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Razavipour SF, Yoon H, Jang K, Kim M, Nawara HM, Bagheri A, Huang WC, Shin M, Zhao D, Zhou Z, Van Boven D, Briegel K, Morey L, Ince TA, Johnson M, Slingerland JM. C-terminally phosphorylated p27 activates self-renewal driver genes to program cancer stem cell expansion, mammary hyperplasia and cancer. Nat Commun 2024; 15:5152. [PMID: 38886396 PMCID: PMC11183067 DOI: 10.1038/s41467-024-48742-y] [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: 07/14/2023] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
In many cancers, a stem-like cell subpopulation mediates tumor initiation, dissemination and drug resistance. Here, we report that cancer stem cell (CSC) abundance is transcriptionally regulated by C-terminally phosphorylated p27 (p27pT157pT198). Mechanistically, this arises through p27 co-recruitment with STAT3/CBP to gene regulators of CSC self-renewal including MYC, the Notch ligand JAG1, and ANGPTL4. p27pTpT/STAT3 also recruits a SIN3A/HDAC1 complex to co-repress the Pyk2 inhibitor, PTPN12. Pyk2, in turn, activates STAT3, creating a feed-forward loop increasing stem-like properties in vitro and tumor-initiating stem cells in vivo. The p27-activated gene profile is over-represented in STAT3 activated human breast cancers. Furthermore, mammary transgenic expression of phosphomimetic, cyclin-CDK-binding defective p27 (p27CK-DD) increases mammary duct branching morphogenesis, yielding hyperplasia and microinvasive cancers that can metastasize to liver, further supporting a role for p27pTpT in CSC expansion. Thus, p27pTpT interacts with STAT3, driving transcriptional programs governing stem cell expansion or maintenance in normal and cancer tissues.
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Affiliation(s)
- Seyedeh Fatemeh Razavipour
- Cancer Host Interactions Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington DC, USA
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
| | - Hyunho Yoon
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon-si, South Korea
| | - Kibeom Jang
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
| | - Minsoon Kim
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
| | - Hend M Nawara
- Cancer Host Interactions Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington DC, USA
| | - Amir Bagheri
- Cancer Host Interactions Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington DC, USA
| | - Wei-Chi Huang
- Cancer Host Interactions Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington DC, USA
| | - Miyoung Shin
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Dekuang Zhao
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
| | - Zhiqun Zhou
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
| | - Derek Van Boven
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Karoline Briegel
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, Fl, USA
| | - Lluis Morey
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Tan A Ince
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael Johnson
- Cancer Host Interactions Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington DC, USA
| | - Joyce M Slingerland
- Cancer Host Interactions Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington DC, USA.
- Braman Family Breast Cancer Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Fl, USA.
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Dix-Peek T, Dickens C, Augustine TN, Phakathi BP, Van Den Berg EJ, Joffe M, Ayeni OA, Cubasch H, Nietz S, Mathew CG, Hayat M, Neugut AI, Jacobson JS, Ruff P, Duarte RA. FGFR2 genetic variants in women with breast cancer. Mol Med Rep 2023; 28:226. [PMID: 37830168 PMCID: PMC10619128 DOI: 10.3892/mmr.2023.13113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/11/2023] [Indexed: 10/14/2023] Open
Abstract
Black African populations are more genetically diverse than others, but genetic variants have been studied primarily in European populations. The present study examined the association of four single nucleotide polymorphisms (SNPs) of the fibroblast growth factor receptor 2, associated with breast cancer in non‑African populations, with breast cancer in Black, southern African women. Genomic DNA was extracted from whole blood samples of 1,001 patients with breast cancer and 1,006 controls (without breast cancer), and the rs2981582, rs35054928, rs2981578, and rs11200014 polymorphisms were analyzed using allele‑specific Kompetitive allele‑specific PCR™, and the χ2 or Fisher's exact tests were used to compare the genotype frequencies. There was no association between those SNPs and breast cancer in the studied cohort, although an association was identified between the C/C homozygote genotype for rs2981578 and invasive lobular carcinoma. These results show that genetic biomarkers of breast cancer risk in European populations are not necessarily associated with risk in sub‑Saharan African populations. African populations are more heterogenous than other populations, and the information from this population can help focus genetic risks of cancer in this understudied population.
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Affiliation(s)
- Thérèse Dix-Peek
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Caroline Dickens
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Tanya N. Augustine
- School of Anatomical Sciences, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Boitumelo P. Phakathi
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa
| | - Eunice J. Van Den Berg
- Department of Histopathology, National Health Laboratory Services, Chris Hani Baragwanath Hospital, Johannesburg 1864, South Africa
- Department of Anatomical Pathology, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Maureen Joffe
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd., Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Oluwatosin A. Ayeni
- Strengthening Oncology Services Research Unit, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd., Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Division of Radiation Oncology, Department of Radiation Sciences, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Herbert Cubasch
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd., Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Batho Pele Breast Unit, Chris Hani Baragwanath Academic Hospital, Soweto 1860, South Africa
- Department of Surgery, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Sarah Nietz
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Department of Surgery, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Christopher G. Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, WC2R 2LS, United Kingdom
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Mahtaab Hayat
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Alfred I. Neugut
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, New York 10032, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York 10032, United States of America
| | - Judith S. Jacobson
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, New York 10032, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York 10032, United States of America
| | - Paul Ruff
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- South African Medical Research Council Common Epithelial Cancer Research Centre, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd., Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
| | - Raquel A.B. Duarte
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of The Witwatersrand, Johannesburg 2193, South Africa
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Drastichova Z, Trubacova R, Novotny J. Regulation of phosphosignaling pathways involved in transcription of cell cycle target genes by TRH receptor activation in GH1 cells. Biomed Pharmacother 2023; 168:115830. [PMID: 37931515 DOI: 10.1016/j.biopha.2023.115830] [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: 08/29/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Thyrotropin-releasing hormone (TRH) is known to activate several cellular signaling pathway, but the activation of the TRH receptor (TRH-R) has not been reported to regulate gene transcription. The aim of this study was to identify phosphosignaling pathways and phosphoprotein complexes associated with gene transcription in GH1 pituitary cells treated with TRH or its analog, taltirelin (TAL), using label-free bottom-up mass spectrometry-based proteomics. Our detailed analysis provided insight into the mechanism through which TRH-R activation may regulate the transcription of genes related to the cell cycle and proliferation. It involves control of the signaling pathways for β-catenin/Tcf, Notch/RBPJ, p53/p21/Rbl2/E2F, Myc, and YY1/Rb1/E2F through phosphorylation and dephosphorylation of their key components. In many instances, the phosphorylation patterns of differentially phosphorylated phosphoproteins in TRH- or TAL-treated cells were identical or displayed a similar trend in phosphorylation. However, some phosphoproteins, especially components of the Wnt/β-catenin/Tcf and YY1/Rb1/E2F pathways, exhibited different phosphorylation patterns in TRH- and TAL-treated cells. This supports the notion that TRH and TAL may act, at least in part, as biased agonists. Additionally, the deficiency of β-arrestin2 resulted in a reduced number of alterations in phosphorylation, highlighting the critical role of β-arrestin2 in the signal transduction from TRH-R in the plasma membrane to transcription factors in the nucleus.
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Affiliation(s)
- Zdenka Drastichova
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia
| | - Radka Trubacova
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia; Institute of Physiology, Czech Academy of Sciences, 142 20 Prague, Czechia
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia.
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4
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Figiel M, Górka AK, Górecki A. Zinc Ions Modulate YY1 Activity: Relevance in Carcinogenesis. Cancers (Basel) 2023; 15:4338. [PMID: 37686614 PMCID: PMC10487186 DOI: 10.3390/cancers15174338] [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: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
YY1 is widely recognized as an intrinsically disordered transcription factor that plays a role in development of many cancers. In most cases, its overexpression is correlated with tumor progression and unfavorable patient outcomes. Our latest research focusing on the role of zinc ions in modulating YY1's interaction with DNA demonstrated that zinc enhances the protein's multimeric state and affinity to its operator. In light of these findings, changes in protein concentration appear to be just one element relevant to modulating YY1-dependent processes. Thus, alterations in zinc ion concentration can directly and specifically impact the regulation of gene expression by YY1, in line with reports indicating a correlation between zinc ion levels and advancement of certain tumors. This review concentrates on other potential consequences of YY1 interaction with zinc ions that may act by altering charge distribution, conformational state distribution, or oligomerization to influence its interactions with molecular partners that can disrupt gene expression patterns.
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Affiliation(s)
| | | | - Andrzej Górecki
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; (M.F.); (A.K.G.)
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Torres T, Barros S, Neuparth T, Ruivo R, Santos MM. Using zebrafish embryo bioassays to identify chemicals modulating the regulation of the epigenome: a case study with simvastatin. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:22913-22928. [PMID: 36307569 DOI: 10.1007/s11356-022-23683-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Contaminants of emerging concern have been increasingly associated with the modulation of the epigenome, leading to potentially inherited and persistent impacts on apical endpoints. Here, we address the performance of the OECD Test No. 236 FET (fish embryo acute toxicity) in the identification of chemicals able to modulate the epigenome. Using zebrafish (Danio rerio) embryos, acute and chronic exposures were performed with the pharmaceutical, simvastatin (SIM), a widely prescribed hypocholesterolemic drug reported to induce inter and transgenerational effects. In the present study, the epigenetic effects of environmentally relevant concentrations of SIM (from 8 ng/L to 2000 ng/L) were addressed following (1) an acute embryo assay based on OECD Test No. 236 FET, (2) a chronic partial life-cycle exposure using adult zebrafish (90 days), and (3) F1 embryos obtained from parental exposed animals. Simvastatin induced significant effects in gene expression of key epigenetic biomarkers (DNA methylation and histone acetylation/deacetylation) in the gonads of exposed adult zebrafish and in 80 hpf zebrafish embryos (acute and chronic parental intergenerational exposure), albeit with distinct effect profiles between biological samples. In the chronic exposure, SIM impacted particularly DNA methyltransferase genes in males and female gonads, whereas in F1 embryos SIM affected mostly genes associated with histone acetylation/deacetylation. In the embryo acute direct exposure, SIM modulated the expression of both genes involved in DNA methylation and histone deacetylase. These findings further support the use of epigenetic biomarkers in zebrafish embryos in a high throughput approach to identify and prioritize epigenome-modulating chemicals.
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Affiliation(s)
- Tiago Torres
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, 4169-007, Porto, Portugal
| | - Susana Barros
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Quinta de Prados, Ed. Blocos Laboratoriais C1.10, 5000-801, Vila Real, Portugal
| | - Teresa Neuparth
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal
| | - Raquel Ruivo
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal.
| | - Miguel Machado Santos
- Group of Endocrine Disruptors and Emerging Contaminants, University of Porto, Avenida General Norton de Matos, 4450-208, Matosinhos, S/N, Portugal.
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, 4169-007, Porto, Portugal.
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Colgan DF, Goodfellow RX, Colgan JD. The transcriptional regulator GON4L is required for viability and hematopoiesis in mice. Exp Hematol 2021; 98:25-35. [PMID: 33864850 DOI: 10.1016/j.exphem.2021.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
The Gon4l gene encodes a putative transcriptional regulator implicated in the control of both cell differentiation and proliferation. Previously, we described a mutant mouse strain called Justy in which splicing of pre-mRNA generated from Gon4l is disrupted. This defect severely reduces, but does not abolish, GON4L protein expression and blocks the formation of early B-lineage progenitors, suggesting Gon4l is required for B-cell development in vertebrates. Yet, mutations that disable Gon4l in zebrafish impair several facets of embryogenesis that include the initiation of primitive hematopoiesis, arguing this gene is needed for multiple vertebrate developmental pathways. To better understand the importance of Gon4l in mammals, we created mice carrying an engineered version of Gon4l that can be completely inactivated by Cre-mediated recombination. Breeding mice heterozygous for the inactivated Gon4l allele failed to yield any homozygous-null offspring, indicating Gon4l is an essential gene in mammals. Consistent with this finding, as well previously published results, cell culture studies revealed that loss of Gon4l blocks cell proliferation and compromises viability, suggesting a fundamental role in the control of cell division and survival. Studies using mixed bone marrow chimeras confirmed Gon4l is required for B-cell development but also found it is needed to maintain definitive hematopoietic stem/progenitor cells that are the source of all hematopoietic cell lineages. Our findings reveal Gon4l is an essential gene in mammals that is required to form the entire hematopoietic system.
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Affiliation(s)
- Diana F Colgan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Renee X Goodfellow
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - John D Colgan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA; Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA; Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA.
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7
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Tsai SM, Chu KC, Jiang YJ. Newly identified Gon4l/Udu-interacting proteins implicate novel functions. Sci Rep 2020; 10:14213. [PMID: 32848183 PMCID: PMC7449961 DOI: 10.1038/s41598-020-70855-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/28/2020] [Indexed: 12/04/2022] Open
Abstract
Mutations of the Gon4l/udu gene in different organisms give rise to diverse phenotypes. Although the effects of Gon4l/Udu in transcriptional regulation have been demonstrated, they cannot solely explain the observed characteristics among species. To further understand the function of Gon4l/Udu, we used yeast two-hybrid (Y2H) screening to identify interacting proteins in zebrafish and mouse systems, confirmed the interactions by co-immunoprecipitation assay, and found four novel Gon4l-interacting proteins: BRCA1 associated protein-1 (Bap1), DNA methyltransferase 1 (Dnmt1), Tho complex 1 (Thoc1, also known as Tho1 or HPR1), and Cryptochrome circadian regulator 3a (Cry3a). Furthermore, all known Gon4l/Udu-interacting proteins—as found in this study, in previous reports, and in online resources—were investigated by Phenotype Enrichment Analysis. The most enriched phenotypes identified include increased embryonic tissue cell apoptosis, embryonic lethality, increased T cell derived lymphoma incidence, decreased cell proliferation, chromosome instability, and abnormal dopamine level, characteristics that largely resemble those observed in reported Gon4l/udu mutant animals. Similar to the expression pattern of udu, those of bap1, dnmt1, thoc1, and cry3a are also found in the brain region and other tissues. Thus, these findings indicate novel mechanisms of Gon4l/Udu in regulating CpG methylation, histone expression/modification, DNA repair/genomic stability, and RNA binding/processing/export.
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Affiliation(s)
- Su-Mei Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Kuo-Chang Chu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Yun-Jin Jiang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan. .,Laboratory of Developmental Signalling and Patterning, Institute of Molecular and Cell Biology, Singapore, Singapore. .,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan. .,Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan. .,Department of Life Science, Tunghai University, Taichung, Taiwan.
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Bucholc K, Skrajna A, Adamska K, Yang XC, Krajewski K, Poznański J, Dadlez M, Domiński Z, Zhukov I. Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations. Int J Mol Sci 2020; 21:ijms21155268. [PMID: 32722282 PMCID: PMC7432317 DOI: 10.3390/ijms21155268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
Abstract
FLICE-associated huge protein (FLASH), Yin Yang 1-Associated Protein-Related Protein (YARP) and Nuclear Protein, Ataxia-Telangiectasia Locus (NPAT) localize to discrete nuclear structures called histone locus bodies (HLBs) where they control various steps in histone gene expression. Near the C-terminus, FLASH and YARP contain a highly homologous domain that interacts with the C-terminal region of NPAT. Structural aspects of the FLASH-NPAT and YARP-NPAT complexes and their role in histone gene expression remain largely unknown. In this study, we used multidimensional NMR spectroscopy and in silico modeling to analyze the C-terminal domain in FLASH and YARP in an unbound form and in a complex with the last 31 amino acids of NPAT. Our results demonstrate that FLASH and YARP domains share the same fold of a triple α -helical bundle that resembles the DNA binding domain of Myb transcriptional factors and the SANT domain found in chromatin-modifying and remodeling complexes. The NPAT peptide contains a single α -helix that makes multiple contacts with α -helices I and III of the FLASH and YARP domains. Surprisingly, in spite of sharing a significant amino acid similarity, each domain likely binds NPAT using a unique network of interactions, yielding two distinct complexes. In silico modeling suggests that both complexes are structurally compatible with DNA binding, raising the possibility that they may function in identifying specific sequences within histone gene clusters, hence initiating the assembly of HLBs and regulating histone gene expression during cell cycle progression.
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Affiliation(s)
- Katarzyna Bucholc
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Aleksandra Skrajna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Kinga Adamska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Zbigniew Domiński
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- NanoBioMedical Centre, Adam Mickiewicz University, ul. Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
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Wang L, Gao Y, Zhao X, Guo C, Wang X, Yang Y, Han C, Zhao L, Qin Y, Liu L, Huang C, Wang W. HOXD3 was negatively regulated by YY1 recruiting HDAC1 to suppress progression of hepatocellular carcinoma cells via ITGA2 pathway. Cell Prolif 2020; 53:e12835. [PMID: 32557953 PMCID: PMC7445403 DOI: 10.1111/cpr.12835] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/24/2022] Open
Abstract
Objectives HOXD3 is associated with progression of multiple types of cancer. This study aimed to identify the association of YY1 with HOXD3‐ITGA2 axis in the progression of hepatocellular carcinoma. Materials and Methods Bioinformatics assay was used to identify the effect of YY1, HOXD3 and ITGA2 expression in HCC tissues. The function of YY1 and HOXD3 in HCCs was determined by qRT‐PCR, MTT, apoptosis, Western blotting, colony formation, immunohistochemistry, and wound‐healing and transwell invasion assays. The relationship between YY1 and HOXD3 or HOXD3 and ITGA2 was explored by RNA‐Seq, ChIP‐PCR, dual luciferase reports and Pearson's assays. The interactions between YY1 and HDAC1 were determined by immunofluorescence microscopy and Co‐IP. Results Herein, we showed that the expression of YY1, HOXD3 and ITGA2 associated with the histologic and pathologic stages of HCC. Moreover, YY1, recruiting HDAC1, can directly target HOXD3 to regulate progression of HCCs. The relationship between YY1 and HOXD3 was unknown until uncovered by our present investigation. Furthermore, HOXD3 bound to promoter region of ITGA2 and up‐regulated the expression, thus activating the ERK1/2 signalling and inducing HCCs proliferation, metastasis and migration in the vitro and vivo. Conclusions Therefore, HOXD3, a target of YY1, facilitates HCC progression via activation of the ERK1/2 signalling by promoting ITGA2. This finding provides a new whole way to HCC therapy by serving YY1‐HOXD3‐ITGA2 regulatory axis as a potential therapeutic target for HCC therapy.
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Affiliation(s)
- Lumin Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yi Gao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Yan'an Key Laboratory of Chronic Disease Prevention and Research, Yan'an, China
| | - Xiaoge Zhao
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chen Guo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaofei Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yang Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Cong Han
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Lingyu Zhao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yannan Qin
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Liying Liu
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Cardiovascular Research Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenjing Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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10
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Budine TE, de Sena-Tomás C, Williams MLK, Sepich DS, Targoff KL, Solnica-Krezel L. Gon4l/Udu regulates cardiomyocyte proliferation and maintenance of ventricular chamber identity during zebrafish development. Dev Biol 2020; 462:223-234. [PMID: 32272116 PMCID: PMC10318589 DOI: 10.1016/j.ydbio.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 01/26/2020] [Accepted: 03/02/2020] [Indexed: 01/03/2023]
Abstract
Vertebrate heart development requires spatiotemporal regulation of gene expression to specify cardiomyocytes, increase the cardiomyocyte population through proliferation, and to establish and maintain atrial and ventricular cardiac chamber identities. The evolutionarily conserved chromatin factor Gon4-like (Gon4l), encoded by the zebrafish ugly duckling (udu) locus, has previously been implicated in cell proliferation, cell survival, and specification of mesoderm-derived tissues including blood and somites, but its role in heart formation has not been studied. Here we report two distinct roles of Gon4l/Udu in heart development: regulation of cell proliferation and maintenance of ventricular identity. We show that zygotic loss of udu expression causes a significant reduction in cardiomyocyte number at one day post fertilization that becomes exacerbated during later development. We present evidence that the cardiomyocyte deficiency in udu mutants results from reduced cell proliferation, unlike hematopoietic deficiencies attributed to TP53-dependent apoptosis. We also demonstrate that expression of the G1/S-phase cell cycle regulator, cyclin E2 (ccne2), is reduced in udu mutant hearts, and that the Gon4l protein associates with regulatory regions of the ccne2 gene during early embryogenesis. Furthermore, udu mutant hearts exhibit a decrease in the proportion of ventricular cardiomyocytes compared to atrial cardiomyocytes, concomitant with progressive reduction of nkx2.5 expression. We further demonstrate that udu and nkx2.5 interact to maintain the proportion of ventricular cardiomyocytes during development. However, we find that ectopic expression of nkx2.5 is not sufficient to restore ventricular chamber identity suggesting that Gon4l regulates cardiac chamber patterning via multiple pathways. Together, our findings define a novel role for zygotically-expressed Gon4l in coordinating cardiomyocyte proliferation and chamber identity maintenance during cardiac development.
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Affiliation(s)
- Terin E Budine
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carmen de Sena-Tomás
- Division of Pediatric Cardiology, Department of Pediatrics, College of Physicians & Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA
| | - Margot L K Williams
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Diane S Sepich
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kimara L Targoff
- Division of Pediatric Cardiology, Department of Pediatrics, College of Physicians & Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA
| | - Lila Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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11
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Fang Z, Yang H, Chen D, Shi X, Wang Q, Gong C, Xu X, Liu H, Lin M, Lin J, Xu C, Shao J. YY1 promotes colorectal cancer proliferation through the miR-526b-3p/E2F1 axis. Am J Cancer Res 2019; 9:2679-2692. [PMID: 31911854 PMCID: PMC6943347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023] Open
Abstract
We previously reported that E2F1 expression is up-regulated and positively correlated with the malignant phenotypes of colorectal cancer (CRC). However, the underlying mechanisms leading to the aberrant up-regulation of E2F1 in CRC have not been clarified. In this study, we observed that miR-526b-3p directly targets the 3'UTR of E2f1 mRNA, leading to reduced E2F1 expression. Overexpression of miR-526b-3p inhibited the proliferation of CRC cells by decreasing the level of E2F1. We also found that the Ying Yang 1 (YY1)-dependent transcriptional suppression of miR-526b-3p is responsible for the up-regulation of E2F1 in CRC, in which YY1 binds to the promoter of miR-526b gene and recruits histone deacetylase (HDAC). Knockdown of YY1 led to cell cycle arrest and diminished colony formation in CRC cells partly through relieving the miR-526b-3p suppression. Clinical analysis showed that YY1 and E2F1 were negatively correlated with miR-526b-3p in CRC tissues. Moreover, a high level of YY1 and E2F1, or a low level of miR-526b-3p, predicted poor survival of CRC patients. In conclusion, our findings highlight the dysregulation of the YY1/miR-526b-3p/E2F1 axis in CRC development, implicating a novel regulatory pathway for E2F1 as a potential therapeutic target in CRC.
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Affiliation(s)
- Zejun Fang
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
- Central Laboratory, Sanmenwan Branch, The First Affiliated Hospital, College of Medicine, Zhejiang UniversitySanmen, China
- Central Laboratory, Sanmen People’s Hospital of Zhejiang ProvinceSanmen, China
| | - Hua Yang
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Dan Chen
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Xiaoying Shi
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Qinqiu Wang
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Chaoju Gong
- Central Laboratory, The Municipal Affiliated Hospital of Xuzhou Medical UniversityXuzhou, China
| | - Xi Xu
- Department of Pathology, The Second Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Hong Liu
- Zhejiang Normal University, Jinhua People’s Hospital Joint Center for Biomedical ResearchJinhua, China
- The Affiliated Hospital of Jinhua Polytechnic CollegeJinhua, China
| | - Min Lin
- Central Laboratory, Sanmenwan Branch, The First Affiliated Hospital, College of Medicine, Zhejiang UniversitySanmen, China
- Central Laboratory, Sanmen People’s Hospital of Zhejiang ProvinceSanmen, China
| | - Junxiao Lin
- Central Laboratory, Sanmenwan Branch, The First Affiliated Hospital, College of Medicine, Zhejiang UniversitySanmen, China
- Central Laboratory, Sanmen People’s Hospital of Zhejiang ProvinceSanmen, China
| | - Chengfu Xu
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Jimin Shao
- Department of Pathology and Pathophysiology, College of Medicine, Zhejiang UniversityHangzhou, China
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12
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Yang Y, Huang W, Qiu R, Liu R, Zeng Y, Gao J, Zheng Y, Hou Y, Wang S, Yu W, Leng S, Feng D, Wang Y. LSD1 coordinates with the SIN3A/HDAC complex and maintains sensitivity to chemotherapy in breast cancer. J Mol Cell Biol 2019; 10:285-301. [PMID: 29741645 DOI: 10.1093/jmcb/mjy021] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 01/21/2018] [Indexed: 01/26/2023] Open
Abstract
Lysine-specific demethylase 1 (LSD1) was the first histone demethylase identified as catalysing the removal of mono- and di-methylation marks on histone H3-K4. Despite the potential broad action of LSD1 in transcription regulation, recent studies indicate that LSD1 may coordinate with multiple epigenetic regulatory complexes including CoREST/HDAC complex, NuRD complex, SIRT1, and PRC2, implying complicated mechanistic actions of this seemingly simple enzyme. Here, we report that LSD1 is also an integral component of the SIN3A/HDAC complex. Transcriptional target analysis using ChIP-on-chip technology revealed that the LSD1/SIN3A/HDAC complex targets several cellular signalling pathways that are critically involved in cell proliferation, survival, metastasis, and apoptosis, especially the p53 signalling pathway. We have demonstrated that LSD1 coordinates with the SIN3A/HDAC complex in inhibiting a series of genes such as CASP7, TGFB2, CDKN1A(p21), HIF1A, TERT, and MDM2, some of which are oncogenic. Our experiments also found that LSD1 and SIN3A are required for optimal survival and growth of breast cancer cells while also essential for the maintenance of epithelial homoeostasis and chemosensitivity. Our data indicate that LSD1 is a functional alternative subunit of the SIN3A/HDAC complex, providing a molecular basis for the interplay of histone demethylation and deacetylation in chromatin remodelling, and suggest that the LSD1/SIN3A/HDAC complex could be a target for breast cancer therapeutic strategies.
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Affiliation(s)
- Yang Yang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Huang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Rongfang Qiu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ruiqiong Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yi Zeng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jie Gao
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yu Zheng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Yongqiang Hou
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shuang Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wenqian Yu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shuai Leng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dandan Feng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yan Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Cellular and Molecular Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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13
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Li Z, Wu J, Chavez L, Hoh R, Deeks SG, Pillai SK, Zhou Q. Reiterative Enrichment and Authentication of CRISPRi Targets (REACT) identifies the proteasome as a key contributor to HIV-1 latency. PLoS Pathog 2019; 15:e1007498. [PMID: 30645648 PMCID: PMC6333332 DOI: 10.1371/journal.ppat.1007498] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023] Open
Abstract
The establishment of HIV-1 latency gives rise to persistent chronic infection that requires life-long treatment. To reverse latency for viral eradiation, the HIV-1 Tat protein and its associated ELL2-containing Super Elongation Complexes (ELL2-SECs) are essential to activate HIV-1 transcription. Despite efforts to identify effective latency-reversing agents (LRA), avenues for exposing latent HIV-1 remain inadequate, prompting the need to identify novel LRA targets. Here, by conducting a CRISPR interference-based screen to reiteratively enrich loss-of-function genotypes that increase HIV-1 transcription in latently infected CD4+ T cells, we have discovered a key role of the proteasome in maintaining viral latency. Downregulating or inhibiting the proteasome promotes Tat-transactivation in cell line models. Furthermore, the FDA-approved proteasome inhibitors bortezomib and carfilzomib strongly synergize with existing LRAs to reactivate HIV-1 in CD4+ T cells from antiretroviral therapy-suppressed individuals without inducing cell activation or proliferation. Mechanistically, downregulating/inhibiting the proteasome elevates the levels of ELL2 and ELL2-SECs to enable Tat-transactivation, indicating the proteasome-ELL2 axis as a key regulator of HIV-1 latency and promising target for therapeutic intervention. To cure chronic HIV-1 infection requires reversal of HIV-1 latency from latently infected CD4+ T cells. A key step in HIV latency reversal is the recruitment of Super Elongation Complexes (SECs) that contain ELL2 by an HIV-encoded protein, Tat, to activate proviral transcription. To identify novel drug targets, we conducted a CRISPRi-based screen to enrich the sgRNAs that increase HIV transcription in latently infected CD4+ T cells. Three of the six most prominent hits in our screen are proteasome subunits. We further proved that antagonizing the proteasome promotes Tat-induced HIV-1 transcription in cell line-based latency models. Furthermore, we found that two FDA-approved proteasome inhibitors strongly synergize with existing LRAs ex vivo without inducing cell activation or proliferation. We further found that antagonizing the proteasome elevates the levels of ELL2 and ELL2-containing SECs in the cells, thus enabling Tat-transactivation. These results indicate that the proteasome-ELL2 axis is a key regulator of HIV-1 latency could potentially be targeted for therapeutic interventions.
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Affiliation(s)
- Zichong Li
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Jun Wu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Leonard Chavez
- Vitalant Research Institute, San Francisco, California, United States of America
- University of California, San Francisco, California, United States of America
| | - Rebecca Hoh
- University of California, San Francisco, California, United States of America
| | - Steven G. Deeks
- University of California, San Francisco, California, United States of America
| | - Satish K. Pillai
- Vitalant Research Institute, San Francisco, California, United States of America
- University of California, San Francisco, California, United States of America
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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14
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Abstract
The reproductive adaptations of land plants have played a key role in their terrestrial colonization and radiation. This encompasses mechanisms used for the production, dispersal and union of gametes to support sexual reproduction. The production of small motile male gametes and larger immotile female gametes (oogamy) in specialized multicellular gametangia evolved in the charophyte algae, the closest extant relatives of land plants. Reliance on water and motile male gametes for sexual reproduction was retained by bryophytes and basal vascular plants, but was overcome in seed plants by the dispersal of pollen and the guided delivery of non-motile sperm to the female gametes. Here we discuss the evolutionary history of male gametogenesis in streptophytes (green plants) and the underlying developmental biology, including recent advances in bryophyte and angiosperm models. We conclude with a perspective on research trends that promise to deliver a deeper understanding of the evolutionary and developmental mechanisms of male gametogenesis in plants.
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Affiliation(s)
- Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.
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15
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Next-generation sequencing analysis of multiplex families with atypical psychosis. Transl Psychiatry 2018; 8:221. [PMID: 30323194 PMCID: PMC6189064 DOI: 10.1038/s41398-018-0272-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/20/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
Atypical psychosis (similar to acute and transient psychotic disorder, brief psychotic disorder) is highly heritable, but the causal genes remain unidentified. We conducted whole-genome sequencing on multiplex Japanese families with atypical psychosis. The patient group of interest shows acute psychotic features including hallucinations, delusions, and catatonic symptoms while they often show good prognosis after the onset. In addition to the next-generation analysis, HLA typing has been conveyed to check the similarity with autoimmune disease, such as systemic lupus erythematosus (SLE). Shared causal polymorphisms in the Deleted in Colorectal Carcinoma, Netrin 1 receptor (DCC) gene were found in one multiplex family with three patients, and variants in the RNA 3'-Terminal Phosphate Cyclase (RTCA) and One Cut Homeobox 2 (ONECUT2) genes were found to be shared in seven patients. Next-generation sequencing analysis of the MHC region (previously suggested to be a hot region in atypical psychosis) using HLA typing (HLA-DRB1) revealed a common vulnerability with SLE (systemic lupus erythematosus) among five patients. This finding demonstrates the shared etiology between psychotic symptoms and autoimmune diseases at the genetic level. Focusing on a specific clinical phenotype is key for elucidating the genetic factors that underlie the complex traits of psychosis.
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16
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Zhang XC, Liang HF, Luo XD, Wang HJ, Gu AP, Zheng CY, Su QZ, Cai J. YY1 promotes IL-6 expression in LPS-stimulated BV2 microglial cells by interacting with p65 to promote transcriptional activation of IL-6. Biochem Biophys Res Commun 2018; 502:269-275. [PMID: 29803672 DOI: 10.1016/j.bbrc.2018.05.159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 12/17/2022]
Abstract
Neuroinflammation plays a critical role in the process of neurodegenerative disorders, during which microglia, the principal resident immune cells in the central nervous system, are activated and produce proinflammatory mediators. Yin-Yang 1 (YY1), a multi-functional transcription factor, is widely expressed in cells of the immune system and participate in various cellular processes. However, whether YY1 is involved in the process of neuroinflammation is still unknown. In the present study, we found that YY1 was progressively up-regulated in BV2 microglial cells stimulated with lipopolysaccharide (LPS), which was dependent on the transactivation function of nuclear factor kappa B (NF-κB). Furthermore, YY1 knockdown notably inhibited LPS-induced the activation of NF-κB signaling and interleukin-6 (IL-6) expression in BV-2 cells, but not mitogen-activated protein kinase (MAPK) signaling. Moreover, YY1 strengthened p65 binding to IL-6 promoter by interacting with p65 but decreased H3K27ac modification on IL-6 promoter, eventually increasing IL-6 transcription. Taken together, these results for the first time uncover the regulatory mechanism of YY1 on IL-6 expression during neuroinflammation responses and provide new lights into neuroinflammation.
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Affiliation(s)
- Xin-Chun Zhang
- Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, PR China
| | - Hong-Feng Liang
- Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, PR China
| | - Xiao-Dong Luo
- Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, PR China
| | - Hua-Jun Wang
- Department of Neurosurgery, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, PR China
| | - Ai-Ping Gu
- Department of Ophthalmology, Guangdong Second Provincial General Hospital, Guangzhou, PR China
| | - Chun-Ye Zheng
- Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, PR China
| | - Qiao-Zhen Su
- Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, PR China
| | - Jun Cai
- Department of Neurosurgery, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, PR China.
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17
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Williams MLK, Sawada A, Budine T, Yin C, Gontarz P, Solnica-Krezel L. Gon4l regulates notochord boundary formation and cell polarity underlying axis extension by repressing adhesion genes. Nat Commun 2018; 9:1319. [PMID: 29615614 PMCID: PMC5882663 DOI: 10.1038/s41467-018-03715-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 03/06/2018] [Indexed: 01/15/2023] Open
Abstract
Anteroposterior (AP) axis extension during gastrulation requires embryonic patterning and morphogenesis to be spatiotemporally coordinated, but the underlying genetic mechanisms remain poorly understood. Here we define a role for the conserved chromatin factor Gon4l, encoded by ugly duckling (udu), in coordinating tissue patterning and axis extension during zebrafish gastrulation through direct positive and negative regulation of gene expression. Although identified as a recessive enhancer of impaired axis extension in planar cell polarity (PCP) mutants, udu functions in a genetically independent, partially overlapping fashion with PCP signaling to regulate mediolateral cell polarity underlying axis extension in part by promoting notochord boundary formation. Gon4l limits expression of the cell–cell and cell–matrix adhesion molecules EpCAM and Integrinα3b, excesses of which perturb the notochord boundary via tension-dependent and -independent mechanisms, respectively. By promoting formation of this AP-aligned boundary and associated cell polarity, Gon4l cooperates with PCP signaling to coordinate morphogenesis along the AP embryonic axis. Anteroposterior axis extension during gastrulation is dynamically coordinated, but how this is regulated at a molecular level is unclear. Here, the authors show in zebrafish that the chromatin factor Gon4l, encoded by ugly duckling, coordinates axis extension by modulating EpCAM and Integrinα3b expression.
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Affiliation(s)
- Margot L K Williams
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Atsushi Sawada
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Terin Budine
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Chunyue Yin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO, 63110, USA. .,Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
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Barr JY, Goodfellow RX, Colgan DF, Colgan JD. Early B Cell Progenitors Deficient for GON4L Fail To Differentiate Due to a Block in Mitotic Cell Division. THE JOURNAL OF IMMUNOLOGY 2017; 198:3978-3988. [PMID: 28381640 DOI: 10.4049/jimmunol.1602054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/14/2017] [Indexed: 11/19/2022]
Abstract
B cell development in Justy mutant mice is blocked due to a precursor mRNA splicing defect that depletes the protein GON4-like (GON4L) in B cell progenitors. Genetic and biochemical studies have suggested that GON4L is a transcriptional regulator that coordinates cell division with differentiation, but its role in B cell development is unknown. To understand the function of GON4L, we characterized B cell differentiation, cell cycle control, and mitotic gene expression in GON4L-deficient B cell progenitors from Justy mice. We found that these cells established key aspects of the transcription factor network that guides B cell development and proliferation and rearranged the IgH gene locus. However, despite intact IL-7 signaling, GON4L-deficient pro-B cell stage precursors failed to undergo a characteristic IL-7-dependent proliferative burst. These cells also failed to upregulate genes required for mitotic division, including those encoding the G1/S cyclin D3 and E2F transcription factors and their targets. Additionally, GON4L-deficient B cell progenitors displayed defects in DNA synthesis and passage through the G1/S transition, contained fragmented DNA, and underwent apoptosis. These phenotypes were not suppressed by transgenic expression of prosurvival factors. However, transgenic expression of cyclin D3 or other regulators of the G1/S transition restored pro-B cell development from Justy progenitor cells, suggesting that GON4L acts at the beginning of the cell cycle. Together, our findings indicate that GON4L is essential for cell cycle progression and division during the early stages of B cell development.
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Affiliation(s)
- Jennifer Y Barr
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Renee X Goodfellow
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242; and
| | - Diana F Colgan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242; and
| | - John D Colgan
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242; .,Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242; and.,Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
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19
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Liu L, Wang JF, Fan J, Rao YS, Liu F, Yan YE, Wang H. Nicotine Suppressed Fetal Adrenal StAR Expression via YY1 Mediated-Histone Deacetylation Modification Mechanism. Int J Mol Sci 2016; 17:ijms17091477. [PMID: 27598153 PMCID: PMC5037755 DOI: 10.3390/ijms17091477] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/10/2016] [Accepted: 08/29/2016] [Indexed: 11/16/2022] Open
Abstract
Steroidogenic acute regulatory (StAR) protein plays a pivotal role in steroidogenesis. Previously, we have demonstrated that prenatal nicotine exposure suppressed fetal adrenal steroidogenesis via steroidogenic factor 1 deacetylation. This study further explored the potential role of the transcriptional repressor Yin Yang 1 (YY1) in nicotine-mediated StAR inhibition. Nicotine was subcutaneously administered (1.0 mg/kg) to pregnant rats twice per day and NCI-H295A cells were treated with nicotine. StAR and YY1 expression were analyzed by real-time PCR, immunohistochemistry, and Western blotting. Histone modifications and the interactions between the YY1 and StAR promoter were assessed using chromatin immunoprecipitation (ChIP). Prenatal nicotine exposure increased YY1 expression and suppressed StAR expression. ChIP assay showed that there was a decreasing trend for histone acetylation at the StAR promoter in fetal adrenal glands, whereas H3 acetyl-K14 at the YY1 promoter presented an increasing trend following nicotine exposure. Furthermore, in nicotine-treated NCI-H295A cells, nicotine enhanced YY1 expression and inhibited StAR expression. ChIP assay showed that histone acetylation decreased at the StAR promoter in NCI-H295A cells and that the interaction between the YY1 and StAR promoter increased. These data indicated that YY1-medicated histone deacetylation modification in StAR promoters might play an important role in the inhibitory effect of nicotine on StAR expression.
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Affiliation(s)
- Lian Liu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China.
- Department of Pharmacology, Medical School of Yangtze University, Jingzhou 434000, China.
| | - Jian-Fei Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China.
| | - Jie Fan
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China.
| | - Yi-Song Rao
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China.
| | - Fang Liu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China.
| | - You-E Yan
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China.
| | - Hui Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071, China.
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20
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Agarwal N, Dancik GM, Goodspeed A, Costello JC, Owens C, Duex JE, Theodorescu D. GON4L Drives Cancer Growth through a YY1-Androgen Receptor-CD24 Axis. Cancer Res 2016; 76:5175-85. [PMID: 27312530 DOI: 10.1158/0008-5472.can-16-1099] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/02/2016] [Indexed: 11/16/2022]
Abstract
In principle, the inhibition of candidate gain-of-function genes defined through genomic analyses of large patient cohorts offers an attractive therapeutic strategy. In this study, we focused on changes in expression of CD24, a well-validated clinical biomarker of poor prognosis and a driver of tumor growth and metastasis, as a benchmark to assess functional relevance. Through this approach, we identified GON4L as a regulator of CD24 from screening a pooled shRNA library of 176 candidate gain-of-function genes. GON4L depletion reduced CD24 expression in human bladder cancer cells and blocked cell proliferation in vitro and tumor xenograft growth in vivo Mechanistically, GON4L interacted with transcription factor YY1, promoting its association with the androgen receptor to drive CD24 expression and cell growth. In clinical bladder cancer specimens, expression of GON4L, YY1, and CD24 was elevated compared with normal bladder urothelium. This pathway is biologically relevant in other cancer types as well, where CD24 and the androgen receptor are clinically prognostic, given that silencing of GON4L and YY1 suppressed CD24 expression and growth of human lung, prostate, and breast cancer cells. Overall, our results define GON4L as a novel driver of cancer growth, offering new biomarker and therapeutic opportunities. Cancer Res; 76(17); 5175-85. ©2016 AACR.
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Affiliation(s)
- Neeraj Agarwal
- Department of Pharmacology, University of Colorado, Denver, Colorado. Department of Surgery (Urology), University of Colorado, Denver, Colorado
| | - Garrett M Dancik
- Department of Mathematics and Computer Science, Eastern Connecticut State University, Willimantic, Connecticut
| | - Andrew Goodspeed
- Department of Pharmacology, University of Colorado, Denver, Colorado
| | - James C Costello
- Department of Pharmacology, University of Colorado, Denver, Colorado. University of Colorado Comprehensive Cancer Center, Denver, Colorado
| | - Charles Owens
- Department of Pharmacology, University of Colorado, Denver, Colorado. Department of Surgery (Urology), University of Colorado, Denver, Colorado
| | - Jason E Duex
- Department of Pharmacology, University of Colorado, Denver, Colorado. Department of Surgery (Urology), University of Colorado, Denver, Colorado
| | - Dan Theodorescu
- Department of Pharmacology, University of Colorado, Denver, Colorado. Department of Surgery (Urology), University of Colorado, Denver, Colorado. University of Colorado Comprehensive Cancer Center, Denver, Colorado.
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21
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Skrajna A, Yang XC, Tarnowski K, Fituch K, Marzluff WF, Dominski Z, Dadlez M. Mapping the Interaction Network of Key Proteins Involved in Histone mRNA Generation: A Hydrogen/Deuterium Exchange Study. J Mol Biol 2016; 428:1180-1196. [PMID: 26860583 DOI: 10.1016/j.jmb.2016.01.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/27/2016] [Accepted: 01/30/2016] [Indexed: 10/22/2022]
Abstract
Histone pre-mRNAs are cleaved at the 3' end by a complex that contains U7 snRNP, the FLICE-associated huge protein (FLASH) and histone pre-mRNA cleavage complex (HCC) consisting of several polyadenylation factors. Within the complex, the N terminus of FLASH interacts with the N terminus of the U7 snRNP protein Lsm11, and together they recruit the HCC. FLASH through its distant C terminus independently interacts with the C-terminal SANT/Myb-like domain of nuclear protein, ataxia-telangiectasia locus (NPAT), a transcriptional co-activator required for expression of histone genes in S phase. To gain structural information on these interactions, we used mass spectrometry to monitor hydrogen/deuterium exchange in various regions of FLASH, Lsm11 and NPAT alone or in the presence of their respective binding partners. Our results indicate that the FLASH-interacting domain in Lsm11 is highly dynamic, while the more downstream region required for recruiting the HCC exchanges deuterium slowly and likely folds into a stable structure. In FLASH, a stable structure is adopted by the domain that interacts with Lsm11 and this domain is further stabilized by binding Lsm11. Notably, both hydrogen/deuterium exchange experiments and in vitro binding assays demonstrate that Lsm11, in addition to interacting with the N-terminal region of FLASH, also contacts the C-terminal SANT/Myb-like domain of FLASH, the same region that binds NPAT. However, while NPAT stabilizes this domain, Lsm11 causes its partial relaxation. These competing reactions may play a role in regulating histone gene expression in vivo.
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Affiliation(s)
- Aleksandra Skrajna
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiao-Cui Yang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Krzysztof Tarnowski
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Kinga Fituch
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - William F Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zbigniew Dominski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Michał Dadlez
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
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22
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Pharmacological modulation of HDAC1 and HDAC6 in vivo in a zebrafish model: Therapeutic implications for Parkinson’s disease. Pharmacol Res 2016; 103:328-39. [DOI: 10.1016/j.phrs.2015.11.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/27/2015] [Accepted: 11/29/2015] [Indexed: 11/22/2022]
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23
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Liu C, Yu Y, Liu F, Wei X, Wrobel JA, Gunawardena HP, Zhou L, Jin J, Chen X. A chromatin activity-based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing. Nat Commun 2014; 5:5733. [PMID: 25502336 PMCID: PMC4360912 DOI: 10.1038/ncomms6733] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 11/02/2014] [Indexed: 12/17/2022] Open
Abstract
Immune cells develop endotoxin tolerance (ET) after prolonged stimulation. ET increases the level of a repression mark H3K9me2 in the transcriptional-silent chromatin specifically associated with pro-inflammatory genes. However, it is not clear what proteins are functionally involved in this process. Here we show that a novel chromatin activity based chemoproteomic (ChaC) approach can dissect the functional chromatin protein complexes that regulate ET-associated inflammation. Using UNC0638 that binds the enzymatically active H3K9-specific methyltransferase G9a/GLP, ChaC reveals that G9a is constitutively active at a G9a-dependent mega-dalton repressome in primary endotoxin-tolerant macrophages. G9a/GLP broadly impacts the ET-specific reprogramming of the histone code landscape, chromatin remodeling, and the activities of select transcription factors. We discover that the G9a-dependent epigenetic environment promotes the transcriptional repression activity of c-Myc for gene-specific co-regulation of chronic inflammation. ChaC may be also applicable to dissect other functional protein complexes in the context of phenotypic chromatin architectures.
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Affiliation(s)
- Cui Liu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Yanbao Yu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Xin Wei
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - John A Wrobel
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Harsha P Gunawardena
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Li Zhou
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jian Jin
- Department of Structural and Chemical Biology, Department of Oncological Sciences, and Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Xian Chen
- 1] Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA [2] Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA [3] Department of Chemistry, Fudan University, Shanghai 200433, China
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24
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Yang XC, Sabath I, Kunduru L, van Wijnen AJ, Marzluff WF, Dominski Z. A conserved interaction that is essential for the biogenesis of histone locus bodies. J Biol Chem 2014; 289:33767-82. [PMID: 25339177 DOI: 10.1074/jbc.m114.616466] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nuclear protein, ataxia-telangiectasia locus (NPAT) and FLICE-associated huge protein (FLASH) are two major components of discrete nuclear structures called histone locus bodies (HLBs). NPAT is a key co-activator of histone gene transcription, whereas FLASH through its N-terminal region functions in 3' end processing of histone primary transcripts. The C-terminal region of FLASH contains a highly conserved domain that is also present at the end of Yin Yang 1-associated protein-related protein (YARP) and its Drosophila homologue, Mute, previously shown to localize to HLBs in Drosophila cells. Here, we show that the C-terminal domain of human FLASH and YARP interacts with the C-terminal region of NPAT and that this interaction is essential and sufficient to drive FLASH and YARP to HLBs in HeLa cells. Strikingly, only the last 16 amino acids of NPAT are sufficient for the interaction. We also show that the C-terminal domain of Mute interacts with a short region at the end of the Drosophila NPAT orthologue, multi sex combs (Mxc). Altogether, our data indicate that the conserved C-terminal domain shared by FLASH, YARP, and Mute recognizes the C-terminal sequence of NPAT orthologues, thus acting as a signal targeting proteins to HLBs. Finally, we demonstrate that the C-terminal domain of human FLASH can be directly joined with its N-terminal region through alternative splicing. The resulting 190-amino acid MiniFLASH, despite lacking 90% of full-length FLASH, contains all regions necessary for 3' end processing of histone pre-mRNA in vitro and accumulates in HLBs.
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Affiliation(s)
- Xiao-cui Yang
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
| | - Ivan Sabath
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
| | - Lalitha Kunduru
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
| | - Andre J van Wijnen
- the Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - William F Marzluff
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
| | - Zbigniew Dominski
- From the Department of Biochemistry and Biophysics, Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and
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25
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Hua L, Zhou P. Combining protein-protein interactions information with support vector machine to identify chronic obstructive pulmonary disease related genes. Mol Biol 2014. [DOI: 10.1134/s0026893314020101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Identification of cellular proteins that interact with human cytomegalovirus immediate-early protein 1 by protein array assay. Viruses 2013; 6:89-105. [PMID: 24385082 PMCID: PMC3917433 DOI: 10.3390/v6010089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/10/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022] Open
Abstract
Human cytomegalovirus (HCMV) gene expression during infection is characterized as a sequential process including immediate-early (IE), early (E), and late (L)-stage gene expression. The most abundantly expressed gene at the IE stage of infection is the major IE (MIE) gene that produces IE1 and IE2. IE1 has been the focus of study because it is an important protein, not only for viral gene expression but also for viral replication. It is believed that IE1 plays important roles in viral gene regulation by interacting with cellular proteins. In the current study, we performed protein array assays and identified 83 cellular proteins that interact with IE1. Among them, seven are RNA-binding proteins that are important in RNA processing; more than half are nuclear proteins that are involved in gene regulations. Tumorigenesis-related proteins are also found to interact with IE1, implying that the role of IE1 in tumorigenesis might need to be reevaluated. Unexpectedly, cytoplasmic proteins, such as Golgi autoantigen and GGA1 (both related to the Golgi trafficking protein), are also found to be associated with IE1. We also employed a coimmunoprecipitation assay to test the interactions of IE1 and some of the proteins identified in the protein array assays and confirmed that the results from the protein array assays are reliable. Many of the proteins identified by the protein array assay have not been previously reported. Therefore, the functions of the IE1-protein interactions need to be further explored in the future.
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27
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Yin Yang 1 (YY1) synergizes with Smad7 to inhibit TGF-β signaling in the nucleus. SCIENCE CHINA-LIFE SCIENCES 2013; 57:128-36. [PMID: 24369345 DOI: 10.1007/s11427-013-4581-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
Abstract
As a prototype of the TGF-β superfamily cytokines, TGF-β is well known for its diverse roles in embryogenesis and adult tissue homeostasis. TGF-β evokes cellular responses by signaling mainly through cell membrane receptors and transcription factor R-Smads and Co-Smad (Smad4), while an inhibitory Smad, Smad7, acts as a critical negative regulator of TGF-β signaling. Smad7 antagonizes TGF-β signaling by regulating the stability or activity of the receptors or blocking the DNA binding of the functional R-Smad-Smad4 complex in the nucleus. However, the function of Smad7 in the nucleus is not fully understood. Yin Yang 1 (YY1) is a ubiquitously expressed transcription factor with multiple functions. It has been reported that YY1 can inhibit Smad-dependent transcriptional responses and TGF-β/BMP-induced cell differentiation independently of its DNA binding ability. In this study, we found that Smad7 interacts with YY1 and the interaction is attenuated by TGF-β signaling. Reporter assays and target gene expression analyses revealed that Smad7 and YY1 act in concert to inhibit TGF-β-induced transcription in the nucleus. Furthermore, Smad7 could enhance the interaction of YY1 with the histone deacetylase HDAC1. Consistently, YY1 and HDAC1 augmented the transcription repression activity of Smad7 in Gal4-luciferase reporter analysis. Therefore, our findings define a novel mechanism of Smad7 and YY1 to antagonize TGF-β signaling.
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28
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The Justy mutant mouse strain produces a spontaneous murine model of salivary gland cancer with myoepithelial and basal cell differentiation. J Transl Med 2013; 93:711-9. [PMID: 23608756 PMCID: PMC3669254 DOI: 10.1038/labinvest.2013.62] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We previously identified a novel mutant mouse strain on the C3HeB/FeJ background named Justy. This strain bears a recessive mutation in the Gon4l gene that greatly reduces expression of the encoded protein, a nuclear factor implicated in transcriptional regulation. Here, we report that Justy mutant mice aged 6 months or older spontaneously developed carcinomas with myoepithelial and basaloid differentiation in salivary glands with an incidence of ∼25%. Tumors developed proximate to submandibular glands and to a lesser extent in the sublingual and parotid glands. Histologically, tumors often had central cavitary lesions filled with necrotic debris that were lined by tumor cells, and had spindle and epithelioid cell differentiation with lesser basaloid to clear cell features. Tumor tissue often had variable evidence of a high mitotic rate, pleomorphism, and invasion into adjacent salivary glands. Neoplastic cells had diffuse immunoreactivity for pancytokeratin (AE1/AE3) and p63. Although CK5/6 immunostaining was seen in the much of the tumor cells, it was often lacking in pleomorphic areas. Tumor cells lacked immunoreactivity for alpha-smooth muscle actin, S100, c-Kit, and glial fibrillary acid protein. In addition, tumors had immunoreactivity for phosphorylated and total epidermal growth factor receptor, suggesting that EGFR signaling may participate in growth regulation of these tumors. These findings indicate that the salivary gland carcinomas occur spontaneously in Justy mice, and that these tumors may offer a valuable model for study of EGFR regulation. In combination, our data suggest that Justy mice warrant further investigation for use as a mouse model for human salivary gland neoplasia.
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29
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Lu P, Hostager BS, Rothman PB, Colgan JD. Sedimentation and immunoprecipitation assays for analyzing complexes that repress transcription. Methods Mol Biol 2013; 977:365-83. [PMID: 23436378 DOI: 10.1007/978-1-62703-284-1_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Co-repressor proteins function as platforms for the assembly of multi-subunit complexes that mediate transcriptional repression. Common components of such complexes are histone deacetylases, which catalyze the removal of acetyl groups from the tails of histones within nucleosomes, resulting in chromatin compaction and gene repression. In addition, co-repressor complexes generally interact with sequence-specific DNA-binding proteins that direct association with regulatory elements in the genome. Thus, identifying proteins that stably associate with co-repressors can provide insights regarding the biochemical function and target gene specificity of these molecules. Here, we describe a density gradient fractionation method for determining whether a co-repressor is incorporated into high-molecular complexes within cells and for identifying potential constituents of these complexes. We also describe a co-immunoprecipitation assay for confirming and further studying interactions between co-repressors and other proteins that may represent functional partners.
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Affiliation(s)
- Ping Lu
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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30
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Wang D, Rendon A, Ouwehand W, Wernisch L. Transcription factor co-localization patterns affect human cell type-specific gene expression. BMC Genomics 2012; 13:263. [PMID: 22721266 PMCID: PMC3441573 DOI: 10.1186/1471-2164-13-263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 06/12/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cellular development requires the precise control of gene expression states. Transcription factors are involved in this regulatory process through their combinatorial binding with DNA. Information about transcription factor binding sites can help determine which combinations of factors work together to regulate a gene, but it is unclear how far the binding data from one cell type can inform about regulation in other cell types. RESULTS By integrating data on co-localized transcription factor binding sites in the K562 cell line with expression data across 38 distinct hematopoietic cell types, we developed regression models to describe the relationship between the expression of target genes and the transcription factors that co-localize nearby. With K562 binding sites identifying the predictors, the proportion of expression explained by the models is statistically significant only for monocytic cells (p-value< 0.001), which are closely related to K562. That is, cell type specific binding patterns are crucial for choosing the correct transcription factors for the model. Comparison of predictors obtained from binding sites in the GM12878 cell line with those from K562 shows that the amount of difference between binding patterns is directly related to the quality of the prediction. By identifying individual genes whose expression is predicted accurately by the binding sites, we are able to link transcription factors FOS, TAF1 and YY1 to a sparsely studied gene LRIG2. We also find that the activity of a transcription factor may be different depending on the cell type and the identity of other co-localized factors. CONCLUSION Our approach shows that gene expression can be explained by a modest number of co-localized transcription factors, however, information on cell-type specific binding is crucial for understanding combinatorial gene regulation.
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Affiliation(s)
- Dennis Wang
- MRC Biostatistics Unit, Institute of Public Health, Robinson Way, Cambridge, UK
| | - Augusto Rendon
- Department of Haematology, University of Cambridge, Long Road, Cambridge, UK
| | - Willem Ouwehand
- Department of Haematology, University of Cambridge, Long Road, Cambridge, UK
| | - Lorenz Wernisch
- Department of Haematology, University of Cambridge, Long Road, Cambridge, UK
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31
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Abstract
Yin Yang 1 (YY1) is a transcription factor with diverse and complex biological functions. YY1 either activates or represses gene transcription, depending on the stimuli received by the cells and its association with other cellular factors. Since its discovery, a biological role for YY1 in tumor development and progression has been suggested because of its regulatory activities toward multiple cancer-related proteins and signaling pathways and its overexpression in most cancers. In this review, we primarily focus on YY1 studies in cancer research, including the regulation of YY1 as a transcription factor, its activities independent of its DNA binding ability, the functions of its associated proteins, and mechanisms regulating YY1 expression and activities. We also discuss the correlation of YY1 expression with clinical outcomes of cancer patients and its target potential in cancer therapy. Although there is not a complete consensus about the role of YY1 in cancers based on its activities of regulating oncogene and tumor suppressor expression, most of the currently available evidence supports a proliferative or oncogenic role of YY1 in tumorigenesis.
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Affiliation(s)
- Qiang Zhang
- Department of Cancer Biology and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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