alexandra Essebier
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Alexander S Brown
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul Ayala Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ameet S Sengar
- Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, M5G 0A8, Canada
| | - YuShan Tu
- Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, M5G 0A8, Canada
| | - Kathleen S Ensbey
- Cell and Molecular Biology Department, Translational Brain Cancer Research Laboratory, QIMR Berghofer MRI, Brisbane, QLD, 4006, Australia
| | - Bryan W Day
- Cell and Molecular Biology Department, Translational Brain Cancer Research Laboratory, QIMR Berghofer MRI, Brisbane, QLD, 4006, Australia
| | - Matthew P Scott
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Mikael Boden
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia. .,Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
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31
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Schanze I, Bunt J, Lim JWC, Schanze D, Dean RJ, Alders M, Blanchet P, Attié-Bitach T, Berland S, Boogert S, Boppudi S, Bridges CJ, Cho MT, Dobyns WB, Donnai D, Douglas J, Earl DL, Edwards TJ, Faivre L, Fregeau B, Genevieve D, Gérard M, Gatinois V, Holder-Espinasse M, Huth SF, Izumi K, Kerr B, Lacaze E, Lakeman P, Mahida S, Mirzaa GM, Morgan SM, Nowak C, Peeters H, Petit F, Pilz DT, Puechberty J, Reinstein E, Rivière JB, Santani AB, Schneider A, Sherr EH, Smith-Hicks C, Wieland I, Zackai E, Zhao X, Gronostajski RM, Zenker M, Richards LJ. NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly. Am J Hum Genet 2018; 103:752-768. [PMID: 30388402 PMCID: PMC6218805 DOI: 10.1016/j.ajhg.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/03/2018] [Indexed: 12/19/2022] Open
Abstract
The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly.
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Affiliation(s)
- Ina Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Jens Bunt
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Jonathan W C Lim
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Ryan J Dean
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marielle Alders
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Patricia Blanchet
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Tania Attié-Bitach
- INSERM U1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris Descartes University, Sorbonne Paris Cité and Imagine Institute, Paris 75015, France
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Steven Boogert
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Sangamitra Boppudi
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Caitlin J Bridges
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | | | - William B Dobyns
- Department of Pediatrics (Genetics), University of Washington and Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Dian Donnai
- Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust; Division of Evolution and Genomic Sciences School of Biological Sciences, and University of Manchester, Manchester M13 9WL, UK
| | - Jessica Douglas
- Boston Children's Hospital - The Feingold Center, Waltham, MA 02115, USA
| | - Dawn L Earl
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Timothy J Edwards
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; The Faculty of Medicine Brisbane, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Laurence Faivre
- UMR1231, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon 21079, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire Dijon, Dijon 21079, France
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David Genevieve
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Marion Gérard
- Service de Génétique, CHU de Caen - Hôpital Clémenceau, Caen Cedex 14000, France
| | - Vincent Gatinois
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Muriel Holder-Espinasse
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille 59000, France; Department of Clinical Genetics, Guy's Hospital, London SE1 9RT, UK
| | - Samuel F Huth
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kosuke Izumi
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust; Division of Evolution and Genomic Sciences School of Biological Sciences, and University of Manchester, Manchester M13 9WL, UK
| | - Elodie Lacaze
- Department of genetics, Le Havre Hospital, 76600 Le Havre, France
| | - Phillis Lakeman
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Sonal Mahida
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ghayda M Mirzaa
- Department of Pediatrics (Genetics), University of Washington and Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Sian M Morgan
- All Wales Genetics Laboratory, Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Catherine Nowak
- Boston Children's Hospital - The Feingold Center, Waltham, MA 02115, USA
| | - Hilde Peeters
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven 3000, Belgium
| | - Florence Petit
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille 59000, France
| | - Daniela T Pilz
- West of Scotland Genetics Service, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Jacques Puechberty
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Eyal Reinstein
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba 4428164, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jean-Baptiste Rivière
- UMR1231, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon 21079, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire Dijon, Dijon 21079, France; Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Avni B Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anouck Schneider
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Ilse Wieland
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Elaine Zackai
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaonan Zhao
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany.
| | - Linda J Richards
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The Faculty of Medicine Brisbane, The University of Queensland, Brisbane, QLD 4072, Australia
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32
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Piper M, Gronostajski R, Messina G. Nuclear Factor One X in Development and Disease. Trends Cell Biol 2018; 29:20-30. [PMID: 30287093 DOI: 10.1016/j.tcb.2018.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023]
Abstract
The past decade has seen incredible advances in the field of stem cell biology that have greatly improved our understanding of development and provided important insights into pathological processes. Transcription factors (TFs) play a central role in mediating stem cell proliferation, quiescence, and differentiation. One TF that contributes to these processes is Nuclear Factor One X (NFIX). Recently, NFIX activity has been shown to be essential in multiple organ systems and to have important translational impacts for human health. Here, we describe recent studies showing the contribution of NFIX to muscle development and muscular dystrophies, hematopoiesis, cancer, and neural stem cell biology, highlighting the importance of this knowledge in the development of therapeutic targets.
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Affiliation(s)
- Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Richard Gronostajski
- Department of Biochemistry, Genetics, Genomics & Bioinformatics Graduate Program, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Graziella Messina
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy.
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33
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Kochmanski J, Marchlewicz EH, Cavalcante RG, Sartor MA, Dolinoy DC. Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood. Epigenetics 2018; 13:779-792. [PMID: 30079798 PMCID: PMC6224215 DOI: 10.1080/15592294.2018.1507198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/13/2018] [Accepted: 07/25/2018] [Indexed: 01/10/2023] Open
Abstract
DNA methylation at cytosine-phosphate-guanine (CpG) dinucleotides changes as a function of age in humans and animal models, a process that may contribute to chronic disease development. Recent studies have investigated the role of an oxidized form of DNA methylation - 5-hydroxymethylcytosine (5hmC) - in the epigenome, but its contribution to age-related DNA methylation remains unclear. We tested the hypothesis that 5hmC changes with age, but in a direction opposite to 5-methylcytosine (5mC), potentially playing a distinct role in aging. To characterize epigenetic aging, genome-wide 5mC and 5hmC were measured in longitudinal blood samples (2, 4, and 10 months of age) from isogenic mice using two sequencing methods - enhanced reduced representation bisulfite sequencing and hydroxymethylated DNA immunoprecipitation sequencing. Examining the epigenome by age, we identified 28,196 unique differentially methylated CpGs (DMCs) and 8,613 differentially hydroxymethylated regions (DHMRs). Mouse blood showed a general pattern of epigenome-wide hypermethylation and hypo-hydroxymethylation with age. Comparing age-related DMCs and DHMRs, 1,854 annotated genes showed both differential 5mC and 5hmC, including one gene - Nfic - at five CpGs in the same 250 bp chromosomal region. At this region, 5mC and 5hmC levels both decreased with age. Reflecting these age-related epigenetic changes, Nfic RNA expression in blood decreased with age, suggesting that age-related regulation of this gene may be driven by 5hmC, not canonical DNA methylation. Combined, our genome-wide results show age-related differential 5mC and 5hmC, as well as some evidence that changes in 5hmC may drive age-related DNA methylation and gene expression.
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Affiliation(s)
- Joseph Kochmanski
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth H. Marchlewicz
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Raymond G. Cavalcante
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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34
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Singh AJ, Chang CN, Ma HY, Ramsey SA, Filtz TM, Kioussi C. FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb. Sci Rep 2018; 8:7670. [PMID: 29769607 PMCID: PMC5956100 DOI: 10.1038/s41598-018-25998-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle in the forelimb develops during embryonic and fetal development and perinatally. While much is known regarding the molecules involved in forelimb myogenesis, little is known about the specific mechanisms and interactions. Migrating skeletal muscle precursor cells express Pax3 as they migrate into the forelimb from the dermomyotome. To compare gene expression profiles of the same cell population over time, we isolated lineage-traced Pax3+ cells (Pax3EGFP) from forelimbs at different embryonic days. We performed whole transcriptome profiling via RNA-Seq of Pax3+ cells to construct gene networks involved in different stages of embryonic and fetal development. With this, we identified genes involved in the skeletal, muscular, vascular, nervous and immune systems. Expression of genes related to the immune, skeletal and vascular systems showed prominent increases over time, suggesting a non-skeletal myogenic context of Pax3-derived cells. Using co-expression analysis, we observed an immune-related gene subnetwork active during fetal myogenesis, further implying that Pax3-derived cells are not a strictly myogenic lineage, and are involved in patterning and three-dimensional formation of the forelimb through multiple systems.
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Affiliation(s)
- Arun J Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Chih-Ning Chang
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA.,Molecular Cell Biology Graduate Program, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Hsiao-Yen Ma
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Stephen A Ramsey
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, 97331, USA.,School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Theresa M Filtz
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Chrissa Kioussi
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA.
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35
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Kim DW, Kim KC, Kim KB, Dunn CT, Park KS. Transcriptional deregulation underlying the pathogenesis of small cell lung cancer. Transl Lung Cancer Res 2018. [PMID: 29535909 DOI: 10.21037/tlcr.2017.10.07] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The discovery of recurrent alterations in genes encoding transcription regulators and chromatin modifiers is one of the most important recent developments in the study of the small cell lung cancer (SCLC) genome. With advances in models and analytical methods, the field of SCLC biology has seen remarkable progress in understanding the deregulated transcription networks linked to the tumor development and malignant progression. This review will discuss recent discoveries on the roles of RB and P53 family of tumor suppressors and MYC family of oncogenes in tumor initiation and development. It will also describe the roles of lineage-specific factors in neuroendocrine (NE) cell differentiation and homeostasis and the roles of epigenetic alterations driven by changes in NFIB and chromatin modifiers in malignant progression and chemoresistance. These recent findings have led to a model of transcriptional network in which multiple pathways converge on regulatory regions of crucial genes linked to tumor development. Validation of this model and characterization of target genes will provide critical insights into the biology of SCLC and novel strategies for tumor intervention.
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Affiliation(s)
- Dong-Wook Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Keun-Cheol Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA.,Department of Biological Sciences, Kangwon National University, Chuncheon, Korea
| | - Kee-Beom Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Colin T Dunn
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
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36
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Kinare V, Shetty AS, Suresh A, Tole S. PAX6 can substitute for LHX2 and override NFIA-induced astrogliogenesis in developing hippocampus in vivo. J Biosci 2018. [DOI: 10.1007/s12038-018-9731-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Transcriptional regulation of Nfix by NFIB drives astrocytic maturation within the developing spinal cord. Dev Biol 2017; 432:286-297. [PMID: 29106906 DOI: 10.1016/j.ydbio.2017.10.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 10/23/2017] [Accepted: 10/23/2017] [Indexed: 01/15/2023]
Abstract
During mouse spinal cord development, ventricular zone progenitor cells transition from producing neurons to producing glia at approximately embryonic day 11.5, a process known as the gliogenic switch. The transcription factors Nuclear Factor I (NFI) A and B initiate this developmental transition, but the contribution of a third NFI member, NFIX, remains unknown. Here, we reveal that ventricular zone progenitor cells within the spinal cord express NFIX after the onset of NFIA and NFIB expression, and after the gliogenic switch has occurred. Mice lacking NFIX exhibit normal neurogenesis within the spinal cord, and, while early astrocytic differentiation proceeds normally, aspects of terminal astrocytic differentiation are impaired. Finally, we report that, in the absence of Nfia or Nfib, there is a marked reduction in the spinal cord expression of NFIX, and that NFIB can transcriptionally activate Nfix expression in vitro. These data demonstrate that NFIX is part of the downstream transcriptional program through which NFIA and NFIB coordinate gliogenesis within the spinal cord. This hierarchical organisation of NFI protein expression and function during spinal cord gliogenesis reveals a previously unrecognised auto-regulatory mechanism within this gene family.
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38
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The convergent roles of the nuclear factor I transcription factors in development and cancer. Cancer Lett 2017; 410:124-138. [PMID: 28962832 DOI: 10.1016/j.canlet.2017.09.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/11/2017] [Accepted: 09/16/2017] [Indexed: 02/07/2023]
Abstract
The nuclear factor I (NFI) transcription factors play important roles during normal development and have been associated with developmental abnormalities in humans. All four family members, NFIA, NFIB, NFIC and NFIX, have a homologous DNA binding domain and function by regulating cell proliferation and differentiation via the transcriptional control of their target genes. More recently, NFI genes have also been implicated in cancer based on genomic analyses and studies of animal models in a variety of tumours across multiple organ systems. However, the association between their functions in development and in cancer is not well described. In this review, we summarise the evidence suggesting a converging role for the NFI genes in development and cancer. Our review includes all cancer types in which the NFI genes are implicated, focusing predominantly on studies demonstrating their oncogenic or tumour-suppressive potential. We conclude by presenting the challenges impeding our understanding of NFI function in cancer biology, and demonstrate how a developmental perspective may contribute towards overcoming such hurdles.
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39
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Khot VV, Yadav DK, Shrestha S, Kaur L, Sundrani DP, Chavan-Gautam PM, Mehendale SS, Chandak GR, Joshi SR. Hypermethylated CpG sites in the MTR gene promoter in preterm placenta. Epigenomics 2017; 9:985-996. [PMID: 28617183 DOI: 10.2217/epi-2016-0173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Altered maternal one-carbon metabolism influences placental DNA methylation patterns and 'programs' the fetus for noncommunicable diseases in adult life. EXPERIMENTAL PROCEDURES Levels of plasma folate, vitamin B12, homocysteine, mRNA and protein levels of MTHFR and MTR enzymes in placenta were compared among women delivering preterm (n = 83) and term (n = 75). MTR promoter CpG methylation was undertaken. RESULTS MTHFR and MTR mRNA levels were higher while protein levels were lower, and MTR CpG sites were hypermethylated in the preterm group, as compared with the term group. Methylated CpG sites were negatively associated with maternal plasma vitamin B12 levels. CONCLUSION Study suggests a dysregulation of enzyme genes in remethylation arm of the one-carbon metabolism in placenta of women delivering preterm.
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Affiliation(s)
- Vinita V Khot
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Dilip K Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Lovejeet Kaur
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Deepali P Sundrani
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Preeti M Chavan-Gautam
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Savita S Mehendale
- Obstetrics & Gynecology, Bharati Medical College & Hospital, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Sadhana R Joshi
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
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40
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Becker-Santos DD, Lonergan KM, Gronostajski RM, Lam WL. Nuclear Factor I/B: A Master Regulator of Cell Differentiation with Paradoxical Roles in Cancer. EBioMedicine 2017; 22:2-9. [PMID: 28596133 PMCID: PMC5552107 DOI: 10.1016/j.ebiom.2017.05.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/19/2017] [Accepted: 05/23/2017] [Indexed: 11/16/2022] Open
Abstract
Emerging evidence indicates that nuclear factor I/B (NFIB), a transcription factor required for proper development and regulation of cellular differentiation in several tissues, also plays critical roles in cancer. Despite being a metastatic driver in small cell lung cancer and melanoma, it has become apparent that NFIB also exhibits tumour suppressive functions in many malignancies. The contradictory contributions of NFIB to both the inhibition and promotion of tumour development and progression, corroborates its diverse and context-dependent roles in many tissues and cell types. Considering the frequent involvement of NFIB in cancer, a better understanding of its multifaceted nature may ultimately benefit the development of novel strategies for the management of a broad spectrum of malignancies. Here we discuss recent findings which bring to light NFIB as a crucial and paradoxical player in cancer. NFIB, a versatile regulator of cell differentiation, is emerging as a crucial driver of cancer metastasis. Paradoxically, NFIB also exhibits tumour suppressive functions in several cancer types. A deeper understanding of the multifaceted and context-dependent nature of NFIB has the potential to improve the clinical management of a variety of cancers.
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Affiliation(s)
- Daiana D Becker-Santos
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
| | - Kim M Lonergan
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
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41
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Roh SY, Park JC. The role of nuclear factor I-C in tooth and bone development. J Korean Assoc Oral Maxillofac Surg 2017; 43:63-69. [PMID: 28462188 PMCID: PMC5410429 DOI: 10.5125/jkaoms.2017.43.2.63] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 01/15/2023] Open
Abstract
Nuclear factor I-C (NFI-C) plays a pivotal role in various cellular processes such as odontoblast and osteoblast differentiation. Nfic-deficient mice showed abnormal tooth and bone formation. The transplantation of Nfic-expressing mouse bone marrow stromal cells rescued the impaired bone formation in Nfic-/- mice. Studies suggest that NFI-C regulate osteogenesis and dentinogenesis in concert with several factors including transforming growth factor-β1, Krüppel-like factor 4, and β-catenin. This review will focus on the function of NFI-C during tooth and bone formation and on the relevant pathways that involve NFI-C.
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Affiliation(s)
- Song Yi Roh
- Department of Oral Histology-Developmental Biology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
| | - Joo-Cheol Park
- Department of Oral Histology-Developmental Biology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Korea
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42
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Chen KS, Harris L, Lim JWC, Harvey TJ, Piper M, Gronostajski RM, Richards LJ, Bunt J. Differential neuronal and glial expression of nuclear factor I proteins in the cerebral cortex of adult mice. J Comp Neurol 2017; 525:2465-2483. [PMID: 28295292 DOI: 10.1002/cne.24206] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 12/31/2022]
Abstract
The nuclear factor I (NFI) family of transcription factors plays an important role in the development of the cerebral cortex in humans and mice. Disruption of nuclear factor IA (NFIA), nuclear factor IB (NFIB), or nuclear factor IX (NFIX) results in abnormal development of the corpus callosum, lateral ventricles, and hippocampus. However, the expression or function of these genes has not been examined in detail in the adult brain, and the cell type-specific expression of NFIA, NFIB, and NFIX is currently unknown. Here, we demonstrate that the expression of each NFI protein shows a distinct laminar pattern in the adult mouse neocortex and that their cell type-specific expression differs depending on the family member. NFIA expression was more frequently observed in astrocytes and oligodendroglia, whereas NFIB expression was predominantly localized to astrocytes and neurons. NFIX expression was most commonly observed in neurons. The NFI proteins were equally distributed within microglia, and the ependymal cells lining the ventricles of the brain expressed all three proteins. In the hippocampus, the NFI proteins were expressed during all stages of neural stem cell differentiation in the dentate gyrus, with higher expression intensity in neuroblast cells as compared to quiescent stem cells and mature granule neurons. These findings suggest that the NFI proteins may play distinct roles in cell lineage specification or maintenance, and establish the basis for further investigation of their function in the adult brain and their emerging role in disease.
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Affiliation(s)
- Kok-Siong Chen
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jonathan W C Lim
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael Piper
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Linda J Richards
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jens Bunt
- The Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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43
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Grabowska MM, Kelly SM, Reese AL, Cates JM, Case TC, Zhang J, DeGraff DJ, Strand DW, Miller NL, Clark PE, Hayward SW, Gronostajski RM, Anderson PD, Matusik RJ. Nfib Regulates Transcriptional Networks That Control the Development of Prostatic Hyperplasia. Endocrinology 2016; 157:1094-109. [PMID: 26677878 PMCID: PMC4769366 DOI: 10.1210/en.2015-1312] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A functional complex consisting of androgen receptor (AR) and forkhead box A1 (FOXA1) proteins supports prostatic development, differentiation, and disease. In addition, the interaction of FOXA1 with cofactors such as nuclear factor I (NFI) family members modulates AR target gene expression. However, the global role of specific NFI family members has yet to be described in the prostate. In these studies, chromatin immunoprecipitation followed by DNA sequencing in androgen-dependent LNCaP prostate cancer cells demonstrated that 64.3% of NFIB binding sites are associated with AR and FOXA1 binding sites. Interrogation of published data revealed that genes associated with NFIB binding sites are predominantly induced after dihydrotestosterone treatment of LNCaP cells, whereas NFIB knockdown studies demonstrated that loss of NFIB drives increased AR expression and superinduction of a subset of AR target genes. Notably, genes bound by NFIB only are associated with cell division and cell cycle. To define the role of NFIB in vivo, mouse Nfib knockout prostatic tissue was rescued via renal capsule engraftment. Loss of Nfib expression resulted in prostatic hyperplasia, which did not resolve in response to castration, and an expansion of an intermediate cell population in a small subset of grafts. In human benign prostatic hyperplasia, luminal NFIB loss correlated with more severe disease. Finally, some areas of intermediate cell expansion were also associated with NFIB loss. Taken together, these results show a fundamental role for NFIB as a coregulator of AR action in the prostate and in controlling prostatic hyperplasia.
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Affiliation(s)
- Magdalena M Grabowska
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Stephen M Kelly
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Amy L Reese
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Justin M Cates
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Tom C Case
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Jianghong Zhang
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - David J DeGraff
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Douglas W Strand
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Nicole L Miller
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Peter E Clark
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Simon W Hayward
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Richard M Gronostajski
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Philip D Anderson
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Robert J Matusik
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
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Lamani E, Gluhak-Heinrich J, MacDougall M. NFI-C2 temporal-spatial expression and cellular localization pattern during tooth formation. Dev Growth Differ 2015; 57:625-38. [PMID: 26687982 DOI: 10.1111/dgd.12253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 01/25/2023]
Abstract
Currently, little is known regarding critical signaling pathways during later stages of tooth development, especially those associated with root formation. Nfi-c null mice, lacking molar roots, have implicated the transcription factor NFI-C as having an essential role in root development. Previously, we identified three NFI-C isoforms expressed in dental tissues with NFI-C2 being the major transcript. However, the expression pattern of the NFI-C2 protein is not characterized. In this study we performed in situ hybridization and immunohistochemistry using isoform specific probes. We show the production of a NFI-C2 peptide antibody, its characterization, the temporal-spatial expression pattern of the NFI-C2 protein during odontogenesis and sub-cellular localization in dental cells. Moderate NFI-C2 staining, as early as bud stage, was detected mostly in the condensing dental ectomesenchyme. This staining intensified within the dental pulp at later stages culminating in high expression in the dentin producing odontoblasts. The dental epithelium showed slight staining until cytodifferentiation of enamel organ into ameloblasts and stratum intermedium. During root formation NFI-C2 expression was high in the Hertwig's epithelial root sheath and later was found in the fully developed root and its supporting tissues. NFI-C2 cellular staining was cytosolic, associated with the Golgi, and nuclear. These data suggest a broader role for NFI-C during tooth formation than limited to root and periodontal ligament development.
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Affiliation(s)
- Ejvis Lamani
- Department of Orthodontics, School of Dentistry, University of Alabama at Birmingham, 1720 2nd Ave South, Birmingham, Alabama, USA.,Institute of Oral Health Research, School of Dentistry, University of Alabama at Birmingham, 1530 3rd Ave South, Birmingham, AL 35294-0007, USA
| | - Jelica Gluhak-Heinrich
- Department of Developmental Dentistry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive Mail code 7894, DTL 4.599U, San Antonio, TX 78229, USA
| | - Mary MacDougall
- Institute of Oral Health Research, School of Dentistry, University of Alabama at Birmingham, 1530 3rd Ave South, Birmingham, AL 35294-0007, USA
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Lee DS, Choung HW, Kim HJ, Gronostajski RM, Yang YI, Ryoo HM, Lee ZH, Kim HH, Cho ES, Park JC. NFI-C regulates osteoblast differentiation via control of osterix expression. Stem Cells 2015; 32:2467-79. [PMID: 24801901 DOI: 10.1002/stem.1733] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 03/30/2014] [Indexed: 01/21/2023]
Abstract
In bone marrow, bone marrow stromal cells (BMSCs) have the capacity to differentiate into osteoblasts and adipocytes. Age-related osteoporosis is associated with a reciprocal decrease of osteogenesis and an increase of adipogenesis in bone marrow. In this study, we demonstrate that disruption of nuclear factor I-C (NFI-C) impairs osteoblast differentiation and bone formation, and increases bone marrow adipocytes. Interestingly, NFI-C controls postnatal bone formation but does not influence prenatal bone development. We also found decreased NFI-C expression in osteogenic cells from human osteoporotic patients. Notably, transplantation of Nfic-overexpressing BMSCs stimulates osteoblast differentiation and new bone formation, but inhibits adipocyte differentiation by suppressing peroxisome proliferator-activated receptor gamma expression in Nfic(-/-) mice showing an age-related osteoporosis-like phenotype. Finally, NFI-C directly regulates Osterix expression but acts downstream of the bone morphogenetic protein-2-Runx2 pathway. These results suggest that NFI-C acts as a transcriptional switch in cell fate determination between osteoblast and adipocyte differentiation in BMSCs. Therefore, regulation of NFI-C expression in BMSCs could be a novel therapeutic approach for treating age-related osteoporosis.
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Affiliation(s)
- Dong-Seol Lee
- Department of Oral Histology-Developmental Biology, Seoul National University, Chongro-gu, Seoul, Korea; Department of Anatomy and Orofacial Development, School of Dentistry, Chosun University, Dong-gu, Gwangju, Korea
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Vidovic D, Harris L, Harvey TJ, Evelyn Heng YH, Smith AG, Osinski J, Hughes J, Thomas P, Gronostajski RM, Bailey TL, Piper M. Expansion of the lateral ventricles and ependymal deficits underlie the hydrocephalus evident in mice lacking the transcription factor NFIX. Brain Res 2015; 1616:71-87. [DOI: 10.1016/j.brainres.2015.04.057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/20/2015] [Accepted: 04/29/2015] [Indexed: 11/29/2022]
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Edelmann S, Fahrner R, Malinka T, Song BH, Stroka D, Mermod N. Nuclear Factor I-C acts as a regulator of hepatocyte proliferation at the onset of liver regeneration. Liver Int 2015; 35:1185-94. [PMID: 25293436 DOI: 10.1111/liv.12697] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 10/01/2014] [Indexed: 02/13/2023]
Abstract
BACKGROUND & AIMS Knockout studies of the murine Nuclear Factor I-C (NFI-C) transcription factor revealed abnormal skin wound healing and growth of its appendages, suggesting a role in controlling cell proliferation in adult regenerative processes. Liver regeneration following partial hepatectomy (PH) is a well-established regenerative model whereby changes elicited in hepatocytes lead to their rapid and phased proliferation. Although NFI-C is highly expressed in the liver, no hepatic function was yet established for this transcription factor. This study aimed to determine whether NFI-C may play a role in hepatocyte proliferation and liver regeneration. METHODS Liver regeneration and cell proliferation pathways following two-thirds PH were investigated in NFI-C knockout (ko) and wild-type (wt) mice. RESULTS We show that the absence of NFI-C impaired hepatocyte proliferation because of plasminogen activator I (PAI-1) overexpression and the subsequent suppression of urokinase plasminogen activator (uPA) activity and hepatocyte growth factor (HGF) signalling, a potent hepatocyte mitogen. This indicated that NFI-C first acts to promote hepatocyte proliferation at the onset of liver regeneration in wt mice. The subsequent transient down regulation of NFI-C, as can be explained by a self-regulatory feedback loop with transforming growth factor beta 1 (TGF-ß1), may limit the number of hepatocytes entering the first wave of cell division and/or prevent late initiations of mitosis. CONCLUSION NFI-C acts as a regulator of the phased hepatocyte proliferation during liver regeneration.
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Affiliation(s)
- Simone Edelmann
- Institute of Biotechnology, University of Lausanne, Lausanne, Switzerland
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Kretova M, Sabova L, Hodny Z, Bartek J, Kollarovic G, Nelson BD, Hubackova S, Luciakova K. TGF-β/NF1/Smad4-mediated suppression of ANT2 contributes to oxidative stress in cellular senescence. Cell Signal 2014; 26:2903-11. [DOI: 10.1016/j.cellsig.2014.08.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/15/2014] [Indexed: 01/15/2023]
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Harris L, Genovesi LA, Gronostajski RM, Wainwright BJ, Piper M. Nuclear factor one transcription factors: Divergent functions in developmental versus adult stem cell populations. Dev Dyn 2014; 244:227-38. [PMID: 25156673 DOI: 10.1002/dvdy.24182] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/18/2014] [Accepted: 08/20/2014] [Indexed: 12/13/2022] Open
Abstract
Nuclear factor one (NFI) transcription factors are a group of site-specific DNA-binding proteins that are emerging as critical regulators of stem cell biology. During development NFIs promote the production of differentiated progeny at the expense of stem cell fate, with Nfi null mice exhibiting defects such as severely delayed brain and lung maturation, skeletomuscular defects and renal abnormalities, phenotypes that are often consistent with patients with congenital Nfi mutations. Intriguingly, recent research suggests that in adult tissues NFI factors play a qualitatively different role than during development, with NFIs serving to promote the survival and maintenance of slow-cycling adult stem cell populations rather than their differentiation. Here we review the role of NFI factors in development, largely focusing on their role as promoters of stem cell differentiation, and attempt to reconcile this with the emerging role of NFIs in adult stem cell niches.
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Affiliation(s)
- Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
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Shaltouki A, Peng J, Liu Q, Rao MS, Zeng X. Efficient generation of astrocytes from human pluripotent stem cells in defined conditions. Stem Cells 2014; 31:941-52. [PMID: 23341249 DOI: 10.1002/stem.1334] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 12/24/2012] [Indexed: 01/07/2023]
Abstract
Astrocytes can be generated from various tissue sources including human pluripotent stem cells (PSC). In this manuscript, we describe a chemically defined xeno-free medium culture system for rapidly generating astrocytes from neural stem cells derived from PSC. We show that astrocyte development in vitro, mimics normal development in vivo, and also passes through a CD44(+) astrocyte precursor stage. Astrocytes generated by our method display similar gene expression patterns, morphological characteristics and functional properties to primary astrocytes, and they survive and integrate after xenotransplantation. Whole genome expression profiling of astrocyte differentiation was performed at several time points of differentiation, and the results indicate the importance of known regulators and identify potential novel regulators and stage-specific lineage markers.
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