1
|
Theusch E, Ting FY, Qin Y, Stevens K, Naidoo D, King SM, Yang NV, Orr J, Han BY, Cyster JG, Chen YDI, Rotter JI, Krauss RM, Medina MW. Participant-derived cell line transcriptomic analyses and mouse studies reveal a role for ZNF335 in plasma cholesterol statin response. Genome Med 2024; 16:93. [PMID: 39061094 PMCID: PMC11282643 DOI: 10.1186/s13073-024-01366-9] [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: 06/27/2023] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Statins lower circulating low-density lipoprotein cholesterol (LDLC) levels and reduce cardiovascular disease risk. Though highly efficacious in general, there is considerable inter-individual variation in statin efficacy that remains largely unexplained. METHODS To identify novel genes that may modulate statin-induced LDLC lowering, we used RNA-sequencing data from 426 control- and 2 µM simvastatin-treated lymphoblastoid cell lines (LCLs) derived from European and African American ancestry participants of the Cholesterol and Pharmacogenetics (CAP) 40 mg/day 6-week simvastatin clinical trial (ClinicalTrials.gov Identifier: NCT00451828). We correlated statin-induced changes in LCL gene expression with plasma LDLC statin response in the corresponding CAP participants. For the most correlated gene identified (ZNF335), we followed up in vivo by comparing plasma cholesterol levels, lipoprotein profiles, and lipid statin response between wild-type mice and carriers of a hypomorphic (partial loss of function) missense mutation in Zfp335 (the mouse homolog of ZNF335). RESULTS The statin-induced expression changes of 147 human LCL genes were significantly correlated to the plasma LDLC statin responses of the corresponding CAP participants in vivo (FDR = 5%). The two genes with the strongest correlations were zinc finger protein 335 (ZNF335 aka NIF-1, rho = 0.237, FDR-adj p = 0.0085) and CCR4-NOT transcription complex subunit 3 (CNOT3, rho = 0.233, FDR-adj p = 0.0085). Chow-fed mice carrying a hypomorphic missense (R1092W; aka bloto) mutation in Zfp335 had significantly lower non-HDL cholesterol levels than wild-type C57BL/6J mice in a sex combined model (p = 0.04). Furthermore, male (but not female) mice carrying the Zfp335R1092W allele had significantly lower total and HDL cholesterol levels than wild-type mice. In a separate experiment, wild-type mice fed a control diet for 4 weeks and a matched simvastatin diet for an additional 4 weeks had significant statin-induced reductions in non-HDLC (-43 ± 18% and -23 ± 19% for males and females, respectively). Wild-type male (but not female) mice experienced significant reductions in plasma LDL particle concentrations, while male mice carrying Zfp335R1092W allele(s) exhibited a significantly blunted LDL statin response. CONCLUSIONS Our in vitro and in vivo studies identified ZNF335 as a novel modulator of plasma cholesterol levels and statin response, suggesting that variation in ZNF335 activity could contribute to inter-individual differences in statin clinical efficacy.
Collapse
Affiliation(s)
- Elizabeth Theusch
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA.
| | - Flora Y Ting
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Yuanyuan Qin
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Kristen Stevens
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Devesh Naidoo
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Sarah M King
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Neil V Yang
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Joseph Orr
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Brenda Y Han
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Jason G Cyster
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Yii-Der I Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ronald M Krauss
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
- Department of Medicine, University of California San Francisco, Oakland, CA, USA
| | - Marisa W Medina
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA.
| |
Collapse
|
2
|
Wang X, Sun L, Yang B, Li W, Zhang C, Yang X, Sun Y, Shen X, Gao Y, Ju B, Gao Y, Liu D, Song J, Jia X, Su Y, Jiao A, Liu H, Zhang L, Lan He, Lei L, Chen W, Zhang B. Zfp335 establishes eTreg lineage and neonatal immune tolerance by targeting Hadha-mediated fatty acid oxidation. J Clin Invest 2023; 133:e166628. [PMID: 37843279 PMCID: PMC10575732 DOI: 10.1172/jci166628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 08/15/2023] [Indexed: 10/17/2023] Open
Abstract
Regulatory T cells (Tregs) are instrumental in maintaining immune tolerance and preventing destructive autoimmunity, but how heterogeneous Treg populations are established remains largely unknown. Here, we show that Zfp335 deletion in Tregs failed to differentiate into effector Tregs (eTregs) and lose Treg-suppressive function and that KO mice exhibited early-onset lethal autoimmune inflammation with unrestricted activation of conventional T cells. Single-cell RNA-Seq analyses revealed that Zfp335-deficient Tregs lacked a eTreg population and showed dramatic accumulation of a dysfunctional Treg subset. Mechanistically, Zfp335-deficient Tregs displayed reduced oxidative phosphorylation and dysfunctional mitochondrial activity. Further studies revealed that Zfp335 controlled eTreg differentiation by regulating fatty acid oxidation (FAO) through direct targeting of the FAO enzyme Hadha. Importantly, we demonstrate a positive correlation between ZNF335 and HADHA expression in human eTregs. Our findings reveal that Zfp335 controls FAO-driven eTreg differentiation to establish immune tolerance.
Collapse
Affiliation(s)
- Xin Wang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Lina Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Biao Yang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Wenhua Li
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Xiaofeng Yang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an, Shaanxi, China
- Xi’an Key Laboratory of Immune-Related Diseases, Xi’an, Shannxi, China
| | - Yae Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Xiaonan Shen
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Yang Gao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Bomiao Ju
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yafeng Gao
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Dan Liu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, China
| | - Jiapeng Song
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Xiaoxuan Jia
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Haiyan Liu
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Lianjun Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Lan He
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Lei Lei
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - WanJun Chen
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, Maryland, USA
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an, Shaanxi, China
- Xi’an Key Laboratory of Immune-Related Diseases, Xi’an, Shannxi, China
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| |
Collapse
|
3
|
Li D, Quan Z, Ni J, Li H, Qing H. The many faces of the zinc finger protein 335 in brain development and immune system. Biomed Pharmacother 2023; 165:115257. [PMID: 37541176 DOI: 10.1016/j.biopha.2023.115257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023] Open
Abstract
Zinc finger protein 335 (ZNF335) plays a crucial role in the methylation and, consequently, regulates the expression of a specific set of genes. Variants of the ZNF335 gene have been identified as risk factors for microcephaly in a variety of populations worldwide. Meanwhile, ZNF335 has also been identified as an essential regulator of T-cell development. However, an in-depth understanding of the role of ZNF335 in brain development and T cell maturation is still lacking. In this review, we summarize current knowledge of the molecular mechanisms underlying the involvement of ZNF335 in neuronal and T cell development across a wide range of pre-clinical, post-mortem, ex vivo, in vivo, and clinical studies. We also review the current limitations regarding the study of the pathophysiological functions of ZNF335. Finally, we hypothesize a potential role for ZNF335 in brain disorders and discuss the rationale of targeting ZNF335 as a therapeutic strategy for preventing brain disorders.
Collapse
Affiliation(s)
- Danyang Li
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Zhenzhen Quan
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Hui Li
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| |
Collapse
|
4
|
Theusch E, Ting FY, Qin Y, Stevens K, Naidoo D, King SM, Yang N, Orr J, Han BY, Cyster JG, Chen YDI, Rotter JI, Krauss RM, Medina MW. Participant-derived cell line transcriptomic analyses and mouse studies reveal a role for ZNF335 in plasma cholesterol statin response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544860. [PMID: 37397985 PMCID: PMC10312755 DOI: 10.1101/2023.06.14.544860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background Statins lower circulating low-density lipoprotein cholesterol (LDLC) levels and reduce cardiovascular disease risk. Though highly efficacious in general, there is considerable inter-individual variation in statin efficacy that remains largely unexplained. Methods To identify novel genes that may modulate statin-induced LDLC lowering, we used RNA-sequencing data from 426 control- and 2 μM simvastatin-treated lymphoblastoid cell lines (LCLs) derived from European and African American ancestry participants of the Cholesterol and Pharmacogenetics (CAP) 40 mg/day 6-week simvastatin clinical trial (ClinicalTrials.gov Identifier: NCT00451828). We correlated statin-induced changes in LCL gene expression with plasma LDLC statin response in the corresponding CAP participants. For the most correlated gene identified (ZNF335), we followed up in vivo by comparing plasma cholesterol levels, lipoprotein profiles, and lipid statin response between wild-type mice and carriers of a hypomorphic (partial loss of function) missense mutation in Zfp335 (the mouse homolog of ZNF335). Results The statin-induced expression changes of 147 human LCL genes were significantly correlated to the plasma LDLC statin responses of the corresponding CAP participants in vivo (FDR=5%). The two genes with the strongest correlations were zinc finger protein 335 (ZNF335 aka NIF-1, rho=0.237, FDR-adj p=0.0085) and CCR4-NOT transcription complex subunit 3 (CNOT3, rho=0.233, FDR-adj p=0.0085). Chow-fed mice carrying a hypomorphic missense (R1092W; aka bloto) mutation in Zfp335 had significantly lower non-HDL cholesterol levels than wild type C57BL/6J mice in a sex combined model (p=0.04). Furthermore, male (but not female) mice carrying the Zfp335R1092W allele had significantly lower total and HDL cholesterol levels than wild-type mice. In a separate experiment, wild-type mice fed a control diet for 4 weeks and a matched simvastatin diet for an additional 4 weeks had significant statin-induced reductions in non-HDLC (-43±18% and -23±19% for males and females, respectively). Wild-type male (but not female) mice experienced significant reductions in plasma LDL particle concentrations, while male mice carrying Zfp335R1092W allele(s) exhibited a significantly blunted LDL statin response. Conclusions Our in vitro and in vivo studies identified ZNF335 as a novel modulator of plasma cholesterol levels and statin response, suggesting that variation in ZNF335 activity could contribute to inter-individual differences in statin clinical efficacy.
Collapse
Affiliation(s)
- Elizabeth Theusch
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Flora Y. Ting
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Yuanyuan Qin
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Kristen Stevens
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Devesh Naidoo
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Sarah M. King
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Neil Yang
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Joseph Orr
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| | - Brenda Y. Han
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA USA
| | - Jason G. Cyster
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA USA
| | - Yii-Der I. Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Ronald M. Krauss
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
- Department of Medicine, University of California San Francisco, Oakland, CA USA
| | - Marisa W. Medina
- Department of Pediatrics, University of California San Francisco, Oakland, CA USA
| |
Collapse
|
5
|
Genomic Structure, Protein Character, Phylogenic Implication, and Embryonic Expression Pattern of a Zebrafish New Member of Zinc Finger BED-Type Gene Family. Genes (Basel) 2023; 14:genes14010179. [PMID: 36672921 PMCID: PMC9859435 DOI: 10.3390/genes14010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
We reported a new member of the C2H2-zinc-finger BED-type (ZBED) protein family found in zebrafish (Danio rerio). It was previously assigned as an uncharacterized protein LOC569044 encoded by the Zgc:161969 gene, the transcripts of which were highly expressed in the CNS after the spinal cord injury of zebrafish. As such, this novel gene deserves a more detailed investigation. The 2.79-kb Zgc:161969 gene contains one intron located on Chromosome 6 at 16,468,776-16,475,879 in the zebrafish genome encoding a 630-aa protein LOC569044. This protein is composed of a DNA-binding BED domain, which is highly conserved among the ZBED protein family, and a catalytic domain consisting of an α-helix structure and an hAT dimerization region. Phylogenetic analysis revealed the LOC569044 protein to be clustered into the monophyletic clade of the ZBED protein family of golden fish. Specifically, the LOC569044 protein was classified as closely related to the monophyletic clades of zebrafish ZBED4-like isoforms and ZBED isoform 2. Furthermore, Zgc:161969 transcripts represented maternal inheritance, expressed in the brain and eyes at early developmental stages and in the telencephalon ventricular zone at late developmental stages. After characterizing the LOC569044 protein encoded by the Zgc:161969 gene, it was identified as a new member of the zebrafish ZBED protein family, named the ZBEDX protein.
Collapse
|
6
|
Liu H, Wang X, Ding R, Jiao A, Zheng H, Zhang C, Feng Z, Su Y, Yang X, Lei L, Sun L, Zhang L, Sun C, Zhang B. The Transcription Factor Zfp335 Promotes Differentiation and Persistence of Memory CD8 +T Cells by Regulating TCF-1. THE JOURNAL OF IMMUNOLOGY 2022; 209:886-895. [DOI: 10.4049/jimmunol.2200026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/17/2022] [Indexed: 11/05/2022]
|
7
|
Wang X, Jiao A, Sun L, Li W, Yang B, Su Y, Ding R, Zhang C, Liu H, Yang X, Sun C, Zhang B. Zinc finger protein Zfp335 controls early T cell development and survival through β-selection-dependent and -independent mechanisms. eLife 2022; 11:75508. [PMID: 35113015 PMCID: PMC8871394 DOI: 10.7554/elife.75508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/03/2022] [Indexed: 11/23/2022] Open
Abstract
T-cell development in the thymus undergoes the process of differentiation, selective proliferation, and survival from CD4−CD8− double negative (DN) stage to CD4+CD8+ double positive (DP) stage prior to the formation of CD4+ helper and CD8+ cytolytic T cells ready for circulation. Each developmental stage is tightly regulated by sequentially operating molecular networks, of which only limited numbers of transcription regulators have been deciphered. Here, we identified Zfp335 transcription factor as a new player in the regulatory network controlling thymocyte development in mice. We demonstrate that Zfp335 intrinsically controls DN to DP transition, as T-cell-specific deficiency in Zfp335 leads to a substantial accumulation of DN3 along with reduction of DP, CD4+, and CD8+ thymocytes. This developmental blockade at DN stage results from the impaired intracellular TCRβ (iTCRβ) expression as well as increased susceptibility to apoptosis in thymocytes. Transcriptomic and ChIP-seq analyses revealed a direct regulation of transcription factors Bcl6 and Rorc by Zfp335. Importantly, enhanced expression of TCRβ and Bcl6/Rorc restores the developmental defect during DN3 to DN4 transition and improves thymocytes survival, respectively. These findings identify a critical role of Zfp335 in controlling T-cell development by maintaining iTCRβ expression-mediated β-selection and independently activating cell survival signaling.
Collapse
Affiliation(s)
- Xin Wang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Lina Sun
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Wenhua Li
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Biao Yang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Renyi Ding
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Haiyan Liu
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Xiaofeng Yang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Chenming Sun
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
8
|
Comprehensive review on the molecular genetics of autosomal recessive primary microcephaly (MCPH). Genet Res (Camb) 2018; 100:e7. [PMID: 30086807 DOI: 10.1017/s0016672318000046] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Primary microcephaly (MCPH) is an autosomal recessive sporadic neurodevelopmental ailment with a trivial head size characteristic that is below 3-4 standard deviations. MCPH is the smaller upshot of an architecturally normal brain; a significant decrease in size is seen in the cerebral cortex. At birth MCPH presents with non-progressive mental retardation, while secondary microcephaly (onset after birth) presents with and without other syndromic features. MCPH is a neurogenic mitotic syndrome nevertheless pretentious patients demonstrate normal neuronal migration, neuronal apoptosis and neural function. Eighteen MCPH loci (MCPH1-MCPH18) have been mapped to date from various populations around the world and contain the following genes: Microcephalin, WDR62, CDK5RAP2, CASC5, ASPM, CENPJ, STIL, CEP135, CEP152, ZNF335, PHC1, CDK6, CENPE, SASS6, MFSD2A, ANKLE2, CIT and WDFY3, clarifying our understanding about the molecular basis of microcephaly genetic disorder. It has previously been reported that phenotype disease is caused by MCB gene mutations and the causes of this phenotype are disarrangement of positions and organization of chromosomes during the cell cycle as a result of mutated DNA, centriole duplication, neurogenesis, neuronal migration, microtubule dynamics, transcriptional control and the cell cycle checkpoint having some invisible centrosomal process that can manage the number of neurons that are produced by neuronal precursor cells. Furthermore, researchers inform us about the clinical management of families that are suffering from MCPH. Establishment of both molecular understanding and genetic advocating may help to decrease the rate of this ailment. This current review study examines newly identified genes along with previously identified genes involved in autosomal recessive MCPH.
Collapse
|
9
|
Han BY, Foo CS, Wu S, Cyster JG. The C2H2-ZF transcription factor Zfp335 recognizes two consensus motifs using separate zinc finger arrays. Genes Dev 2017; 30:1509-14. [PMID: 27401554 PMCID: PMC4949324 DOI: 10.1101/gad.279406.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 06/15/2016] [Indexed: 12/22/2022]
Abstract
Here, Han et al. show that transcription factor Zfp335 binds DNA and drives transcription via recognition of two distinct consensus motifs by separate ZF clusters and identify the specific motif interaction disrupted by the mutation R1092W. This study presents Zfp335 as a model for understanding how C2H2-ZF TFs may use multiple recognition motifs to control gene expression. The complexities of DNA recognition by transcription factors (TFs) with multiple Cys2–His2 zinc fingers (C2H2-ZFs) remain poorly studied. We previously reported a mutation (R1092W) in the C2H2-ZF TF Zfp335 that led to selective loss of binding at a subset of targets, although the basis for this effect was unclear. We show that Zfp335 binds DNA and drives transcription via recognition of two distinct consensus motifs by separate ZF clusters and identify the specific motif interaction disrupted by R1092W. Our work presents Zfp335 as a model for understanding how C2H2-ZF TFs may use multiple recognition motifs to control gene expression.
Collapse
Affiliation(s)
- Brenda Yuyuan Han
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| | - Chuan-Sheng Foo
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Shuang Wu
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jason G Cyster
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94143, USA; Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94143, USA
| |
Collapse
|
10
|
Common polygenic variation in coeliac disease and confirmation of ZNF335 and NIFA as disease susceptibility loci. Eur J Hum Genet 2015; 24:291-7. [PMID: 25920553 PMCID: PMC4717209 DOI: 10.1038/ejhg.2015.87] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 03/05/2015] [Accepted: 03/10/2015] [Indexed: 12/22/2022] Open
Abstract
Coeliac disease (CD) is a chronic immune-mediated disease triggered by the ingestion of gluten. It has an estimated prevalence of approximately 1% in European populations. Specific HLA-DQA1 and HLA-DQB1 alleles are established coeliac susceptibility genes and are required for the presentation of gliadin to the immune system resulting in damage to the intestinal mucosa. In the largest association analysis of CD to date, 39 non-HLA risk loci were identified, 13 of which were new, in a sample of 12 014 individuals with CD and 12 228 controls using the Immunochip genotyping platform. Including the HLA, this brings the total number of known CD loci to 40. We have replicated this study in an independent Irish CD case–control population of 425 CD and 453 controls using the Immunochip platform. Using a binomial sign test, we show that the direction of the effects of previously described risk alleles were highly correlated with those reported in the Irish population, (P=2.2 × 10−16). Using the Polygene Risk Score (PRS) approach, we estimated that up to 35% of the genetic variance could be explained by loci present on the Immunochip (P=9 × 10−75). When this is limited to non-HLA loci, we explain a maximum of 4.5% of the genetic variance (P=3.6 × 10−18). Finally, we performed a meta-analysis of our data with the previous reports, identifying two further loci harbouring the ZNF335 and NIFA genes which now exceed genome-wide significance, taking the total number of CD susceptibility loci to 42.
Collapse
|
11
|
Zhao XS, Fu WY, Hung KW, Chien WWY, Li Z, Fu AK, Ip NY. NRC-interacting factor directs neurite outgrowth in an activity-dependent manner. Neuroscience 2015; 289:207-13. [PMID: 25573434 DOI: 10.1016/j.neuroscience.2014.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/05/2014] [Accepted: 12/24/2014] [Indexed: 11/18/2022]
Abstract
Nuclear hormone receptor coregulator-interacting factor 1 (NIF-1) is a zinc finger nuclear protein that was initially identified to enhance nuclear hormone receptor transcription via its interaction with nuclear hormone receptor coregulator (NRC). NIF-1 may regulate gene transcription either by modulating general transcriptional machinery or remodeling chromatin structure through interactions with specific protein partners. We previously reported that the cytoplasmic/nuclear localization of NIF-1 is regulated by the neuronal Cdk5 activator p35, suggesting potential neuronal functions for NIF-1. The present study reveals that NIF-1 plays critical roles in regulating neuronal morphogenesis at early stages. NIF-1 was prominently expressed in the nuclei of developing rat cortical neurons. Knockdown of NIF-1 expression attenuated both neurite outgrowth in cultured cortical neurons and retinoic acid (RA)-treated Neuro-2a neuroblastoma cells. Furthermore, activity-induced Ca(2+) influx, which is critical for neuronal morphogenesis, stimulated the nuclear localization of NIF-1 in cortical neurons. Suppression of NIF-1 expression reduced the up-regulation of neuronal activity-dependent gene transcription. These findings collectively suggest that NIF-1 directs neuronal morphogenesis during early developmental stages through modulating activity-dependent gene transcription.
Collapse
Affiliation(s)
- X-S Zhao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - W-Y Fu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - K-W Hung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - W W Y Chien
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Z Li
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - A K Fu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - N Y Ip
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| |
Collapse
|
12
|
TLR4/NF-κB-responsive microRNAs and their potential target genes: a mouse model of skeletal muscle ischemia-reperfusion injury. BIOMED RESEARCH INTERNATIONAL 2015; 2015:410721. [PMID: 25692136 PMCID: PMC4321099 DOI: 10.1155/2015/410721] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/01/2014] [Accepted: 10/13/2014] [Indexed: 12/20/2022]
Abstract
Background. The aim of this study was to profile TLR4/NF-κB-responsive microRNAs (miRNAs) and their potential target genes in the skeletal muscles of mice following ischemia-reperfusion injury. Methods. Thigh skeletal muscles of C57BL/6, Tlr4−/−, and NF-κB−/− mice isolated based on femoral artery perfusion were subjected to ischemia for 2 h and reperfusion for 0 h, 4 h, 1 d, and 7 d. The muscle specimens were analyzed with miRNA arrays. Immunoprecipitation with an argonaute 2- (Ago2-) specific monoclonal antibody followed by whole genome microarray was performed to identify mRNA associated with the RNA-silencing machinery. The potential targets of each upregulated miRNA were identified by combined analysis involving the bioinformatics algorithm miRanda and whole genome expression. Results. Three TLR4/NF-κB-responsive miRNAs (miR-15a, miR-744, and miR-1196) were significantly upregulated in the muscles following ischemia-reperfusion injury. The combined in silico and whole genome microarray approaches identified 5, 4, and 20 potential target genes for miR-15a, miR-744, and miR-1196, respectively. Among the 3 genes (Zbed4, Lrsam1, and Ddx21) regulated by at least 2 of the 3 upregulated miRNAs, Lrsam1 and Ddx21 are known to be associated with the innate immunity pathway. Conclusions. This study profiled TLR4/NF-κB-responsive miRNAs and their potential target genes in mouse skeletal muscle subjected to ischemia-reperfusion injury.
Collapse
|
13
|
Shortt K, Chaudhary S, Grigoryev D, Heruth DP, Venkitachalam L, Zhang LQ, Ye SQ. Identification of novel single nucleotide polymorphisms associated with acute respiratory distress syndrome by exome-seq. PLoS One 2014; 9:e111953. [PMID: 25372662 PMCID: PMC4221189 DOI: 10.1371/journal.pone.0111953] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/29/2014] [Indexed: 12/26/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a lung condition characterized by impaired gas exchange with systemic release of inflammatory mediators, causing pulmonary inflammation, vascular leak and hypoxemia. Existing biomarkers have limited effectiveness as diagnostic and therapeutic targets. To identify disease-associating variants in ARDS patients, whole-exome sequencing was performed on 96 ARDS patients, detecting 1,382,399 SNPs. By comparing these exome data to those of the 1000 Genomes Project, we identified a number of single nucleotide polymorphisms (SNP) which are potentially associated with ARDS. 50,190SNPs were found in all case subgroups and controls, of which89 SNPs were associated with susceptibility. We validated three SNPs (rs78142040, rs9605146 and rs3848719) in additional ARDS patients to substantiate their associations with susceptibility, severity and outcome of ARDS. rs78142040 (C>T) occurs within a histone mark (intron 6) of the Arylsulfatase D gene. rs9605146 (G>A) causes a deleterious coding change (proline to leucine) in the XK, Kell blood group complex subunit-related family, member 3 gene. rs3848719 (G>A) is a synonymous SNP in the Zinc-Finger/Leucine-Zipper Co-Transducer NIF1 gene. rs78142040, rs9605146, and rs3848719 are associated significantly with susceptibility to ARDS. rs3848719 is associated with APACHE II score quartile. rs78142040 is associated with 60-day mortality in the overall ARDS patient population. Exome-seq is a powerful tool to identify potential new biomarkers for ARDS. We selectively validated three SNPs which have not been previously associated with ARDS and represent potential new genetic biomarkers for ARDS. Additional validation in larger patient populations and further exploration of underlying molecular mechanisms are warranted.
Collapse
Affiliation(s)
- Katherine Shortt
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
- Department of Biomedical and Health Informatics, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Suman Chaudhary
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Dmitry Grigoryev
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
- Department of Biomedical and Health Informatics, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Daniel P. Heruth
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Lakshmi Venkitachalam
- Department of Biomedical and Health Informatics, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Li Q. Zhang
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
| | - Shui Q. Ye
- Department of Pediatrics, Division of Experimental and Translational Genetics, Children's Mercy Hospital, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
- Department of Biomedical and Health Informatics, University of Missouri - Kansas City School of Medicine, Kansas City, Missouri, United States of America
- * E-mail:
| |
Collapse
|
14
|
Han BY, Wu S, Foo CS, Horton RM, Jenne CN, Watson SR, Whittle B, Goodnow CC, Cyster JG. Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment. eLife 2014; 3. [PMID: 25343476 PMCID: PMC4371841 DOI: 10.7554/elife.03549] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 09/24/2014] [Indexed: 12/26/2022] Open
Abstract
The generation of naïve T lymphocytes is critical for immune function yet the
mechanisms governing their maturation remain incompletely understood. We have
identified a mouse mutant, bloto, that harbors a hypomorphic
mutation in the zinc finger protein Zfp335.
Zfp335bloto/bloto mice exhibit a naïve T cell
deficiency due to an intrinsic developmental defect that begins to manifest in the
thymus and continues into the periphery, affecting T cells that have recently
undergone thymic egress. The effects of Zfp335bloto are multigenic and
cannot be attributed to altered thymic selection, proliferation or Bcl2-dependent
survival. Zfp335 binds to promoter regions via a consensus motif, and its target
genes are enriched in categories related to protein metabolism, mitochondrial
function, and transcriptional regulation. Restoring the expression of one target,
Ankle2, partially rescues T cell maturation. These findings identify Zfp335 as a
transcription factor and essential regulator of late-stage intrathymic and
post-thymic T cell maturation. DOI:http://dx.doi.org/10.7554/eLife.03549.001 To defend our bodies against a variety of foreign microbes, our immune system makes
cells called T cells that can identify these invaders and help to destroy them. There
are several types of T cells that play different roles in the immune response: some
activate other immune cells, while others destroy cells that have been infected by
viruses or other pathogens. T cells develop in a specialized organ called the thymus, where they go through a
rigorous selection process before being released as mature T cells into the rest of
the body. This selection process includes eliminating individual T cells that are
found to be sub-standard, perhaps because they might mistake our own cells for enemy
cells. However, many of the details of the later stages of T cell development are not
fully understood. Han et al. have now found that a protein called Zfp335 that is involved in the
production of mature T cells. Mice carrying a mutation in the gene that makes this
protein have fewer mature T cells than normal mice. Han et al. also reveal that
Zfp335 is a transcription factor that can control whether or not other genes are
expressed as proteins, and further show that one of these proteins, Ankle2, has an
important role in the production of mature T cells. A next step in the work is to define exactly how Zfp335 controls the expression of
these genes. It will also be important to determine whether mutations in Zfp335
contribute to human T-cell immunodeficiency. DOI:http://dx.doi.org/10.7554/eLife.03549.002
Collapse
Affiliation(s)
- Brenda Y Han
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Shuang Wu
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Chuan-Sheng Foo
- Department of Computer Science, Stanford University, Stanford, United States
| | - Robert M Horton
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Craig N Jenne
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Susan R Watson
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Belinda Whittle
- Australian Phenomics Facility, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Chris C Goodnow
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Jason G Cyster
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
15
|
Zhao XS, Fu WY, Chien WWY, Li Z, Fu AKY, Ip NY. p35 regulates the CRM1-dependent nucleocytoplasmic shuttling of nuclear hormone receptor coregulator-interacting factor 1 (NIF-1). PLoS One 2014; 9:e110584. [PMID: 25329792 PMCID: PMC4199748 DOI: 10.1371/journal.pone.0110584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/22/2014] [Indexed: 01/02/2023] Open
Abstract
Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase, which plays critical roles in a wide spectrum of neuronal functions including neuronal survival, neurite outgrowth, and synapse development and plasticity. Cdk5 activity is controlled by its specific activators: p35 or p39. While knockout studies reveal that Cdk5/p35 is critical for neuronal migration during early brain development, functions of Cdk5/p35 have been unraveled through the identification of the interacting proteins of p35, most of which are Cdk5/p35 substrates. However, it remains unclear whether p35 can regulate neuronal functions independent of Cdk5 activity. Here, we report that a nuclear protein, nuclear hormone receptor coregulator (NRC)-interacting factor 1 (NIF-1), is a new interacting partner of p35. Interestingly, p35 regulates the functions of NIF-1 independent of Cdk5 activity. NIF-1 was initially discovered as a transcriptional regulator that enhances the transcriptional activity of nuclear hormone receptors. Our results show that p35 interacts with NIF-1 and regulates its nucleocytoplasmic trafficking via the nuclear export pathway. Furthermore, we identified a nuclear export signal on p35; mutation of this site or blockade of the CRM1/exportin-dependent nuclear export pathway resulted in the nuclear accumulation of p35. Intriguingly, blocking the nuclear export of p35 attenuated the nuclear accumulation of NIF-1. These findings reveal a new p35-dependent mechanism in transcriptional regulation that involves the nucleocytoplasmic shuttling of transcription regulators.
Collapse
Affiliation(s)
- Xiao-Su Zhao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wing-Yu Fu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Winnie W. Y. Chien
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Zhen Li
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Amy K. Y. Fu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Nancy Y. Ip
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| |
Collapse
|
16
|
Shirai YT, Suzuki T, Morita M, Takahashi A, Yamamoto T. Multifunctional roles of the mammalian CCR4-NOT complex in physiological phenomena. Front Genet 2014; 5:286. [PMID: 25191340 PMCID: PMC4139912 DOI: 10.3389/fgene.2014.00286] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/04/2014] [Indexed: 01/12/2023] Open
Abstract
The carbon catabolite repression 4 (CCR4)–negative on TATA-less (NOT) complex serves as one of the major deadenylases of eukaryotes. Although it was originally identified and characterized in yeast, recent studies have revealed that the CCR4–NOT complex also exerts important functions in mammals, -including humans. However, there are some differences in the composition and functions of the CCR4–NOT complex between mammals and yeast. It is noteworthy that each subunit of the CCR4–NOT complex has unique, multifunctional roles and is responsible for various physiological phenomena. This heterogeneity and versatility of the CCR4–NOT complex makes an overall understanding of this complex difficult. Here, we describe the functions of each subunit of the mammalian CCR4–NOT complex and discuss the molecular mechanisms by which it regulates homeostasis in mammals. Furthermore, a possible link between the disruption of the CCR4–NOT complex and various diseases will be discussed. Finally, we propose that the analysis of mice with each CCR4–NOT subunit knocked out is an effective strategy for clarifying its complicated functions and networks in mammals.
Collapse
Affiliation(s)
- Yo-Taro Shirai
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University Onna-son, Japan
| | - Toru Suzuki
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University Onna-son, Japan
| | - Masahiro Morita
- Department of Biochemistry, McGill University Montreal, QC, Canada ; Goodman Cancer Research Centre, McGill University Montreal, QC, Canada
| | - Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University Onna-son, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University Onna-son, Japan
| |
Collapse
|
17
|
Frantzi M, Zoidakis J, Papadopoulos T, Zürbig P, Katafigiotis I, Stravodimos K, Lazaris A, Giannopoulou I, Ploumidis A, Mischak H, Mullen W, Vlahou A. IMAC fractionation in combination with LC-MS reveals H2B and NIF-1 peptides as potential bladder cancer biomarkers. J Proteome Res 2013; 12:3969-79. [PMID: 23924207 DOI: 10.1021/pr400255h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Improvement in bladder cancer (BC) management requires more effective diagnosis and prognosis of disease recurrence and progression. Urinary biomarkers attract special interest because of the noninvasive means of urine collection. Proteomic analysis of urine entails the adoption of a fractionation methodology to reduce sample complexity. In this study, we applied immobilized metal affinity chromatography in combination with high-resolution LC-MS/MS for the discovery of native urinary peptides potentially associated with BC aggressiveness. This approach was employed toward urine samples from patients with invasive BC, noninvasive BC, and benign urogenital diseases. A total of 1845 peptides were identified, corresponding to a total of 638 precursor proteins. Specific enrichment for proteins involved in nucleosome assembly and for zinc-finger transcription factors was observed. The differential expression of two candidate biomarkers, histone H2B and NIF-1 (zinc finger 335) in BC, was verified in independent sets of urine samples by ELISA and by immunohistochemical analysis of BC tissue. The results collectively support changes in the expression of both of these proteins with tumor progression, suggesting their potential role as markers for discriminating BC stages. In addition, the data indicate a possible involvement of NIF-1 in BC progression, likely as a suppressor and through interactions with Sox9 and HoxA1.
Collapse
Affiliation(s)
- Maria Frantzi
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Mokhonov VV, Theendakara VP, Gribanova YE, Ahmedli NB, Farber DB. Sequence-specific binding of recombinant Zbed4 to DNA: insights into Zbed4 participation in gene transcription and its association with other proteins. PLoS One 2012; 7:e35317. [PMID: 22693546 PMCID: PMC3365051 DOI: 10.1371/journal.pone.0035317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/15/2012] [Indexed: 11/19/2022] Open
Abstract
Zbed4, a member of the BED subclass of Zinc-finger proteins, is expressed in cone photoreceptors and glial Müller cells of human retina whereas it is only present in Müller cells of mouse retina. To characterize structural and functional properties of Zbed4, enough amounts of purified protein were needed. Thus, recombinant Zbed4 was expressed in E. coli and its refolding conditions optimized for the production of homogenous and functionally active protein. Zbed4’s secondary structure, determined by circular dichroism spectroscopy, showed that this protein contains 32% α-helices, 18% β-sheets, 20% turns and 30% unordered structures. CASTing was used to identify the target sites of Zbed4 in DNA. The majority of the DNA fragments obtained contained poly-Gs and some of them had, in addition, the core signature of GC boxes; a few clones had only GC-boxes. With electrophoretic mobility shift assays we demonstrated that Zbed4 binds both not only to DNA and but also to RNA oligonucleotides with very high affinity, interacting with poly-G tracts that have a minimum of 5 Gs; its binding to and GC-box consensus sequences. However, the latter binding depends on the GC-box flanking nucleotides. We also found that Zbed4 interacts in Y79 retinoblastoma cells with nuclear and cytoplasmic proteins Scaffold Attachment Factor B1 (SAFB1), estrogen receptor alpha (ERα), and cellular myosin 9 (MYH9), as shown with immunoprecipitation and mass spectrometry studies as well as gel overlay assays. In addition, immunostaining corroborated the co-localization of Zbed4 with these proteins. Most importantly, in vitro experiments using constructs containing promoters of genes directing expression of the luciferase gene, showed that Zbed4 transactivates the transcription of those promoters with poly-G tracts.
Collapse
Affiliation(s)
- Vladislav V. Mokhonov
- Jules Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Veena P. Theendakara
- Jules Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yekaterina E. Gribanova
- Jules Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Novruz B. Ahmedli
- Jules Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (DBF); (NBA)
| | - Debora B. Farber
- Jules Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- Brain Research Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (DBF); (NBA)
| |
Collapse
|
19
|
Alberts R, Chen H, Pommerenke C, Smit AB, Spijker S, Williams RW, Geffers R, Bruder D, Schughart K. Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease. BMC Genomics 2011; 12:610. [PMID: 22182475 PMCID: PMC3277499 DOI: 10.1186/1471-2164-12-610] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/19/2011] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Regulatory T cells (Tregs) play an essential role in the control of the immune response. Treg cells represent important targets for therapeutic interventions of the immune system. Therefore, it will be very important to understand in more detail which genes are specifically activated in Treg cells versus T helper (Th) cells, and which gene regulatory circuits may be involved in specifying and maintaining Treg cell homeostasis. RESULTS We isolated Treg and Th cells from a genetically diverse family of 31 BXD type recombinant inbred strains and the fully inbred parental strains of this family--C57BL/6J and DBA/2J. Subsequently genome-wide gene expression studies were performed from the isolated Treg and Th cells. A comparative analysis of the transcriptomes of these cell populations allowed us to identify many novel differentially expressed genes. Analysis of cis- and trans-expression Quantitative Trait Loci (eQTLs) highlighted common and unique regulatory mechanisms that are active in the two cell types. Trans-eQTL regions were found for the Treg functional genes Nrp1, Stat3 and Ikzf4. Analyses of the respective QTL intervals suggested several candidate genes that may be involved in regulating these genes in Treg cells. Similarly, possible candidate genes were found which may regulate the expression of F2rl1, Ctla4, Klrb1f. In addition, we identified a focused group of candidate genes that may be important for the maintenance of self-tolerance and the prevention of allergy. CONCLUSIONS Variation of expression across the strains allowed us to find many novel gene-interaction networks in both T cell subsets. In addition, these two data sets enabled us to identify many differentially expressed genes and to nominate candidate genes that may have important functions for the maintenance of self-tolerance and the prevention of allergy.
Collapse
Affiliation(s)
- Rudi Alberts
- Department of Infection Genetics, University of Veterinary Medicine Hannover, Braunschweig, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Saghizadeh M, Gribanova Y, Akhmedov NB, Farber DB. ZBED4, a cone and Müller cell protein in human retina, has a different cellular expression in mouse. Mol Vis 2011; 17:2011-8. [PMID: 21850176 PMCID: PMC3154125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 07/18/2011] [Indexed: 11/17/2022] Open
Abstract
PURPOSE ZBED4, a protein in cones and Müller cells of human retina, may play important functions as a transcriptional activator of genes expressed in those cells or as a co-activator/repressor of their nuclear hormone receptors. To begin investigating these potential roles of ZBED4, we studied the developmental expression and localization of both the Zbed4 mRNA and protein of mouse retina. METHODS northern blots showed the presence of Zbed4 mRNA in retina and other mouse tissues, and western blots showed the nuclear and cytoplasmic expression of Zbed4 at different developmental times. Antibodies against Zbed4 and specific retinal cell markers were used for retinal immunohistochemistry. RESULTS Zbed4 mRNA was present at different levels in all the mouse tissues analyzed. The Zbed4 protein was barely detectable at embryonic day (E)14.5 but was clearly seen at E16 at both retinal outer and vitreal borders and throughout the retina by E18 and postnatal day 0 (P0). Thereafter, Zbed4 expression was more restricted to the inner retina. While ZBED4 is localized in cones and endfeet of Müller cells of human retina, in adult mouse retina Zbed4 is only detected in Müller cell endfeet and processes. The same localization of Zbed4 was observed in rat retina. In early development, Zbed4 is mainly present in the nuclear fraction of the mouse retina, and in adulthood it becomes more enriched in the cytoplasmic fraction. CONCLUSIONS The patterns of spatial and temporal expression of Zbed4 in the mouse retina suggest a possible involvement of this protein in retinal morphogenesis and Müller cell function.
Collapse
Affiliation(s)
- Mehrnoosh Saghizadeh
- Jules Stein Eye Institute, UCLA, Los Angeles, CA,Molecular Biology Institute, UCLA, Los Angeles, CA
| | | | | | - Debora B. Farber
- Jules Stein Eye Institute, UCLA, Los Angeles, CA,Molecular Biology Institute, UCLA, Los Angeles, CA
| |
Collapse
|
21
|
Saghizadeh M, Akhmedov NB, Yamashita CK, Gribanova Y, Theendakara V, Mendoza E, Nelson SF, Ljubimov AV, Farber DB. ZBED4, a BED-type zinc-finger protein in the cones of the human retina. Invest Ophthalmol Vis Sci 2009; 50:3580-8. [PMID: 19369242 DOI: 10.1167/iovs.08-2751] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To characterize the ZBED4 cDNA identified by subtractive hybridization and microarray of retinal cone degeneration (cd) adult dog mRNA from mRNA of normal dog retina. METHODS The cDNA library obtained from subtractive hybridization was arrayed and screened with labeled amplicons from normal and cd dog retinas. Northern blot analysis was used to verify ZBED4 mRNA expression in human retina. Flow cytometry sorted peanut agglutinin (PNA)-labeled cones from dissociated mouse retinas, and quantitative RT-PCR (QPCR) was used to measure ZBED4 mRNA levels in these cone cells. Immunohistochemistry localized ZBED4 in human retinas. Expression of ZBED4 mRNA transiently transfected into HEK293 cells was analyzed by immunofluorescence. ZBED4 subcellular localization was determined with Western blot analysis. RESULTS One of 80 cDNAs differentially expressed in normal and cd dog retinas corresponded to a novel gene, ZBED4, which is also expressed in human and mouse retinas. ZBED4 mRNA was found to be present in cone photoreceptors. When ZBED4 cDNA was transfected into HEK293 cells, the expressed protein showed nuclear localization. However, in human retinas, ZBED4 was localized to cone nuclei, inner segments, and pedicles, as well as to Müller cell endfeet. Confirming these immunohistochemical results, the 135-kDa ZBED4 was found in both the nuclear and cytosolic extracts of human retinas. ZBED4 has four predicted DNA-binding domains, a dimerization domain, and two LXXLL motifs characteristic of coactivators/corepressors of nuclear hormone receptors. CONCLUSIONS ZBED4 cellular/subcellular localization and domains suggest a regulatory role for this protein, which may exert its effects in cones and Müller cells through multiple ways of action.
Collapse
Affiliation(s)
- Mehrnoosh Saghizadeh
- Jules Stein Eye Institute, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
Background We present a systematic search for regulatory elements in a 3.5 Mb region on human chromosome 20q13.12, a region associated with a number of medical conditions such as type II diabetes and obesity. Methodology/Principal Findings We profiled six histone modifications alongside RNA polymerase II (PolII) and CTCF in two cell lines, HeLa S3 and NTERA-2 clone D1 (NT2/D1), by chromatin immunoprecipitation using an in-house spotted DNA array, constructed with 1.8 kb overlapping plasmid clones. In both cells, more than 90% of transcription start sites (TSSs) of expressed genes showed enrichments with PolII, di-methylated lysine 4 of histone H3 (H3K4me2), tri-methylated lysine 4 of histone H3 (H3K4me3) or acetylated H3 (H3Ac), whereas mono-methylated lysine 4 of histone H3 (H3K4me1) signals did not correlate with expression. No TSSs were enriched with tri-methylated lysine 27 of histone H3 (H3K27me3) in HeLa S3, while eight TSSs (4 expressed) showed enrichments in NT2/D1. We have also located several CTCF binding sites that are potential insulator elements. Conclusions/Significance In summary, we annotated a number of putative regulatory elements in 20q13.12 and went on to verify experimentally a subset of them using dual luciferase reporter assays. Correlating this data to sequence variation can aid identification of disease causing variants.
Collapse
|
23
|
Garapaty S, Xu CF, Trojer P, Mahajan MA, Neubert TA, Samuels HH. Identification and characterization of a novel nuclear protein complex involved in nuclear hormone receptor-mediated gene regulation. J Biol Chem 2009; 284:7542-52. [PMID: 19131338 DOI: 10.1074/jbc.m805872200] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NRC/NCoA6 plays an important role in mediating the effects of ligand-bound nuclear hormone receptors as well as other transcription factors. NRC interacting factor 1 (NIF-1) was cloned as a novel factor that interacts in vivo with NRC. Although NIF-1 does not directly interact with nuclear hormone receptors, it enhances activation by nuclear hormone receptors presumably through its interaction with NRC. To further understand the cellular and biological function of NIF-1, we identified NIF-1-associated proteins by in-solution proteolysis followed by mass spectrometry. The identified components revealed factors involved in histone methylation and cell cycle control and include Ash2L, RbBP5, WDR5, HCF-1, DBC-1, and EMSY. Although the NIF-1 complex contains Ash2L, RbBP5, and WDR5, suggesting that the complex might methylate histone H3-Lys-4, we found that the complex contains a H3 methyltransferase activity that modifies a residue other than H3-Lys-4. The identified components form at least two distinctly sized NIF-1 complexes. DBC-1 and EMSY were identified as integral components of an NIF-1 complex of approximately 1.5 MDa and were found to play an important role in the regulation of nuclear receptor-mediated transcription. Stimulation of the Sox9 and HoxA1 genes by retinoic acid receptor-alpha was found to require both DBC-1 and EMSY in addition to NIF-1 for maximal transcriptional activation. Interestingly, NRC was not identified as a component of the NIF-1 complex, suggesting that NIF-1 and NRC do not exist as stable in vitro purified complexes, although the separate NIF-1 and NRC complexes appear to functionally interact in the cell.
Collapse
Affiliation(s)
- Shivani Garapaty
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | | | | | | | | | | |
Collapse
|
24
|
Garapaty S, Mahajan MA, Samuels HH. Components of the CCR4-NOT Complex Function as Nuclear Hormone Receptor Coactivators via Association with the NRC-interacting Factor NIF-1. J Biol Chem 2008; 283:6806-16. [DOI: 10.1074/jbc.m706986200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
25
|
Brayer KJ, Segal DJ. Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem Biophys 2008; 50:111-31. [PMID: 18253864 DOI: 10.1007/s12013-008-9008-5] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 12/28/2007] [Indexed: 11/28/2022]
Abstract
Cys2-His2 (C2H2) zinc finger domains (ZFs) were originally identified as DNA-binding domains, and uncharacterized domains are typically assumed to function in DNA binding. However, a growing body of evidence suggests an important and widespread role for these domains in protein binding. There are even examples of zinc fingers that support both DNA and protein interactions, which can be found in well-known DNA-binding proteins such as Sp1, Zif268, and Ying Yang 1 (YY1). C2H2 protein-protein interactions (PPIs) are proving to be more abundant than previously appreciated, more plastic than their DNA-binding counterparts, and more variable and complex in their interactions surfaces. Here we review the current knowledge of over 100 C2H2 zinc finger-mediated PPIs, focusing on what is known about the binding surface, contributions of individual fingers to the interaction, and function. An accurate understanding of zinc finger biology will likely require greater insights into the potential protein interaction capabilities of C2H2 ZFs.
Collapse
Affiliation(s)
- Kathryn J Brayer
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | | |
Collapse
|
26
|
Mahajan MA, Samuels HH. Nuclear receptor coactivator/coregulator NCoA6(NRC) is a pleiotropic coregulator involved in transcription, cell survival, growth and development. NUCLEAR RECEPTOR SIGNALING 2008; 6:e002. [PMID: 18301782 PMCID: PMC2254332 DOI: 10.1621/nrs.06002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 12/11/2007] [Indexed: 11/20/2022]
Abstract
NCoA6 (also referred to as NRC, ASC-2, TRBP, PRIP and RAP250) was originally isolated as a ligand-dependent nuclear receptor interacting protein. However, NCoA6 is a multifunctional coregulator or coactivator necessary for transcriptional activation of a wide spectrum of target genes. The NCoA6 gene is amplified and overexpressed in breast, colon and lung cancers. NCoA6 is a 250 kDa protein which harbors a potent N-terminal activation domain, AD1; and a second, centrally-located activation domain, AD2, which is necessary for nuclear receptor signaling. The intrinsic activation potential of NCoA6 is regulated by its C-terminal STL regulatory domain. Near AD2 is an LxxLL-1 motif which interacts with a wide spectrum of ligand-bound NRs with high-affinity. A second LxxLL motif (LxxLL-2) located towards the C-terminal region is more restricted in its NR specificity. The potential role of NCoA6 as a co-integrator is suggested by its ability to enhance transcriptional activation of a wide variety of transcription factors and from its in vivo association with a number of known cofactors including CBP/p300. NCoA6 has been shown to associate with at least three distinct coactivator complexes containing Set methyltransferases as core polypeptides. The composition of these complexes suggests that NCoA6 may play a fundamental role in transcriptional activation by modulating chromatin structure through histone methylation. Knockout studies in mice suggest that NCoA6 is an essential coactivator. NCoA6-/- embryos die between 8.5-12.5 dpc from general growth retardation coupled with developmental defects in the heart, liver, brain and placenta. NCoA6-/- MEFs grow at a reduced rate compared to WT MEFs and spontaneously undergo apoptosis, indicating the importance of NCoA6 as a prosurvival and anti-apoptotic gene. Studies with NCoA6+/- and conditional knockout mice suggest that NCoA6 is a pleiotropic coregulator involved in growth, development, wound healing and maintenance of energy homeostasis.
Collapse
Affiliation(s)
- Muktar A Mahajan
- Department of Pharmacology, NYU School of Medicine, New York, New York, USA.
| | | |
Collapse
|
27
|
Das S, Schapira M, Tomic-Canic M, Goyanka R, Cardozo T, Samuels HH. Farnesyl Pyrophosphate Is a Novel Transcriptional Activator for a Subset of Nuclear Hormone Receptors. Mol Endocrinol 2007; 21:2672-86. [PMID: 17666588 DOI: 10.1210/me.2007-0080] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In silico docking of a chemical library with the ligand-binding domain of thyroid hormone nuclear receptor-beta (TRbeta) suggested that farnesyl pyrophosphate (FPP), a key intermediate in cholesterol synthesis and protein farnesylation, might function as an agonist. Surprisingly, addition of FPP to cells activated TR as well as the classical steroid hormone receptors but not peroxisome proliferative-activating receptors, farnesoid X receptor, liver X receptor, or several orphan nuclear receptors the ligands of which are unknown. FPP enhanced receptor-coactivator binding in vitro and in vivo, and elevation of FPP levels in cells by squalene synthetase or farnesyl transferase inhibitors leads to activation. The FPP effect was blocked by selective receptor antagonists, and in silico docking with 143 nuclear receptor ligand-binding domain structures revealed that FPP only docked with the agonist conformation of those receptors activated by FPP. Our results suggest that certain nuclear receptors maintain a common structural feature that may reflect an action of FPP on an ancient nuclear receptor or that FPP could function as a ligand for one of the many orphan nuclear receptors the ligands of which have not yet been identified. This finding also has potential interesting implications that may, in part, explain the pleotropic effects of statins as well as certain actions of farnesylation inhibitors in cells.
Collapse
Affiliation(s)
- Sharmistha Das
- Department of Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA
| | | | | | | | | | | |
Collapse
|
28
|
Nuclear receptor transcriptional coactivators in development and metabolism. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1574-3349(06)16012-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
29
|
Mahajan MA, Samuels HH. Nuclear hormone receptor coregulator: role in hormone action, metabolism, growth, and development. Endocr Rev 2005; 26:583-97. [PMID: 15561801 DOI: 10.1210/er.2004-0012] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nuclear hormone receptor coregulator (NRC) (also referred to as activating signal cointegrator-2, thyroid hormone receptor-binding protein, peroxisome proliferator activating receptor-interacting protein, and 250-kDa receptor associated protein) belongs to a growing class of nuclear cofactors widely known as coregulators or coactivators that are necessary for transcriptional activation of target genes. The NRC gene is also amplified and overexpressed in breast, colon, and lung cancers. NRC is a 2063-amino acid protein that harbors a potent N-terminal activation domain (AD1) and a second more centrally located activation domain (AD2) that is rich in Glu and Pro. Near AD2 is a receptor-interacting domain containing an LxxLL motif (LxxLL-1), which interacts with a wide variety of ligand-bound nuclear hormone receptors with high affinity. A second LxxLL motif (LxxLL-2) located in the C-terminal region of NRC is more restricted in its nuclear hormone receptor specificity. The intrinsic activation potential of NRC is regulated by a C-terminal serine, threonine, leucine-regulatory domain. The potential role of NRC as a cointegrator is suggested by its ability to enhance transcriptional activation of a wide variety of transcription factors and from its in vivo association with a number of known transcriptional regulators including CBP/p300. Recent studies in mice indicate that deletion of both NRC alleles leads to embryonic lethality resulting from general growth retardation coupled with developmental defects in the heart, liver, brain, and placenta. NRC(-/-) mouse embryo fibroblasts spontaneously undergo apoptosis, indicating the importance of NRC as a prosurvival and antiapoptotic gene. Studies with 129S6 NRC(+/-) mice indicate that NRC is a pleiotropic regulator that is involved in growth, development, reproduction, metabolism, and wound healing.
Collapse
Affiliation(s)
- Muktar A Mahajan
- Departments of Pharmacology and Medicine, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA.
| | | |
Collapse
|
30
|
Lee B, Vouthounis C, Stojadinovic O, Brem H, Im M, Tomic-Canic M. From an Enhanceosome to a Repressosome: Molecular Antagonism between Glucocorticoids and EGF Leads to Inhibition of Wound Healing. J Mol Biol 2005; 345:1083-97. [PMID: 15644206 DOI: 10.1016/j.jmb.2004.11.027] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 11/10/2004] [Accepted: 11/12/2004] [Indexed: 11/19/2022]
Abstract
Wound healing in its complexity depends on the concerted activity of many signaling pathways. Here, we analyzed how the simultaneous presence of glucocorticoids (GC), retinoic acid (RA) and epidermal growth factor (EGF) affect wound healing at the molecular, cellular and tissue levels. We found that GC inhibit wound healing by inhibiting keratinocyte migration, whereas RA does not. Furthermore, GC block EGF-mediated migration, whereas RA does not. On the molecular level, these compounds target expression of one of the earliest markers of wound healing, cytoskeletal components, keratins K6 and K16. Both GC and RA repress their transcription, whereas EGF induces it. Interestingly, the GC inhibition is mediated by a repressosome complex consisting of four monomers of the GC receptor, beta-catenin and coactivator-associated-arginine-methyltransferase-1. GC are dominant, EGF cannot rescue GC-mediated inhibition. Pre-treatment of keratinocytes with GC shifts the balance towards the repressosome, allowing for dominant inhibition of K6 even in the presence of EGF or c-fos/c-jun. Although RA receptor gamma and glucocorticoid receptor bind to the same response element repressing transcription of keratins K6/K16, RA receptor interacts with the components of the EGF-enhanceosome (co-activators: glucocorticoid-receptor-interactive protein-1(GRIP-1)/steroid-receptors coactivator-1 (SRC-1)) without breaking it. Consequently, RA has a co-dominant effect with EGF: when present simultaneously, their effects balance each other. When keratinocytes are pre-treated with mitogen-activated protein kinase (MAPK) inhibitor, thus blocking EGF, the balance is shifted towards the RA repression. Similar to clinical findings, pre-treatment of keratinocytes with RA blocks GC-mediated inhibition. In summary, our results identify complex molecular mechanisms through which RA alleviates GC-mediated inhibition of wound healing.
Collapse
Affiliation(s)
- Brian Lee
- New York University School of Medicine, The Ronald O. Perelman Department of Dermatology, 550 First Avenue, New York, NY 10016, USA
| | | | | | | | | | | |
Collapse
|
31
|
Mahajan MA, Das S, Zhu H, Tomic-Canic M, Samuels HH. The nuclear hormone receptor coactivator NRC is a pleiotropic modulator affecting growth, development, apoptosis, reproduction, and wound repair. Mol Cell Biol 2004; 24:4994-5004. [PMID: 15143190 PMCID: PMC416394 DOI: 10.1128/mcb.24.11.4994-5004.2004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Revised: 02/04/2004] [Accepted: 03/18/2004] [Indexed: 12/27/2022] Open
Abstract
Nuclear hormone receptor coregulator (NRC) is a 2,063-amino-acid coregulator of nuclear hormone receptors and other transcription factors (e.g., c-Fos, c-Jun, and NF-kappaB). We and others have generated C57BL/6-129S6 hybrid (C57/129) NRC(+/-) mice that appear outwardly normal and grow and reproduce. In contrast, homozygous deletion of the NRC gene is embryonic lethal. NRC(-/-) embryos are always smaller than NRC(+/+) embryos, and NRC(-/-) embryos die between 8.5 and 12.5 days postcoitus (dpc), suggesting that NRC has a pleotrophic effect on growth. To study this, we derived mouse embryonic fibroblasts (MEFs) from 12.5-dpc embryos, which revealed that NRC(-/-) MEFs exhibit a high rate of apoptosis. Furthermore, a small interfering RNA that targets mouse NRC leads to enhanced apoptosis of wild-type MEFs. The finding that C57/129 NRC(+/-) mice exhibit no apparent phenotype prompted us to develop 129S6 NRC(+/-) mice, since the phenotype(s) of certain gene deletions may be strain dependent. In contrast with C57/129 NRC(+/-) females, 20% of 129S6 NRC(+/-) females are infertile while 80% are hypofertile. The 129S6 NRC(+/-) males produce offspring when crossed with wild-type 129S6 females, although fertility is reduced. The 129S6 NRC(+/-) mice tend to be stunted in their growth compared with their wild-type littermates and exhibit increased postnatal mortality. Lastly, both C57/129 NRC(+/-) and 129S6 NRC(+/-) mice exhibit a spontaneous wound healing defect, indicating that NRC plays an important role in that process. Our findings reveal that NRC is a coregulator that controls many cellular and physiologic processes ranging from growth and development to reproduction and wound repair.
Collapse
Affiliation(s)
- Muktar A Mahajan
- Department of Pharmacology and Medicine, New York University School of Medicine, 550 First Ave., New York, NY 10016, USA
| | | | | | | | | |
Collapse
|
32
|
Steffensen KR, Nilsson M, Schuster GU, Stulnig TM, Dahlman-Wright K, Gustafsson JA. Gene expression profiling in adipose tissue indicates different transcriptional mechanisms of liver X receptors alpha and beta, respectively. Biochem Biophys Res Commun 2003; 310:589-93. [PMID: 14521951 DOI: 10.1016/j.bbrc.2003.08.139] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The nuclear receptors liver X receptors (LXR) alpha and beta are important regulators of genes involved in lipid, cholesterol, and carbohydrate metabolism and are highly expressed in mature adipocyte tissue. In this study we show that LXRalpha and LXRbeta are more expressed in brown adipose tissue and subcutaneous white adipose tissue than visceral (gonadal) adipose tissue. Furthermore, we report differences between LXRalpha and LXRbeta in their ability to alter expression of target genes. Gene expression profiling analysis of gonadal white adipose tissue from LXRalpha(-/-) mice and LXRbeta(-/-) mice shows different gene expression patterns in the two LXR-deficient mouse strains. Genes regulated similarly in both KO mouse strains as well as genes regulated in one, but not the other LXR-deficient mouse strain were seen. A number of genes were regulated in opposite directions by the respective LXR isoform. Taken together this suggests that the LXR isoforms might operate through different transcriptional mechanisms as well as common mechanisms. These results are in consonance with the growing body of evidence reporting differences in regulation of gene expression between the two isoforms. Furthermore, gene expression profiling shows altered gene expression patterns in primary mouse embryonic fibroblasts (MEFs) from wild type versus LXRbeta(-/-) mice; MEFs are pluripotent cells with the potential to differentiate into mature adipocytes. These results indicate a role of LXR in early developmental stages of adipose tissue.
Collapse
Affiliation(s)
- Knut R Steffensen
- Department of Biosciences, Karolinska Institutet at NOVUM, Huddinge, Sweden.
| | | | | | | | | | | |
Collapse
|
33
|
Mathur M, Das S, Samuels HH. PSF-TFE3 oncoprotein in papillary renal cell carcinoma inactivates TFE3 and p53 through cytoplasmic sequestration. Oncogene 2003; 22:5031-44. [PMID: 12902986 DOI: 10.1038/sj.onc.1206643] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Papillary renal cell carcinomas are associated with chromosomal translocations involving the helix-loop-helix leucine-zipper region of the TFE3 gene on the X chromosome. These translocations lead to the expression of TFE3 chimeras of PRCC, RCC17, NonO and PSF (PTB-associated splicing factor). In this study, we explored the role of PSF-TFE3 fusion protein in mediating cell transformation. Unlike wild-type TFE3 or PSF, which are nuclear proteins, PSF-TFE3 is not a nuclear protein and is targeted to the endosomal compartment. Although PSF-TFE3 has no effect on the nuclear localization of wild-type PSF, it sequesters wild-type TFE3 as well as p53 in the extranuclear compartment leading to functionally null p53 and TFE3 cells. In UOK-145 papillary renal carcinoma cells, which endogenously express PSF-TFE3, siRNA complementary to the PSF-TFE3 fusion junction leads to a reduction in PSF-TFE3 and redistribution of endogenous TFE3 and p53 from the cytoplasmic compartment to the nucleus. Our results indicate that PSF-TFE3 acts through a novel mechanism, and exports TFE3, p53 and possibly other factors from the nucleus to the cytoplasm for degradation leading to the transformed phenotype. Thus, PSF-TFE3 is a promising target for the treatment for a subset of renal cell carcinomas.
Collapse
Affiliation(s)
- Mukul Mathur
- Departments of Pharmacology and Medicine, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA.
| | | | | |
Collapse
|