151
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The role of MYB proto-oncogene like 2 in tamoxifen resistance in breast cancer. J Mol Histol 2020; 52:21-30. [PMID: 33141360 DOI: 10.1007/s10735-020-09920-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022]
Abstract
Despite the efficacy of tamoxifen in preventing disease relapse, a large portion of breast cancer patients show intrinsic or acquired resistance to tamoxifen, leading to treatment failure and unfavorable clinical outcome. MYB proto-oncogene like 2 (MYBL2) is a transcription factor implicated in the initiation and progression of various human cancers. However, its role in tamoxifen resistance in breast cancer remained largely unknown. In the present study, by analyzing public transcriptome dataset, we found that MYBL2 is overexpressed in breast cancer and is associated with the poor prognosis of breast cancer patients. By establishing tamoxifen-resistant breast cancer cell lines, we also provided evidence that MYBL2 overexpression contributes to tamoxifen resistance by up-regulating its downstream transcriptional effectors involved in cell proliferation (PLK1, PRC1), survival (BIRC5) and metastasis (HMMR). In contrast, inhibiting those genes via MYBL2 depletion suppresses cancer progression, restores tamoxifen and eventually reduces the risk of disease recurrence. All these findings revealed a critical role of MYBL2 in promoting tamoxifen resistance and exacerbating the progression of breast cancer, which may serve as a novel therapeutic target to overcome drug resistance and improve the prognosis of breast cancer patients.
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152
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Caldwell AB, Liu Q, Schroth GP, Galasko DR, Yuan SH, Wagner SL, Subramaniam S. Dedifferentiation and neuronal repression define familial Alzheimer's disease. SCIENCE ADVANCES 2020; 6:6/46/eaba5933. [PMID: 33188013 PMCID: PMC7673760 DOI: 10.1126/sciadv.aba5933] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 09/23/2020] [Indexed: 05/05/2023]
Abstract
Identifying the systems-level mechanisms that lead to Alzheimer's disease, an unmet need, is an essential step toward the development of therapeutics. In this work, we report that the key disease-causative mechanisms, including dedifferentiation and repression of neuronal identity, are triggered by changes in chromatin topology. Here, we generated human induced pluripotent stem cell (hiPSC)-derived neurons from donor patients with early-onset familial Alzheimer's disease (EOFAD) and used a multiomics approach to mechanistically characterize the modulation of disease-associated gene regulatory programs. We demonstrate that EOFAD neurons dedifferentiate to a precursor-like state with signatures of ectoderm and nonectoderm lineages. RNA-seq, ATAC-seq, and ChIP-seq analysis reveals that transcriptional alterations in the cellular state are orchestrated by changes in histone methylation and chromatin topology. Furthermore, we demonstrate that these mechanisms are observed in EOFAD-patient brains, validating our hiPSC-derived neuron models. The mechanistic endotypes of Alzheimer's disease uncovered here offer key insights for therapeutic interventions.
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Affiliation(s)
- Andrew B Caldwell
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Qing Liu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Douglas R Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Shauna H Yuan
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Steven L Wagner
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- VA San Diego Healthcare System, La Jolla, CA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
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153
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Ray M, Larschan E. Getting started: altering promoter choice as a mechanism for cell type differentiation. Genes Dev 2020; 34:619-620. [PMID: 32358039 PMCID: PMC7197355 DOI: 10.1101/gad.338723.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this issue of Genes & Development, Lu and colleagues (pp. 663-677) have discovered a key new mechanism of alternative promoter choice that is involved in differentiation of spermatocytes. Promoter choice has strong potential as mechanism for differentiation of many different cell types.
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Affiliation(s)
- Mukulika Ray
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Erica Larschan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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154
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p130 And pRb in the Maintenance of Transient Quiescence of Mesenchymal Stem Cells. Stem Cells Int 2020; 2020:8883436. [PMID: 33014072 PMCID: PMC7519995 DOI: 10.1155/2020/8883436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/11/2020] [Accepted: 09/03/2020] [Indexed: 11/17/2022] Open
Abstract
An effective regulation of quiescence plays a key role in the differentiation, plasticity, and prevention of stem cells from becoming malignant. The state of quiescence is being controlled by the pRb family proteins which show overlapping functions in cell cycle regulation; however, their roles in controlling the proliferation of mesenchymal stem cells (MSCs) remain to be understood. This study investigated the regulation of transient quiescence using growth curves, proliferation assay, the cytometric evaluation of cell cycle, Western blotting, and the electromobility gel shift assay (EMSA) on synchronized MSCs of the C3H10Т1/2 and control cells with different statuses of pRb proteins. It has been found that functional steady-state level of p130 but not pRb plays a critical role for entering, exiting, and maintenance of transient quiescence in multipotent mesenchymal stem cells.
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155
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Desvoyes B, Gutierrez C. Roles of plant retinoblastoma protein: cell cycle and beyond. EMBO J 2020; 39:e105802. [PMID: 32865261 PMCID: PMC7527812 DOI: 10.15252/embj.2020105802] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
The human retinoblastoma (RB1) protein is a tumor suppressor that negatively regulates cell cycle progression through its interaction with members of the E2F/DP family of transcription factors. However, RB-related (RBR) proteins are an early acquisition during eukaryote evolution present in plant lineages, including unicellular algae, ancient plants (ferns, lycophytes, liverworts, mosses), gymnosperms, and angiosperms. The main RBR protein domains and interactions with E2Fs are conserved in all eukaryotes and not only regulate the G1/S transition but also the G2/M transition, as part of DREAM complexes. RBR proteins are also important for asymmetric cell division, stem cell maintenance, and the DNA damage response (DDR). RBR proteins play crucial roles at every developmental phase transition, in association with chromatin factors, as well as during the reproductive phase during female and male gametes production and embryo development. Here, we review the processes where plant RBR proteins play a role and discuss possible avenues of research to obtain a full picture of the multifunctional roles of RBR for plant life.
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156
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Cui H, Zuo S, Liu Z, Liu H, Wang J, You T, Zheng Z, Zhou Y, Qian X, Yao H, Xie L, Liu T, Sham PC, Yu Y, Li MJ. The support of genetic evidence for cardiovascular risk induced by antineoplastic drugs. SCIENCE ADVANCES 2020; 6:eabb8543. [PMID: 33055159 PMCID: PMC7556838 DOI: 10.1126/sciadv.abb8543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/28/2020] [Indexed: 05/04/2023]
Abstract
Cardiovascular dysfunction is one of the most common complications of long-term cancer treatment. Growing evidence has shown that antineoplastic drugs can increase cardiovascular risk during cancer therapy, seriously affecting patient survival. However, little is known about the genetic factors associated with the cardiovascular risk of antineoplastic drugs. We established a compendium of genetic evidence that supports cardiovascular risk induced by antineoplastic drugs. Most of this genetic evidence is attributed to causal alleles altering the expression of cardiovascular disease genes. We found that antineoplastic drugs predicted to induce cardiovascular risk are significantly enriched in drugs associated with cardiovascular adverse reactions, including many first-line cancer treatments. Functional experiments validated that retinoid X receptor agonists can reduce triglyceride lipolysis, thus modulating cardiovascular risk. Our results establish a link between the causal allele of cardiovascular disease genes and the direction of pharmacological modulation, which could facilitate cancer drug discovery and clinical trial design.
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Affiliation(s)
- Hui Cui
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Key Laboratory of Food Safety Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute for Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shengkai Zuo
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zipeng Liu
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Huanhuan Liu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jianhua Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianyi You
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhanye Zheng
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yao Zhou
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xinyi Qian
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hongcheng Yao
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Tong Liu
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, Tianjin, China
| | - Pak Chung Sham
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Yu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Key Laboratory of Food Safety Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute for Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mulin Jun Li
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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157
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Roelofs PA, Goh CY, Chua BH, Jarvis MC, Stewart TA, McCann JL, McDougle RM, Carpenter MA, Martens JW, Span PN, Kappei D, Harris RS. Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B. eLife 2020; 9:61287. [PMID: 32985974 PMCID: PMC7553775 DOI: 10.7554/elife.61287] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022] Open
Abstract
APOBEC3B (A3B)-catalyzed DNA cytosine deamination contributes to the overall mutational landscape in breast cancer. Molecular mechanisms responsible for A3B upregulation in cancer are poorly understood. Here we show that a single E2F cis-element mediates repression in normal cells and that expression is activated by its mutational disruption in a reporter construct or the endogenous A3B gene. The same E2F site is required for A3B induction by polyomavirus T antigen indicating a shared molecular mechanism. Proteomic and biochemical experiments demonstrate the binding of wildtype but not mutant E2F promoters by repressive PRC1.6/E2F6 and DREAM/E2F4 complexes. Knockdown and overexpression studies confirm the involvement of these repressive complexes in regulating A3B expression. Altogether, these studies demonstrate that A3B expression is suppressed in normal cells by repressive E2F complexes and that viral or mutational disruption of this regulatory network triggers overexpression in breast cancer and provides fuel for tumor evolution.
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Affiliation(s)
- Pieter A Roelofs
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Chai Yeen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Haow Chua
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States
| | - Teneale A Stewart
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Mater Research Institute, The University of Queensland, Faculty of Medicine, Brisbane, Australia
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
| | - Rebecca M McDougle
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Hennepin Healthcare, Minneapolis, United States
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
| | - John Wm Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Paul N Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
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158
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Martínez-Cué C, Rueda N. Signalling Pathways Implicated in Alzheimer's Disease Neurodegeneration in Individuals with and without Down Syndrome. Int J Mol Sci 2020; 21:E6906. [PMID: 32962300 PMCID: PMC7555886 DOI: 10.3390/ijms21186906] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
Down syndrome (DS), the most common cause of intellectual disability of genetic origin, is characterized by alterations in central nervous system morphology and function that appear from early prenatal stages. However, by the fourth decade of life, all individuals with DS develop neuropathology identical to that found in sporadic Alzheimer's disease (AD), including the development of amyloid plaques and neurofibrillary tangles due to hyperphosphorylation of tau protein, loss of neurons and synapses, reduced neurogenesis, enhanced oxidative stress, and mitochondrial dysfunction and neuroinflammation. It has been proposed that DS could be a useful model for studying the etiopathology of AD and to search for therapeutic targets. There is increasing evidence that the neuropathological events associated with AD are interrelated and that many of them not only are implicated in the onset of this pathology but are also a consequence of other alterations. Thus, a feedback mechanism exists between them. In this review, we summarize the signalling pathways implicated in each of the main neuropathological aspects of AD in individuals with and without DS as well as the interrelation of these pathways.
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Affiliation(s)
- Carmen Martínez-Cué
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, 39011 Santander, Spain;
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159
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Nientiedt M, Müller K, Nitschke K, Erben P, Steidler A, Porubsky S, Popovic ZV, Waldbillig F, Mühlbauer J, Kriegmair MC. B-MYB-p53-related relevant regulator for the progression of clear cell renal cell carcinoma. J Cancer Res Clin Oncol 2020; 147:129-138. [PMID: 32951068 DOI: 10.1007/s00432-020-03392-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/10/2020] [Indexed: 01/10/2023]
Abstract
PURPOSE To investigate the mRNA expression of B-MYB and MDM2 together with their p53 relatedness in clear cell renal cell carcinoma (ccRCC). METHODS Genes were screened for their mRNA expression from 529 patients in a publicly available ccRCC cohort (TCGA). A cohort of 101 patients with ccRCC served as validation by qRT-PCR mRNA tissue expression analysis. RESULTS Expression: B-MYB expression was significantly higher in high-grade tumours (p < 0.0001 and p = 0.048) and in advanced stages (p = 0.005 and p = 0.037) in both cohorts. Correlation: p53-B-MYB as well as MDM2-B-MYB showed significant correlations in local and low-grade ccRCCs, but not in high grade tumours or advanced stages (r < 0.3 and/or p > 0.05). Survival: Multivariable Cox regression of the TCGA cohort revealed B-MYB upregulation and low MDM2 expression as predictors for an impaired overall survival (OS) (HR 1.97; p = 0.0003; HR 2.94, p < 0.0001) and progression-free survival (PFS) (HR 2.86; p = 0.0005; HR 1.58, p = 0.046). In the validation cohort, the results were confirmed for OS by univariable, but not multivariable regression: high B-MYB expression (HR = 3.05, p = 0.035) and low MDM2 expression (HR 3.81, p value 0.036). CONCLUSION In ccRCC patients with high-grade tumours and advanced stages, high B-MYB expression is common and is associated with poorer OS and PFS. These patients show a loss of their physiological B-MYB-p53 network correlation, suggesting an additional, alternative regulatory, oncogenic mechanism. Assuming further characterization of its signalling pathways, B-MYB could be a potential therapy target for ccRCC.
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Affiliation(s)
- M Nientiedt
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
| | - K Müller
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - K Nitschke
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - P Erben
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - A Steidler
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - S Porubsky
- Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Z V Popovic
- Institute of Pathology, University Medical Centre Mannheim, University of Heidelberg, Mannheim, Germany
| | - F Waldbillig
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - J Mühlbauer
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - M C Kriegmair
- Department of Urology and Urosurgery, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
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160
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Cho B, Yoon SH, Lee D, Koranteng F, Tattikota SG, Cha N, Shin M, Do H, Hu Y, Oh SY, Lee D, Vipin Menon A, Moon SJ, Perrimon N, Nam JW, Shim J. Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila. Nat Commun 2020; 11:4483. [PMID: 32900993 PMCID: PMC7479620 DOI: 10.1038/s41467-020-18135-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/06/2020] [Indexed: 11/22/2022] Open
Abstract
The Drosophila lymph gland, the larval hematopoietic organ comprised of prohemocytes and mature hemocytes, has been a valuable model for understanding mechanisms underlying hematopoiesis and immunity. Three types of mature hemocytes have been characterized in the lymph gland: plasmatocytes, lamellocytes, and crystal cells, which are analogous to vertebrate myeloid cells, yet molecular underpinnings of the lymph gland hemocytes have been less investigated. Here, we use single-cell RNA sequencing to comprehensively analyze heterogeneity of developing hemocytes in the lymph gland, and discover previously undescribed hemocyte types including adipohemocytes, stem-like prohemocytes, and intermediate prohemocytes. Additionally, we identify the developmental trajectory of hemocytes during normal development as well as the emergence of the lamellocyte lineage following active cellular immunity caused by wasp infestation. Finally, we establish similarities and differences between embryonically derived- and larval lymph gland hemocytes. Altogether, our study provides detailed insights into the hemocyte development and cellular immune responses at single-cell resolution. How the Drosophila lymph gland hemocytes develop and are regulated at a single-cell level is unclear. Here, the authors use single-cell RNA sequencing to show heterogeneity of developing hemocytes in the lymph gland and how they react to wasp infestation, and compare hemocytes from two independent origins.
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Affiliation(s)
- Bumsik Cho
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | - Sang-Ho Yoon
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | - Daewon Lee
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | - Ferdinand Koranteng
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | | | - Nuri Cha
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | - Mingyu Shin
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | - Hobin Do
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sue Young Oh
- Department of Oral Biology, Yonsei University, College of Dentistry, Seoul, 03722, Republic of Korea
| | - Daehan Lee
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | - A Vipin Menon
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea
| | - Seok Jun Moon
- Department of Oral Biology, Yonsei University, College of Dentistry, Seoul, 03722, Republic of Korea
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Jin-Wu Nam
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea. .,Research Institute for Natural Sciences, Hanyang University, Seoul, 04736, Republic of Korea. .,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04736, Republic of Korea.
| | - Jiwon Shim
- Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea. .,Research Institute for Natural Sciences, Hanyang University, Seoul, 04736, Republic of Korea. .,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04736, Republic of Korea.
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161
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Kang K, Choi Y, Kim HH, Yoo KH, Yu S. Predicting FOXM1-Mediated Gene Regulation through the Analysis of Genome-Wide FOXM1 Binding Sites in MCF-7, K562, SK-N-SH, GM12878 and ECC-1 Cell Lines. Int J Mol Sci 2020; 21:ijms21176141. [PMID: 32858881 PMCID: PMC7503762 DOI: 10.3390/ijms21176141] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/16/2020] [Accepted: 08/24/2020] [Indexed: 12/25/2022] Open
Abstract
Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. However, the mechanism by which FOXM1 controls the common gene set in different cellular contexts is unclear. In this study, a comprehensive meta-analysis of genome-wide FOXM1 binding sites in ECC-1, GM12878, K562, MCF-7, and SK-N-SH cell lines was conducted to predict FOXM1-driven gene regulation. Consistent with previous studies, different TF binding motifs were identified at FOXM1 binding sites, while the NFY binding motif was found at 81% of common FOXM1 binding sites in promoters of cell cycle-related genes. The results indicated that FOXM1 might control the gene set through interaction with the NFY proteins, while cell type-specific genes were predicted to be regulated by enhancers with FOXM1 and cell type-specific TFs. We also found that the high expression level of FOXM1 was significantly associated with poor prognosis in nine types of cancer. Overall, these results suggest that FOXM1 is predicted to function as a master regulator of the cell cycle through the interaction of NFY-family proteins, and therefore the inhibition of FOXM1 could be an attractive strategy for cancer therapy.
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Affiliation(s)
- Keunsoo Kang
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea;
- Correspondence: (K.K.); (S.Y.); Tel.: +82-41-550-3456 (K.K.); +82-43-649-1418 (S.Y.)
| | | | - Hoo Hyun Kim
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea;
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea;
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Korea
| | - Sungryul Yu
- Department of Clinical Laboratory Science, Semyung University, Jecheon 27136, Korea
- Correspondence: (K.K.); (S.Y.); Tel.: +82-41-550-3456 (K.K.); +82-43-649-1418 (S.Y.)
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Pattschull G, Walz S, Gründl M, Schwab M, Rühl E, Baluapuri A, Cindric-Vranesic A, Kneitz S, Wolf E, Ade CP, Rosenwald A, von Eyss B, Gaubatz S. The Myb-MuvB Complex Is Required for YAP-Dependent Transcription of Mitotic Genes. Cell Rep 2020; 27:3533-3546.e7. [PMID: 31216474 DOI: 10.1016/j.celrep.2019.05.071] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/18/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
YAP and TAZ, downstream effectors of the Hippo pathway, are important regulators of proliferation. Here, we show that the ability of YAP to activate mitotic gene expression is dependent on the Myb-MuvB (MMB) complex, a master regulator of genes expressed in the G2/M phase of the cell cycle. By carrying out genome-wide expression and binding analyses, we found that YAP promotes binding of the MMB subunit B-MYB to the promoters of mitotic target genes. YAP binds to B-MYB and stimulates B-MYB chromatin association through distal enhancer elements that interact with MMB-regulated promoters through chromatin looping. The cooperation between YAP and B-MYB is critical for YAP-mediated entry into mitosis. Furthermore, the expression of genes coactivated by YAP and B-MYB is associated with poor survival of cancer patients. Our findings provide a molecular mechanism by which YAP and MMB regulate mitotic gene expression and suggest a link between two cancer-relevant signaling pathways.
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Affiliation(s)
- Grit Pattschull
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Susanne Walz
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Marco Gründl
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Melissa Schwab
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Eva Rühl
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Wuerzburg, Wuerzburg 97074, Germany
| | | | - Susanne Kneitz
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Carsten P Ade
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Andreas Rosenwald
- Institute of Pathology and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg 97080, Germany
| | - Björn von Eyss
- Leibniz Institute on Aging, Fritz Lipmann Institute e.V., Jena 07745, Germany
| | - Stefan Gaubatz
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany.
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163
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Zhao W, Wang M, Wang C, Liu Y, Liu H, Luo S. RACGAP1 is transcriptionally regulated by E2F3, and its depletion leads to mitotic catastrophe in esophageal squamous cell carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:950. [PMID: 32953750 PMCID: PMC7475413 DOI: 10.21037/atm-20-2901] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Background RACGAP1 has significant involvement in tumorigenesis of cancers, including liver cancer, stomach cancer, and colon cancer. However, the role and the exact mechanism of RACGAP1 in esophageal squamous cell carcinoma (ESCC) has not been explored. Methods QPCR and Western blots analysis was performed to analyze the expression of RACGAP1 in ESCC. MTT assays and colony formation assays were performed to explore the functional role of RACGAP1 in ESCC. Cell cycle analysis and immunofluorescence assays were used to investigate the function of RACGAP1 involvement in mitotic catastrophe. At last, we conducted the public datasets mining to explore the expression status and prognosis value of RACGAP1 as well as the correlation between RACGAP1 and E2F3 in various cancers. Results The high abnormal expression of RACGAP1 is observed in ESCC and associated with worse clinical outcomes of patients with ESCC. RACGAP1, a novel cell cycle associated gene regulated by E2F3, acts as an oncogenic driver in ESCC cell lines. Notably, for the first time, RACGAP1 depletion induced severe mitotic catastrophe, followed by massive cell death. Conclusions Our findings showed the essential role of RACGAP1 in ESCC cancer cell survival and the therapeutic potential of RACGAP1 as a molecular target for ESCC.
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Affiliation(s)
- Weifeng Zhao
- Department of Medical Oncology, the Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,Department of Oncology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China
| | - Mengyao Wang
- Radiation Oncology Department, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Chaojie Wang
- Department of Oncology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yingjun Liu
- Department of General Surgery, the Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Huimin Liu
- Department of Oncology, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China
| | - Suxia Luo
- Department of Medical Oncology, the Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
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164
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Emanuele MJ, Enrico TP, Mouery RD, Wasserman D, Nachum S, Tzur A. Complex Cartography: Regulation of E2F Transcription Factors by Cyclin F and Ubiquitin. Trends Cell Biol 2020; 30:640-652. [PMID: 32513610 PMCID: PMC7859860 DOI: 10.1016/j.tcb.2020.05.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
The E2F family of transcriptional regulators sits at the center of cell cycle gene expression and plays vital roles in normal and cancer cell cycles. Whereas control of E2Fs by the retinoblastoma family of proteins is well established, much less is known about their regulation by ubiquitin pathways. Recent studies placed the Skp1-Cul1-F-box-protein (SCF) family of E3 ubiquitin ligases with the F-box protein Cyclin F at the center of E2F regulation, demonstrating temporal proteolysis of both activator and atypical repressor E2Fs. Importantly, these E2F members, in particular activator E2F1 and repressors E2F7 and E2F8, form a feedback circuit at the crossroads of cell cycle and cell death. Moreover, Cyclin F functions in a reciprocal circuit with the cell cycle E3 ligase anaphase-promoting complex/cyclosome (APC/C), which also controls E2F7 and E2F8. This review focuses on the complex contours of feedback within this circuit, highlighting the deep crosstalk between E2F, SCF-Cyclin F, and APC/C in regulating the oscillator underlying human cell cycles.
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Affiliation(s)
- Michael J Emanuele
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Taylor P Enrico
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D Mouery
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Genetics and Molecular Biology Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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165
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Thiecke MJ, Wutz G, Muhar M, Tang W, Bevan S, Malysheva V, Stocsits R, Neumann T, Zuber J, Fraser P, Schoenfelder S, Peters JM, Spivakov M. Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers. Cell Rep 2020; 32:107929. [PMID: 32698000 PMCID: PMC7383238 DOI: 10.1016/j.celrep.2020.107929] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/01/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
It is currently assumed that 3D chromosomal organization plays a central role in transcriptional control. However, depletion of cohesin and CTCF affects the steady-state levels of only a minority of transcripts. Here, we use high-resolution Capture Hi-C to interrogate the dynamics of chromosomal contacts of all annotated human gene promoters upon degradation of cohesin and CTCF. We show that a majority of promoter-anchored contacts are lost in these conditions, but many contacts with distinct properties are maintained, and some new ones are gained. The rewiring of contacts between promoters and active enhancers upon cohesin degradation associates with rapid changes in target gene transcription as detected by SLAM sequencing (SLAM-seq). These results provide a mechanistic explanation for the limited, but consistent, effects of cohesin and CTCF depletion on steady-state transcription and suggest the existence of both cohesin-dependent and -independent mechanisms of enhancer-promoter pairing.
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Affiliation(s)
- Michiel J Thiecke
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna 1030, Austria
| | - Matthias Muhar
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna 1030, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna 1030, Austria
| | - Stephen Bevan
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Valeriya Malysheva
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK
| | - Roman Stocsits
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna 1030, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna 1030, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna 1030, Austria
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Department of Biological Science, Florida State University, Tallahassee, FL 32301, USA
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna 1030, Austria
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London W12 0NN, UK.
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166
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Abstract
Disparities in cancer patient responses have prompted widespread searches to identify differences in sensitive vs. nonsensitive populations and form the basis of personalized medicine. This customized approach is dependent upon the development of pathway-specific therapeutics in conjunction with biomarkers that predict patient responses. Here, we show that Cdk5 drives growth in subgroups of patients with multiple types of neuroendocrine neoplasms. Phosphoproteomics and high throughput screening identified phosphorylation sites downstream of Cdk5. These phosphorylation events serve as biomarkers and effectively pinpoint Cdk5-driven tumors. Toward achieving targeted therapy, we demonstrate that mouse models of neuroendocrine cancer are responsive to selective Cdk5 inhibitors and biomimetic nanoparticles are effective vehicles for enhanced tumor targeting and reduction of drug toxicity. Finally, we show that biomarkers of Cdk5-dependent tumors effectively predict response to anti-Cdk5 therapy in patient-derived xenografts. Thus, a phosphoprotein-based diagnostic assay combined with Cdk5-targeted therapy is a rational treatment approach for neuroendocrine malignancies.
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167
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Zluhan-Martínez E, Pérez-Koldenkova V, Ponce-Castañeda MV, Sánchez MDLP, García-Ponce B, Miguel-Hernández S, Álvarez-Buylla ER, Garay-Arroyo A. Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation. Int J Mol Sci 2020; 21:E4925. [PMID: 32664691 PMCID: PMC7404004 DOI: 10.3390/ijms21144925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/29/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb's functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals.
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Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
- Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán 04510, Mexico
| | - Vadim Pérez-Koldenkova
- Laboratorio Nacional de Microscopía Avanzada, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc, 330. Col. Doctores, Alc. Cuauhtémoc 06720, Mexico;
| | - Martha Verónica Ponce-Castañeda
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Sergio Miguel-Hernández
- Laboratorio de Citopatología Ambiental, Departamento de Morfología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda, Manuel Stampa 07738, Mexico;
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
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168
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Wahab S, Saettone A, Nabeel-Shah S, Dannah N, Fillingham J. Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila. Front Cell Dev Biol 2020; 8:509. [PMID: 32695779 PMCID: PMC7339932 DOI: 10.3389/fcell.2020.00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic histone acetylation cycle is composed of three classes of proteins, histone acetyltransferases (HATs) that add acetyl groups to lysine amino acids, bromodomain (BRD) containing proteins that are one of the most characterized of several protein domains that recognize acetyl-lysine (Kac) and effect downstream function, and histone deacetylases (HDACs) that catalyze the reverse reaction. Dysfunction of selected proteins of these three classes is associated with human disease such as cancer. Additionally, the HATs, BRDs, and HDACs of fungi and parasitic protozoa present potential drug targets. Despite their importance, the function and mechanisms of HATs, BRDs, and HDACs and how they relate to chromatin remodeling (CR) remain incompletely understood. Tetrahymena thermophila (Tt) provides a highly tractable single-celled free-living protozoan model for studying histone acetylation, featuring a massively acetylated somatic genome, a property that was exploited in the identification of the first nuclear/type A HAT Gcn5 in the 1990s. Since then, Tetrahymena remains an under-explored model for the molecular analysis of HATs, BRDs, and HDACs. Studies of HATs, BRDs, and HDACs in Tetrahymena have the potential to reveal the function of HATs and BRDs relevant to both fundamental eukaryotic biology and to the study of disease mechanisms in parasitic protozoa.
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Affiliation(s)
| | | | | | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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169
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Dhuppar S, Mazumder A. Investigating cell cycle-dependent gene expression in the context of nuclear architecture at single-allele resolution. J Cell Sci 2020; 133:jcs246330. [PMID: 32467328 DOI: 10.1242/jcs.246330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/10/2020] [Indexed: 12/20/2022] Open
Abstract
Nuclear architecture is the organization of the genome within a cell nucleus with respect to different nuclear landmarks such as the nuclear lamina, nuclear matrix or nucleoli. Recently, nuclear architecture has emerged as a major regulator of gene expression in mammalian cells. However, studies connecting nuclear architecture with gene expression are largely population-averaged and do not report on the heterogeneity in genome organization or gene expression within a population. In this report we present a method for combining 3D DNA fluorescence in situ hybridization (FISH) with single-molecule RNA FISH (smFISH) and immunofluorescence to study nuclear architecture-dependent gene regulation on a cell-by-cell basis. We further combine our method with imaging-based cell cycle staging to correlate nuclear architecture with gene expression across the cell cycle. We present this in the context of the cyclin-A2 (CCNA2) gene, which has known cell cycle-dependent expression. We show that, across the cell cycle, the expression of a CCNA2 gene copy is stochastic and depends neither on its sub-nuclear position - which usually lies close to nuclear lamina - nor on the expression from other copies of the gene.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Shivnarayan Dhuppar
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500046, Telangana, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500046, Telangana, India
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170
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Schade AE, Fischer M, DeCaprio JA. RB, p130 and p107 differentially repress G1/S and G2/M genes after p53 activation. Nucleic Acids Res 2020; 47:11197-11208. [PMID: 31667499 PMCID: PMC6868438 DOI: 10.1093/nar/gkz961] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/09/2019] [Accepted: 10/26/2019] [Indexed: 12/19/2022] Open
Abstract
Cell cycle gene expression occurs in two waves. The G1/S genes encode factors required for DNA synthesis and the G2/M genes contribute to mitosis. The Retinoblastoma protein (RB) and DREAM complex (DP, RB-like, E2F4 and MuvB) cooperate to repress all cell cycle genes during G1 and inhibit entry into the cell cycle. DNA damage activates p53 leading to increased levels of p21 and inhibition of cell cycle progression. Whether the G1/S and G2/M genes are differentially repressed by RB and the RB-like proteins p130 and p107 in response to DNA damage is not known. We performed gene expression profiling of primary human fibroblasts upon DNA damage and assessed the effects on G1/S and G2/M genes. Upon p53 activation, p130 and RB cooperated to repress the G1/S genes. In addition, in the absence of RB and p130, p107 contributed to repression of G1/S genes. In contrast, G2/M genes were repressed by p130 and p107 after p53 activation. Furthermore, repression of G2/M genes by p107 and p130 led to reduced entry into mitosis. Our data demonstrates specific roles for RB, p130-DREAM, and p107-DREAM in p53 and p21 mediated repression of cell cycle genes.
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Affiliation(s)
- Amy E Schade
- Program in Virology, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Boston, MA 02115, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Martin Fischer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany
| | - James A DeCaprio
- Program in Virology, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Boston, MA 02115, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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171
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Gründl M, Walz S, Hauf L, Schwab M, Werner KM, Spahr S, Schulte C, Maric HM, Ade CP, Gaubatz S. Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes. PLoS Genet 2020; 16:e1008818. [PMID: 32469866 PMCID: PMC7286521 DOI: 10.1371/journal.pgen.1008818] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/10/2020] [Accepted: 05/01/2020] [Indexed: 01/14/2023] Open
Abstract
The Hippo signalling pathway and its central effector YAP regulate proliferation of cardiomyocytes and growth of the heart. Using genetic models in mice we show that the increased proliferation of embryonal and postnatal cardiomyocytes due to loss of the Hippo-signaling component SAV1 depends on the Myb-MuvB (MMB) complex. Similarly, proliferation of postnatal cardiomyocytes induced by constitutive active YAP requires MMB. Genome studies revealed that YAP and MMB regulate an overlapping set of cell cycle genes in cardiomyocytes. Protein-protein interaction studies in cell lines and with recombinant proteins showed that YAP binds directly to B-MYB, a subunit of MMB, in a manner dependent on the YAP WW domains and a PPXY motif in B-MYB. Disruption of the interaction by overexpression of the YAP binding domain of B-MYB strongly inhibits the proliferation of cardiomyocytes. Our results point to MMB as a critical downstream effector of YAP in the control of cardiomyocyte proliferation. YAP, the major downstream transducer of the Hippo pathway, is a potent inducer of proliferation. Here we show that the Myb-MuvB complex (MMB) mediates cardiomyocyte proliferation by YAP. We find that YAP and MMB regulate an overlapping set of pro-proliferative genes which involves binding of MMB to the promoters of these genes. We also identified a direct interaction between the B-MYB subunit of MMB and YAP. Based on the binding studies, we created a tool called MY-COMP that interferes with the association YAP to B-MYB and strongly inhibits proliferation of cardiomyocytes. Together, our data suggests that the YAP-MMB interaction is essential for division of cardiomyocytes, underscoring the functional relevance of the crosstalk between these two pathways for proper heart development.
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Affiliation(s)
- Marco Gründl
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter University of Wuerzburg, Wuerzburg, Germany
| | - Susanne Walz
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Laura Hauf
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter University of Wuerzburg, Wuerzburg, Germany
| | - Melissa Schwab
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter University of Wuerzburg, Wuerzburg, Germany
| | - Kerstin Marcela Werner
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter University of Wuerzburg, Wuerzburg, Germany
| | - Susanne Spahr
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter University of Wuerzburg, Wuerzburg, Germany
| | - Clemens Schulte
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Wuerzburg, Germany
| | - Hans Michael Maric
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Wuerzburg, Germany
| | - Carsten P. Ade
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter University of Wuerzburg, Wuerzburg, Germany
| | - Stefan Gaubatz
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter University of Wuerzburg, Wuerzburg, Germany
- * E-mail:
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172
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Niu Y, Wu L, Li Y, Huang H, Qian M, Sun W, Zhu H, Xu Y, Fan Y, Mahmood U, Xu B, Zhang K, Qu C, Li J, Lu K. Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:90. [PMID: 32467731 PMCID: PMC7236191 DOI: 10.1186/s13068-020-01728-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/09/2020] [Indexed: 06/02/2023]
Abstract
BACKGROUND Brassica rapa is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed Brassica crops, Brassica napus and Brassica juncea. Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in Brassica crops remain unclear. RESULTS We collected seeds from a pair of B. rapa accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 28,954 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. K-means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of B. rapa. A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G2/M cell cycle transition, and the transcription factor Bra.A05TSO1 seemed to positively stimulate the expression of two CYCB1;2 genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of TT8 and its target genes TT3, TT18, and ANR. In the third module, WRI1 and FUS3 were conserved to increase the seed OC, and Bra.A03GRF5 was revealed as a key transcription factor on lipid biosynthesis. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in B. rapa. CONCLUSIONS This study provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants based on transcriptome comparison. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.
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Affiliation(s)
- Yue Niu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Limin Wu
- InnoTech Alberta, Hwy 16A & 75 St., PO Bag 4000, Vegreville, AB Canada
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK Canada
| | - Yanhua Li
- Institute of Characteristic Crop Research, Chongqing Academy of Agricultural Sciences, Chongqing, 402160 China
| | - Hualei Huang
- Institute of Characteristic Crop Research, Chongqing Academy of Agricultural Sciences, Chongqing, 402160 China
| | - Mingchao Qian
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Hong Zhu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Yuanfang Xu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Umer Mahmood
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
| | - Benbo Xu
- College of Life Sciences, Yangtze University, Jingzhou, 434025 Hubei China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715 China
- College of Life Sciences, Yangtze University, Jingzhou, 434025 Hubei China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
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173
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Voutsadakis IA. Clinical Implications of Chromosomal Instability (CIN) and Kinetochore Abnormalities in Breast Cancers. Mol Diagn Ther 2020; 23:707-721. [PMID: 31372940 DOI: 10.1007/s40291-019-00420-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Genetic instability is a defining property of cancer cells and is the basis of various lesions including point mutations, copy number alterations and translocations. Chromosomal instability (CIN) is part of the genetic instability of cancer and consists of copy number alterations in whole or parts of cancer cell chromosomes. CIN is observed in differing degrees in most cancers. In breast cancer, CIN is commonly part of the genomic landscape of the disease and has a higher incidence in aggressive sub-types. Tumor suppressors that are commonly mutated or disabled in cancer, such as p53 and pRB, play roles in protection against CIN, and as a result, their dysfunction contributes to the establishment or tolerance of CIN. Several structural and regulatory proteins of the centromeres and kinetochore, the complex structure that is responsible for the correct distribution of genetic material in the daughter cells during mitosis, are direct or, mostly, indirect transcription targets of p53 and pRB. Thus, despite the absence of structural defects in genes encoding for centromere and kinetochore components, dysfunction of these tumor suppressors may have profound implications for the correct function of the mitotic apparatus contributing to CIN. CIN and its prognostic and therapeutic implications in breast cancer are discussed in this article.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, 750 Great Northern Road, Sault Ste Marie, ON, P6B 0A8, Canada. .,Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON, Canada.
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174
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Vorster PJ, Goetsch P, Wijeratne TU, Guiley KZ, Andrejka L, Tripathi S, Larson BJ, Rubin SM, Strome S, Lipsick JS. A long lost key opens an ancient lock: Drosophila Myb causes a synthetic multivulval phenotype in nematodes. Biol Open 2020; 9:bio051508. [PMID: 32295830 PMCID: PMC7225089 DOI: 10.1242/bio.051508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/05/2020] [Indexed: 01/14/2023] Open
Abstract
The five-protein MuvB core complex is highly conserved in animals. This nuclear complex interacts with RB-family tumor suppressor proteins and E2F-DP transcription factors to form DREAM complexes that repress genes that regulate cell cycle progression and cell fate. The MuvB core complex also interacts with Myb family oncoproteins to form the Myb-MuvB complexes that activate many of the same genes. We show that animal-type Myb genes are present in Bilateria, Cnidaria and Placozoa, the latter including the simplest known animal species. However, bilaterian nematode worms lost their animal-type Myb genes hundreds of millions of years ago. Nevertheless, amino acids in the LIN9 and LIN52 proteins that directly interact with the MuvB-binding domains of human B-Myb and Drosophila Myb are conserved in Caenorhabditiselegans Here, we show that, despite greater than 500 million years since their last common ancestor, the Drosophila melanogaster Myb protein can bind to the nematode LIN9-LIN52 proteins in vitro and can cause a synthetic multivulval (synMuv) phenotype in vivo This phenotype is similar to that caused by loss-of-function mutations in C. elegans synMuvB-class genes including those that encode homologs of the MuvB core, RB, E2F and DP. Furthermore, amino acid substitutions in the MuvB-binding domain of Drosophila Myb that disrupt its functions in vitro and in vivo also disrupt these activities in C. elegans We speculate that nematodes and other animals may contain another protein that can bind to LIN9 and LIN52 in order to activate transcription of genes repressed by DREAM complexes.
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Affiliation(s)
- Paul J Vorster
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Paul Goetsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tilini U Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Keelan Z Guiley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Laura Andrejka
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Braden J Larson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Susan Strome
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joseph S Lipsick
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
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175
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Jiang S, Williams K, Kong X, Zeng W, Nguyen NV, Ma X, Tawil R, Yokomori K, Mortazavi A. Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei. PLoS Genet 2020; 16:e1008754. [PMID: 32365093 PMCID: PMC7224571 DOI: 10.1371/journal.pgen.1008754] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/14/2020] [Accepted: 04/03/2020] [Indexed: 12/22/2022] Open
Abstract
FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is thought to be the pathogenic cause of FSHD, DUX4 is lowly expressed in patient samples, and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we performed bulk RNA-seq on a 6-day differentiation time-course in primary FSHD2 patient myoblasts. We identify a set of 54 genes upregulated in FSHD2 cells, termed FSHD-induced genes. Using single-cell and single-nucleus RNA-seq on myoblasts and differentiated myotubes, respectively, we captured, for the first time, DUX4 expressed at the single-nucleus level in a native state. We identified two populations of FSHD myotube nuclei based on low or high enrichment of DUX4 and FSHD-induced genes ("FSHD-Lo" and "FSHD Hi", respectively). FSHD-Hi myotube nuclei coexpress multiple DUX4 target genes including DUXA, LEUTX and ZSCAN4, and also upregulate cell cycle-related genes with significant enrichment of E2F target genes and p53 signaling activation. We found more FSHD-Hi nuclei than DUX4-positive nuclei, and confirmed with in situ RNA/protein detection that DUX4 transcribed in only one or two nuclei is sufficient for DUX4 protein to activate target genes across multiple nuclei within the same myotube. DUXA (the DUX4 paralog) is more widely expressed than DUX4, and depletion of DUXA suppressed the expression of LEUTX and ZSCAN4 in late, but not early, differentiation. The results suggest that the DUXA can take over the role of DUX4 to maintain target gene expression. These results provide a possible explanation as to why it is easier to detect DUX4 target genes than DUX4 itself in patient cells and raise the possibility of a self-sustaining network of gene dysregulation triggered by the limited DUX4 expression.
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Affiliation(s)
- Shan Jiang
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Katherine Williams
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Weihua Zeng
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Nam Viet Nguyen
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Xinyi Ma
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KY); (AM)
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KY); (AM)
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176
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Lu D, Sin HS, Lu C, Fuller MT. Developmental regulation of cell type-specific transcription by novel promoter-proximal sequence elements. Genes Dev 2020; 34:663-677. [PMID: 32217666 PMCID: PMC7197356 DOI: 10.1101/gad.335331.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
Cell type-specific transcriptional programs that drive differentiation of specialized cell types are key players in development and tissue regeneration. One of the most dramatic changes in the transcription program in Drosophila occurs with the transition from proliferating spermatogonia to differentiating spermatocytes, with >3000 genes either newly expressed or expressed from new alternative promoters in spermatocytes. Here we show that opening of these promoters from their closed state in precursor cells requires function of the spermatocyte-specific tMAC complex, localized at the promoters. The spermatocyte-specific promoters lack the previously identified canonical core promoter elements except for the Inr. Instead, these promoters are enriched for the binding site for the TALE-class homeodomain transcription factors Achi/Vis and for a motif originally identified under tMAC ChIP-seq peaks. The tMAC motif resembles part of the previously identified 14-bp β2UE1 element critical for spermatocyte-specific expression. Analysis of downstream sequences relative to transcription start site usage suggested that ACA and CNAAATT motifs at specific positions can help promote efficient transcription initiation. Our results reveal how promoter-proximal sequence elements that recruit and are acted upon by cell type-specific chromatin binding complexes help establish a robust, cell type-specific transcription program for terminal differentiation.
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Affiliation(s)
- Dan Lu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ho-Su Sin
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Chenggang Lu
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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177
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Morita K, He S, Nowak RP, Wang J, Zimmerman MW, Fu C, Durbin AD, Martel MW, Prutsch N, Gray NS, Fischer ES, Look AT. Retracted: Allosteric Activators of Protein Phosphatase 2A Display Broad Antitumor Activity Mediated by Dephosphorylation of MYBL2. Cell 2020; 181:702-715.e20. [PMID: 32315619 PMCID: PMC7397863 DOI: 10.1016/j.cell.2020.03.051] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/02/2020] [Accepted: 03/20/2020] [Indexed: 11/21/2022]
Abstract
Protein phosphatase 2A (PP2A) enzymes can suppress tumors, but they are often inactivated in human cancers overexpressing inhibitory proteins. Here, we identify a class of small-molecule iHAPs (improved heterocyclic activators of PP2A) that kill leukemia cells by allosterically assembling a specific heterotrimeric PP2A holoenzyme consisting of PPP2R1A (scaffold), PPP2R5E (B56ε, regulatory), and PPP2CA (catalytic) subunits. One compound, iHAP1, activates this complex but does not inhibit dopamine receptor D2, a mediator of neurologic toxicity induced by perphenazine and related neuroleptics. The PP2A complex activated by iHAP1 dephosphorylates the MYBL2 transcription factor on Ser241, causing irreversible arrest of leukemia and other cancer cells in prometaphase. In contrast, SMAPs, a separate class of compounds, activate PP2A holoenzymes containing a different regulatory subunit, do not dephosphorylate MYBL2, and arrest tumor cells in G1 phase. Our findings demonstrate that small molecules can serve as allosteric switches to activate distinct PP2A complexes with unique substrates.
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Affiliation(s)
- Ken Morita
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Cong Fu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Adam D Durbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Megan W Martel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Nicole Prutsch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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178
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Leech CM, Flynn MJ, Arsenault HE, Ou J, Liu H, Zhu LJ, Benanti JA. The coordinate actions of calcineurin and Hog1 mediate the stress response through multiple nodes of the cell cycle network. PLoS Genet 2020; 16:e1008600. [PMID: 32343701 PMCID: PMC7209309 DOI: 10.1371/journal.pgen.1008600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/08/2020] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
Upon exposure to environmental stressors, cells transiently arrest the cell cycle while they adapt and restore homeostasis. A challenge for all cells is to distinguish between stress signals and coordinate the appropriate adaptive response with cell cycle arrest. Here we investigate the role of the phosphatase calcineurin (CN) in the stress response and demonstrate that CN activates the Hog1/p38 pathway in both yeast and human cells. In yeast, the MAPK Hog1 is transiently activated in response to several well-studied osmostressors. We show that when a stressor simultaneously activates CN and Hog1, CN disrupts Hog1-stimulated negative feedback to prolong Hog1 activation and the period of cell cycle arrest. Regulation of Hog1 by CN also contributes to inactivation of multiple cell cycle-regulatory transcription factors (TFs) and the decreased expression of cell cycle-regulated genes. CN-dependent downregulation of G1/S genes is dependent upon Hog1 activation, whereas CN inactivates G2/M TFs through a combination of Hog1-dependent and -independent mechanisms. These findings demonstrate that CN and Hog1 act in a coordinated manner to inhibit multiple nodes of the cell cycle-regulatory network. Our results suggest that crosstalk between CN and stress-activated MAPKs helps cells tailor their adaptive responses to specific stressors. In order to survive exposure to environmental stress, cells transiently arrest the cell division cycle while they adapt to the stress. Several kinases and phosphatases are known to control stress adaptation programs, but the extent to which these signaling pathways work together to tune the stress response is not well understood. This study investigates the role of the phosphatase calcineurin in the stress response and shows that calcineurin inhibits the cell cycle in part by stimulating the activity of the Hog1/p-38 stress-activated MAPK in both yeast and human cells. Crosstalk between stress response pathways may help cells mount specific responses to diverse stressors and to survive changes in their environment.
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Affiliation(s)
- Cassandra M. Leech
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Mackenzie J. Flynn
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Heather E. Arsenault
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jianhong Ou
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Haibo Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Bioinformatics and Integrative Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jennifer A. Benanti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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179
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Knudsen ES, Nambiar R, Rosario SR, Smiraglia DJ, Goodrich DW, Witkiewicz AK. Pan-cancer molecular analysis of the RB tumor suppressor pathway. Commun Biol 2020; 3:158. [PMID: 32242058 PMCID: PMC7118159 DOI: 10.1038/s42003-020-0873-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/26/2020] [Indexed: 12/21/2022] Open
Abstract
The retinoblastoma tumor suppressor gene (RB1) plays a critical role in coordinating multiple pathways that impact cancer initiation, disease progression, and therapeutic responses. Here we probed molecular features associated with the RB-pathway across 31 tumor-types. While the RB-pathway has been purported to exhibit multiple mutually exclusive genetic events, only RB1 alteration is mutually exclusive with deregulation of CDK4/6 activity. An ER+ breast cancer model with targeted RB1 deletion was used to identify signatures of CDK4/6 activity and RB-dependency (CDK4/6-RB integrated signature). This signature was prognostic in tumor-types with gene expression features indicative of slower growth. Single copy loss on chromosome 13q encompassing the RB1 locus is prevalent in many cancers, yielding reduced expression of multiple genes in cis, and is inversely related to the CDK4/6-RB integrated signature supporting a cause-effect relationship. Genes that are positively and inversely correlated with the CDK4/6-RB integrated signature define new tumor-specific pathways associated with RB-pathway activity.
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Affiliation(s)
- Erik S Knudsen
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA. .,Department of Molecular and Cellular Biology, Buffalo, USA. .,Center for Personalized Medicine, Buffalo, USA.
| | - Ram Nambiar
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Molecular and Cellular Biology, Buffalo, USA
| | - Spencer R Rosario
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Genetics and Genomics, Buffalo, USA
| | - Dominic J Smiraglia
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Genetics and Genomics, Buffalo, USA
| | - David W Goodrich
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.,Department of Pharmacology and Therapeutics, Buffalo, USA
| | - Agnieszka K Witkiewicz
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA. .,Center for Personalized Medicine, Buffalo, USA. .,Department of Pathology, Buffalo, USA.
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180
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Takeuchi T, Sears BB, Lindeboom C, Lin YT, Fekaris N, Zienkiewicz K, Zienkiewicz A, Poliner E, Benning C. Chlamydomonas CHT7 Is Required for an Effective Quiescent State by Regulating Nutrient-Responsive Cell Cycle Gene Expression. THE PLANT CELL 2020; 32:1240-1269. [PMID: 32001503 PMCID: PMC7145468 DOI: 10.1105/tpc.19.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
COMPROMISED HYDROLYSIS OF TRIACYLGLYCEROLS7 (CHT7) in Chlamydomonas (Chlamydomonas reinhardtii) was previously shown to affect the transcription of a subset of genes during nitrogen (N)-replete growth and following N refeeding. Here, we show that an extensive derepression of genes involved in DNA metabolism and cell cycle-related processes, as well as downregulation of genes encoding oxidoreductases and nutrient transporters, occurs in the cht7 mutant during N deprivation. Cellular mutant phenotypes are consistent with the observed transcriptome misregulation, as cht7 cells fail to properly arrest growth, nuclear replication, and cell division following N deprivation. Reduction in cht7 colony formation following N refeeding is explained by its compromised viability during N deprivation and by the occurrence of abortive divisions during N refeeding. Surprisingly, the largely unstructured C-terminal half of CHT7 with predicted protein binding domains, but not the canonical CXC DNA binding domain, is essential for the ability of CHT7 to form stable complexes and reverse the cellular phenotypes and transcription levels in the cht7 mutant. Hence, although lacking the presumed DNA binding domain, CHT7 modulates the expression of cell cycle genes in response to N availability, which is essential for establishing an effective quiescent state and the coordinated resumption of growth following N refeeding.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Barbara B Sears
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Chase Lindeboom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Yang-Tsung Lin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Nicholas Fekaris
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Krzysztof Zienkiewicz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
| | - Agnieszka Zienkiewicz
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | - Eric Poliner
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
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181
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Belizário J, Destro Rodrigues MF. Checkpoint inhibitor blockade and epigenetic reprogrammability in CD8 + T-cell activation and exhaustion. Ther Adv Vaccines Immunother 2020; 8:2515135520904238. [PMID: 32206744 PMCID: PMC7074507 DOI: 10.1177/2515135520904238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/19/2019] [Indexed: 11/17/2022] Open
Abstract
CD8+ T-cell exhaustion is a dysfunctional state that is regulated through the expression of inhibitory checkpoint receptor genes including the cytotoxic T-lymphocyte–associated antigen 4, programmed death 1, and DNA methylation of effector genes interferon-γ, perforin, and granzyme B. Different strategies have been used to reverse T-cell exhaustion, which is an adverse event of checkpoint inhibitor blockade. Here, we present the mechanisms by which DNA methyltransferase inhibitors and Simian virus 40 large T antigen through viral mimicry can promote the reversion of exhausted CD8+ T cells. We examine how these pharmacological strategies can work together to improve the clinical efficacy of immunotherapies.
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Affiliation(s)
- José Belizário
- Department of Pharmacology, Institute Biomedical Sciences of the University of Sao Paulo, Avenida Lineu Prestes, 1524, São Paulo, CEP 05508-900, Brazil
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182
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Wong CO, Venkatachalam K. Motor neurons from ALS patients with mutations in C9ORF72 and SOD1 exhibit distinct transcriptional landscapes. Hum Mol Genet 2020; 28:2799-2810. [PMID: 31107959 DOI: 10.1093/hmg/ddz104] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease that culminates in paralysis and death. Here, we present our analyses of publicly available multiOMIC data sets generated using motor neurons from ALS patients and control cohorts. Functional annotation of differentially expressed genes in induced pluripotent stem cell (iPSC)-derived motor neurons generated from patients with mutations in C9ORF72 (C9-ALS) suggests elevated expression of genes that pertain to extracellular matrix (ECM) and cell adhesion, inflammation and TGFβ targets. On the other end of the continuum, we detected diminished expression of genes repressed by quiescence-promoting E2F4/DREAM complex. Proteins whose abundance was significantly altered in C9-ALS neurons faithfully recapitulated the transcriptional aberrations. Importantly, patterns of gene expression in spinal motor neurons dissected from C9-ALS or sporadic ALS patients were highly concordant with each other and with the C9-ALS iPSC neurons. In contrast, motor neurons from patients with mutations in SOD1 exhibited dramatically different signatures. Elevated expression of gene sets such as ECM and cell adhesion genes occurs in C9 and sporadic ALS but not SOD1-ALS. These analyses indicate that despite the similarities in outward manifestations, transcriptional and proteomic signatures in ALS motor neurons can vary significantly depending on the identity of the causal mutations.
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Affiliation(s)
- Ching-On Wong
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX 77030, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Kartik Venkatachalam
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX 77030, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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183
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PDCD4 controls the G1/S-phase transition in a telomerase-immortalized epithelial cell line and affects the expression level and translation of multiple mRNAs. Sci Rep 2020; 10:2758. [PMID: 32066800 PMCID: PMC7026441 DOI: 10.1038/s41598-020-59678-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/27/2019] [Indexed: 12/11/2022] Open
Abstract
PDCD4, the protein encoded by the tumor suppressor gene PDCD4 (programmed cell death 4) has been implicated in the control of cellular transcription and translation by modulating the activity of specific transcription factors and suppressing the translation of mRNAs with structured 5′-UTRs. Most studies of human PDCD4 have employed tumor cell lines, possibly resulting in a biased picture of its role in normal cells. Here, we have studied the function of PDCD4 in a telomerase-immortalized human epithelial cell line. We show for the first time that PDCD4 is required for the G1/S-transition, demonstrating its crucial role in the cell cycle. Inhibition of p53-dependent activation of p21WAF1/CIP1 overrides the requirement for PDCD4 for the G1/S-transition, suggesting that PDCD4 counteracts basal p53 activity to prevent activation of the G1/S checkpoint by p53. Transcriptome and ribosome profiling data show that silencing of PDCD4 changes the expression levels and translation of many mRNAs, providing an unbiased view of the cellular processes that are affected by PDCD4 in an epithelial cell line. Our data identify PDCD4 as a key regulator of cell cycle- and DNA-related functions that are inhibited when it is silenced, suggesting that decreased expression of PDCD4 might contribute to tumor development by compromising genomic integrity.
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184
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Cherian JR, Adams KV, Petrella LN. Wnt Signaling Drives Ectopic Gene Expression and Larval Arrest in the Absence of the Caenorhabditis elegans DREAM Repressor Complex. G3 (BETHESDA, MD.) 2020; 10:863-874. [PMID: 31843805 PMCID: PMC7003081 DOI: 10.1534/g3.119.400850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/08/2019] [Indexed: 11/18/2022]
Abstract
Establishment and maintenance of proper gene expression is a requirement for normal growth and development. The DREAM complex in Caenorhabditis elegans functions as a transcriptional repressor of germline genes in somatic cells. At 26°, DREAM complex mutants show increased misexpression of germline genes in somatic cells and High Temperature Arrest (HTA) of worms at the first larval stage. To identify transcription factors required for the ectopic expression of germline genes in DREAM complex mutants, we conducted an RNA interference screen against 123 transcription factors capable of binding DREAM target promoter loci for suppression of the HTA phenotype in lin-54 mutants. We found that knock-down of 15 embryonically expressed transcription factors suppress the HTA phenotype in lin-54 mutants. Five of the transcription factors found in the initial screen have associations with Wnt signaling pathways. In a subsequent RNAi suppression screen of Wnt signaling factors we found that knock-down of the non-canonical Wnt/PCP pathway factors vang-1, prkl-1 and fmi-1 in a lin-54 mutant background resulted in strong suppression of the HTA phenotype. Animals mutant for both lin-54 and vang-1 showed almost complete suppression of the HTA phenotype, pgl-1 misexpression, and fertility defects associated with lin-54 single mutants at 26°. We propose a model whereby a set of embryonically expressed transcription factors, and the Wnt/PCP pathway, act opportunistically to activate DREAM complex target genes in somatic cells of DREAM complex mutants at 26°.
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Affiliation(s)
- Jerrin R Cherian
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Katherine V Adams
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
| | - Lisa N Petrella
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233
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185
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Higurashi M, Maruyama T, Nogami Y, Ishikawa F, Yoshida Y, Mori K, Fujita KI, Shibanuma M. High expression of FOXM1 critical for sustaining cell proliferation in mitochondrial DNA-less liver cancer cells. Exp Cell Res 2020; 389:111889. [PMID: 32032602 DOI: 10.1016/j.yexcr.2020.111889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/06/2020] [Accepted: 02/03/2020] [Indexed: 12/16/2022]
Abstract
The copy number of mitochondrial DNA (mtDNA) is decreased in most cancer types, including hepatocellular carcinoma (HCC), compared to normal counterparts. However, a decrease in mtDNA usually leads to defects in cell proliferation, which contradicts the robustness of cancer cell proliferation. In this study, we found that four out of seven HCC cell lines were of the mtDNA-less type. Interestingly, FOXM1, a member of the FOX transcription factor family, was highly expressed in a subset of them with proliferative potential maintained. B-MYB, a partner of FOXM1, was also expressed in the same cell lines. RNAi-mediated experiments demonstrated that when FOXM1/B-MYB was silenced in the cell lines, cell cycle-related genes were downregulated, while p21Cip1 was induced with senescence-associated β-galactosidase, resulting in G1/S cell cycle arrest. These results suggest that high expression of FOXM1/B-MYB is critical for sustaining cell proliferation in mtDNA-less cells. In addition, we found that high expression of FOXM1 was mediated by the deubiquitinating enzyme, OTUB1, in one cell line. Thus, interference with FOXM1/B-MYB expression, such as through OTUB1 inhibition, may induce a dormant state of senescence-like proliferation arrest in mtDNA-less cancer cells. This finding may be utilized for the development of precision medicine for relevant cancers.
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Affiliation(s)
- Masato Higurashi
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Tsuyoshi Maruyama
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Yusuke Nogami
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Fumihiro Ishikawa
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Yukiko Yoshida
- Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Kazunori Mori
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Ken-Ichi Fujita
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Motoko Shibanuma
- Division of Cancer Cell Biology, Department of Pharmaceutical Sciences, Showa University School of Pharmacy, Tokyo, 142-8555, Japan.
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186
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Pal A, Kundu R. Human Papillomavirus E6 and E7: The Cervical Cancer Hallmarks and Targets for Therapy. Front Microbiol 2020; 10:3116. [PMID: 32038557 PMCID: PMC6985034 DOI: 10.3389/fmicb.2019.03116] [Citation(s) in RCA: 252] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/24/2019] [Indexed: 01/14/2023] Open
Abstract
Human papillomavirus (HPV)-induced cervical cancer is a major health issue among women from the poorly/under-developed sectors of the world. It accounts for a high-mortality rate because of its late diagnosis and poor prognosis. Initial establishment and subsequent progression of this form of cancer are completely dependent on two major oncogenes E6 and E7, which are expressed constitutively leading to tumorigenesis. Thus, manipulation of these genes represents the most successful form of cervical cancer therapy. In the present article, information on structural, functional, and clinical dimensions of E6 and E7 activity has been reviewed. The genome organization and protein structure of E6 and E7 have been discussed followed by their mechanism to establish the six major cancer hallmarks in cervical tissues for tumor propagation. The later section of this review article deals with the different modes of therapeutics, which functions by deregulating E6 and E7 activity. Since E6 and E7 are the biomarkers of a cervical cancer cell and are the ones driving the cancer progression, therapeutic approaches targeting E6 and E7 have been proved to be highly efficient in terms of focused removal of abnormally propagating malignant cells. Therapeutics including different forms of vaccines to advanced genome editing techniques, which suppress E6 and E7 activity, have been found to successfully bring down the population of cervical cancer cells infected with HPV. T-cell mediated immunotherapy is another upcoming successful form of treatment to eradicate HPV-infected tumorigenic cells. Additionally, therapeutics using natural compounds from plants or other natural repositories, i.e., phytotherapeutic approaches have also been reviewed here, which prove their anticancer potential through E6 and E7 inhibitory effects. Thus, E6 and E7 repression through any of these methods is a significant approach toward cervical cancer therapy, described in details in this review along with an insight into the signaling pathways and molecular mechanistic of E6 and E7 action.
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Affiliation(s)
| | - Rita Kundu
- Cell Biology Laboratory, Department of Botany, Centre of Advanced Studies, University of Calcutta, Kolkata, India
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187
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Ackeifi C, Swartz E, Kumar K, Liu H, Chalada S, Karakose E, Scott DK, Garcia-Ocaña A, Sanchez R, DeVita RJ, Stewart AF, Wang P. Pharmacologic and genetic approaches define human pancreatic β cell mitogenic targets of DYRK1A inhibitors. JCI Insight 2020; 5:132594. [PMID: 31821176 PMCID: PMC7030849 DOI: 10.1172/jci.insight.132594] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/04/2019] [Indexed: 01/09/2023] Open
Abstract
Small molecule inhibitors of dual specificity, tyrosine phosphorylation-regulated kinase 1A (DYRK1A), including harmine and others, are able to drive human β cell regeneration. While DYRK1A is certainly a target of this class, whether it is the only or the most important target is uncertain. Here, we employ a combined pharmacologic and genetic approach to refine the potential mitogenic targets of the DYRK1A inhibitor family in human islets. A combination of human β cell RNA sequencing, DYRK1A inhibitor kinome screens, pharmacologic inhibitors, and targeted silencing of candidate genes confirms that DYRK1A is a central target. Surprisingly, however, DYRK1B also proves to be an important target: silencing DYRK1A results in an increase in DYRK1B. Simultaneous silencing of both DYRK1A and DYRK1B yields greater β cell proliferation than silencing either individually. Importantly, other potential kinases, such as the CLK and the GSK3 families, are excluded as important harmine targets. Finally, we describe adenoviruses that are able to silence up to 7 targets simultaneously. Collectively, we report that inhibition of both DYRK1A and DYRK1B is required for induction of maximal rates of human β cell proliferation, and we provide clarity for future efforts in structure-based drug design for human β cell regenerative drugs.
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Affiliation(s)
| | | | - Kunal Kumar
- Drug Discovery Institute, and
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Suebsuwong Chalada
- Drug Discovery Institute, and
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Roberto Sanchez
- Drug Discovery Institute, and
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert J. DeVita
- Drug Discovery Institute, and
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Peng Wang
- Diabetes Obesity Metabolism Institute
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188
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Kosti A, Du L, Shivram H, Qiao M, Burns S, Garcia JG, Pertsemlidis A, Iyer VR, Kokovay E, Penalva LOF. ELF4 Is a Target of miR-124 and Promotes Neuroblastoma Proliferation and Undifferentiated State. Mol Cancer Res 2020; 18:68-78. [PMID: 31624087 PMCID: PMC6942226 DOI: 10.1158/1541-7786.mcr-19-0187] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/06/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022]
Abstract
13-Cis-retinoic acid (RA) is typically used in postremission maintenance therapy in patients with neuroblastoma. However, side effects and recurrence are often observed. We investigated the use of miRNAs as a strategy to replace RA as promoters of differentiation. miR-124 was identified as the top candidate in a functional screen. Genomic target analysis indicated that repression of a network of transcription factors (TF) could be mediating most of miR-124's effect in driving differentiation. To advance miR-124 mimic use in therapy and better define its mechanism of action, a high-throughput siRNA morphologic screen focusing on its TF targets was conducted and ELF4 was identified as a leading candidate for miR-124 repression. By altering its expression levels, we showed that ELF4 maintains neuroblastoma in an undifferentiated state and promotes proliferation. Moreover, ELF4 transgenic expression was able to counteract the neurogenic effect of miR-124 in neuroblastoma cells. With RNA sequencing, we established the main role of ELF4 to be regulation of cell-cycle progression, specifically through the DREAM complex. Interestingly, several cell-cycle genes activated by ELF4 are repressed by miR-124, suggesting that they might form a TF-miRNA regulatory loop. Finally, we showed that high ELF4 expression is often observed in neuroblastomas and is associated with poor survival. IMPLICATIONS: miR-124 induces neuroblastoma differentiation partially through the downregulation of TF ELF4, which drives neuroblastoma proliferation and its undifferentiated phenotype.
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Affiliation(s)
- Adam Kosti
- Department of Cell Systems and Anatomy, UT Health Science Center at San Antonio, San Antonio, Texas
- Greehey Children's Cancer Research Institute, UT Health Science Center at San Antonio, San Antonio, Texas
| | - Liqin Du
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Haridha Shivram
- Department of Molecular Biosciences and Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Mei Qiao
- Greehey Children's Cancer Research Institute, UT Health Science Center at San Antonio, San Antonio, Texas
| | - Suzanne Burns
- Greehey Children's Cancer Research Institute, UT Health Science Center at San Antonio, San Antonio, Texas
| | - Juan Gabriel Garcia
- Department of Cell Systems and Anatomy, UT Health Science Center at San Antonio, San Antonio, Texas
| | - Alexander Pertsemlidis
- Department of Cell Systems and Anatomy, UT Health Science Center at San Antonio, San Antonio, Texas
- Greehey Children's Cancer Research Institute, UT Health Science Center at San Antonio, San Antonio, Texas
- Department of Pediatrics, UT Health Science Center at San Antonio, San Antonio, Texas
| | - Vishwanath R Iyer
- Department of Molecular Biosciences and Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Erzsebet Kokovay
- Department of Cell Systems and Anatomy, UT Health Science Center at San Antonio, San Antonio, Texas
| | - Luiz O F Penalva
- Department of Cell Systems and Anatomy, UT Health Science Center at San Antonio, San Antonio, Texas.
- Greehey Children's Cancer Research Institute, UT Health Science Center at San Antonio, San Antonio, Texas
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189
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Allegretti PA, Horton TM, Abdolazimi Y, Moeller HP, Yeh B, Caffet M, Michel G, Smith M, Annes JP. Generation of highly potent DYRK1A-dependent inducers of human β-Cell replication via Multi-Dimensional compound optimization. Bioorg Med Chem 2020; 28:115193. [PMID: 31757680 PMCID: PMC6941846 DOI: 10.1016/j.bmc.2019.115193] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/20/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
Small molecule stimulation of β-cell regeneration has emerged as a promising therapeutic strategy for diabetes. Although chemical inhibition of dual specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) is sufficient to enhance β-cell replication, current lead compounds have inadequate cellular potency for in vivo application. Herein, we report the clinical stage anti-cancer kinase inhibitor OTS167 as a structurally novel, remarkably potent DYRK1A inhibitor and inducer of human β-cell replication. Unfortunately, OTS167's target promiscuity and cytotoxicity curtails utility. To tailor kinase selectivity towards DYRK1A and reduce cytotoxicity we designed a library of fifty-one OTS167 derivatives based upon a modeled structure of the DYRK1A-OTS167 complex. Indeed, derivative characterization yielded several leads with exceptional DYRK1A inhibition and human β-cell replication promoting potencies but substantially reduced cytotoxicity. These compounds are the most potent human β-cell replication-promoting compounds yet described and exemplify the potential to purposefully leverage off-target activities of advanced stage compounds for a desired application.
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Affiliation(s)
- Paul A Allegretti
- Department of Medicine and Division of Endocrinology, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Timothy M Horton
- Department of Medicine and Division of Endocrinology, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Yassan Abdolazimi
- Department of Medicine and Division of Endocrinology, Stanford University, Stanford, CA 94305, USA
| | - Hannah P Moeller
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Medicine and Division of Endocrinology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin Yeh
- Department of Medicine and Division of Endocrinology, Stanford University, Stanford, CA 94305, USA
| | - Matthew Caffet
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Guillermina Michel
- Department of Medicine and Division of Endocrinology, Stanford University, Stanford, CA 94305, USA
| | - Mark Smith
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Justin P Annes
- Department of Medicine and Division of Endocrinology, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA.
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190
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Őszi E, Papdi C, Mohammed B, Petkó-Szandtner A, Leviczky T, Molnár E, Galvan-Ampudia C, Khan S, Juez EL, Horváth B, Bögre L, Magyar Z. E2FB Interacts with RETINOBLASTOMA RELATED and Regulates Cell Proliferation during Leaf Development. PLANT PHYSIOLOGY 2020; 182:518-533. [PMID: 31694902 PMCID: PMC6945829 DOI: 10.1104/pp.19.00212] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 10/24/2019] [Indexed: 05/31/2023]
Abstract
Cell cycle entry and quiescence are regulated by the E2F transcription factors in association with RETINOBLASTOMA-RELATED (RBR). E2FB is considered to be a transcriptional activator of cell cycle genes, but its function during development remains poorly understood. Here, by studying E2FB-RBR interaction, E2F target gene expression, and epidermal cell number and shape in e2fb mutant and overexpression lines during leaf development in Arabidopsis (Arabidopsis thaliana), we show that E2FB in association with RBR plays a role in the inhibition of cell proliferation to establish quiescence. In young leaves, both RBR and E2FB are abundant and form a repressor complex that is reinforced by an autoregulatory loop. Increased E2FB levels, either by expression driven by its own promoter or ectopically together with DIMERIZATION PARTNER A, further elevate the amount of this repressor complex, leading to reduced leaf cell number. Cell overproliferation in e2fb mutants and in plants overexpressing a truncated form of E2FB lacking the RBR binding domain strongly suggested that RBR repression specifically acts through E2FB. The increased number of small cells below the guard cells and of fully developed stomata indicated that meristemoids preferentially hyperproliferate. As leaf development progresses and cells differentiate, the amount of RBR and E2FB gradually declined. At this stage, elevation of E2FB level can overcome RBR repression, leading to reactivation of cell division in pavement cells. In summary, E2FB in association with RBR is central to regulating cell proliferation during organ development to determine final leaf cell number.
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Affiliation(s)
- Erika Őszi
- Institute of Plant Biology, Biological Research Centre, Szeged, 6726, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary
| | - Csaba Papdi
- Royal Holloway University of London, School of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, TW20 0EX, United Kingdom
| | - Binish Mohammed
- Royal Holloway University of London, School of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, TW20 0EX, United Kingdom
| | - Aladár Petkó-Szandtner
- Institute of Plant Biology, Biological Research Centre, Szeged, 6726, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, 6726, Hungary
| | - Tünde Leviczky
- Institute of Plant Biology, Biological Research Centre, Szeged, 6726, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary
| | - Eszter Molnár
- Institute of Plant Biology, Biological Research Centre, Szeged, 6726, Hungary
| | - Carlos Galvan-Ampudia
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, F-69364 Lyon, France
| | - Safina Khan
- Royal Holloway University of London, School of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, TW20 0EX, United Kingdom
| | - Enrique Lopez Juez
- Royal Holloway University of London, School of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, TW20 0EX, United Kingdom
| | - Beatrix Horváth
- Royal Holloway University of London, School of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, TW20 0EX, United Kingdom
| | - László Bögre
- Royal Holloway University of London, School of Biological Sciences, Centre for Systems and Synthetic Biology, Egham, TW20 0EX, United Kingdom
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, 6726, Hungary
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191
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Uxa S, Bernhart SH, Mages CFS, Fischer M, Kohler R, Hoffmann S, Stadler PF, Engeland K, Müller GA. DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation. Nucleic Acids Res 2019; 47:9087-9103. [PMID: 31400114 PMCID: PMC6753476 DOI: 10.1093/nar/gkz635] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/07/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
Most human cancers acquire mutations causing defects in the p53 signaling pathway. The tumor suppressor p53 becomes activated in response to genotoxic stress and is essential for arresting the cell cycle to facilitate DNA repair or to initiate apoptosis. p53-induced cell cycle-arrest is mediated by expression of the CDK inhibitor p21WAF1/Cip1, which prevents phosphorylation and inactivation of the pocket proteins RB, p130, and p107. In a hypophosphorylated state, pocket proteins bind to E2F factors forming RB-E2F and DREAM transcriptional repressor complexes. Here, we analyze the influence of RB and DREAM on p53-induced gene repression and cell-cycle arrest. We show that abrogation of DREAM function by knockout of the DREAM component LIN37 results in a reduced repression of cell-cycle genes. We identify the genes repressed by the p53-DREAM pathway and describe a set of genes that is downregulated by p53 independent of LIN37/DREAM. Most strikingly, p53-dependent repression of cell-cycle genes is completely abrogated in LIN37-/-;RB-/- cells leading to a loss of the G1/S checkpoint. Taken together, we show that DREAM and RB are key factors in the p53 signaling pathway to downregulate a large number of cell-cycle genes and to arrest the cell cycle at the G1/S transition.
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Affiliation(s)
- Sigrid Uxa
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany
| | - Christina F S Mages
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Robin Kohler
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Peter F Stadler
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Research Center for Civilization Diseases; and Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Leipzig University, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, A-1090 Wien, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogota, Colombia.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Kurt Engeland
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany
| | - Gerd A Müller
- Molecular Oncology, Department of Gynaecology, Medical School, Leipzig University, 04103 Leipzig, Germany.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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192
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Clark NM, Buckner E, Fisher AP, Nelson EC, Nguyen TT, Simmons AR, de Luis Balaguer MA, Butler-Smith T, Sheldon PJ, Bergmann DC, Williams CM, Sozzani R. Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks. Nat Commun 2019. [PMID: 31811116 DOI: 10.1101/517250v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood. Here, we find that, in the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks. Development of a mathematical model of TCX2 expression allows us to show that TCX2 orchestrates the coordinated division of different stem cell types. Our results highlight that genes expressed across different stem cell types ensure cross-communication among cells, allowing them to divide and develop harmonically together.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
- Biomathematics Graduate Program, North Carolina State University, Raleigh, NC, 27695, United States
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, United States
| | - Eli Buckner
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, 27695, United States
| | - Adam P Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Emily C Nelson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Thomas T Nguyen
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Abigail R Simmons
- Department of Biology, Stanford University, Stanford, CA, 94305, United States
| | - Maria A de Luis Balaguer
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Tiara Butler-Smith
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Parnell J Sheldon
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
- Department of Biology, Denison University, Granville, OH, 43023, United States
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA, 94305, United States
- Howard Hughes Medical Institute (HHMI), Stanford University, Stanford, CA, 94305, United States
| | - Cranos M Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, 27695, United States
| | - Rossangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States.
- Biomathematics Graduate Program, North Carolina State University, Raleigh, NC, 27695, United States.
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193
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Clark NM, Buckner E, Fisher AP, Nelson EC, Nguyen TT, Simmons AR, de Luis Balaguer MA, Butler-Smith T, Sheldon PJ, Bergmann DC, Williams CM, Sozzani R. Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks. Nat Commun 2019; 10:5574. [PMID: 31811116 PMCID: PMC6897965 DOI: 10.1038/s41467-019-13132-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 10/19/2019] [Indexed: 12/21/2022] Open
Abstract
Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood. Here, we find that, in the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks. Development of a mathematical model of TCX2 expression allows us to show that TCX2 orchestrates the coordinated division of different stem cell types. Our results highlight that genes expressed across different stem cell types ensure cross-communication among cells, allowing them to divide and develop harmonically together.
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Affiliation(s)
- Natalie M. Clark
- 0000 0001 2173 6074grid.40803.3fDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 United States ,0000 0001 2173 6074grid.40803.3fBiomathematics Graduate Program, North Carolina State University, Raleigh, NC 27695 United States ,0000 0004 1936 7312grid.34421.30Present Address: Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 United States
| | - Eli Buckner
- 0000 0001 2173 6074grid.40803.3fDepartment of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695 United States
| | - Adam P. Fisher
- 0000 0001 2173 6074grid.40803.3fDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 United States
| | - Emily C. Nelson
- 0000 0001 2173 6074grid.40803.3fDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 United States
| | - Thomas T. Nguyen
- 0000 0001 2173 6074grid.40803.3fDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 United States
| | - Abigail R. Simmons
- 0000000419368956grid.168010.eDepartment of Biology, Stanford University, Stanford, CA 94305 United States
| | - Maria A. de Luis Balaguer
- 0000 0001 2173 6074grid.40803.3fDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 United States
| | - Tiara Butler-Smith
- 0000 0001 2173 6074grid.40803.3fDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 United States
| | - Parnell J. Sheldon
- 0000 0001 2173 6074grid.40803.3fDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 United States ,0000 0001 2185 2366grid.255014.7Department of Biology, Denison University, Granville, OH 43023 United States
| | - Dominique C. Bergmann
- 0000000419368956grid.168010.eDepartment of Biology, Stanford University, Stanford, CA 94305 United States ,0000000419368956grid.168010.eHoward Hughes Medical Institute (HHMI), Stanford University, Stanford, CA 94305 United States
| | - Cranos M. Williams
- 0000 0001 2173 6074grid.40803.3fDepartment of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695 United States
| | - Rossangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States. .,Biomathematics Graduate Program, North Carolina State University, Raleigh, NC, 27695, United States.
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194
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Wang TY, Wang YF, Zhang Y, Shen JJ, Guo M, Yang J, Lau YL, Yang W. Identification of Regulatory Modules That Stratify Lupus Disease Mechanism through Integrating Multi-Omics Data. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 19:318-329. [PMID: 31877408 PMCID: PMC6938958 DOI: 10.1016/j.omtn.2019.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 11/05/2022]
Abstract
Although recent advances in genetic studies have shed light on systemic lupus erythematosus (SLE), its detailed mechanisms remain elusive. In this study, using datasets on SLE transcriptomic profiles, we identified 750 differentially expressed genes (DEGs) in T and B lymphocytes and peripheral blood cells. Using transcription factor (TF) binding data derived from chromatin immunoprecipitation sequencing (ChIP-seq) experiments from the Encyclopedia of DNA Elements (ENCODE) project, we inferred networks of co-regulated genes (NcRGs) based on binding profiles of the upregulated DEGs by significantly enriched TFs. Modularization analysis of NcRGs identified co-regulatory modules among the DEGs and master TFs vital for each module. Remarkably, the co-regulatory modules stratified the common SLE interferon (IFN) signature and revealed SLE pathogenesis pathways, including the complement cascade, cell cycle regulation, NETosis, and epigenetic regulation. By integrative analyses of disease-associated genes (DAGs), DEGs, and enriched TFs, as well as proteins interacting with them, we identified a hierarchical regulatory cascade with TFs regulated by DAGs, which in turn regulates gene expression. Integrative analysis of multi-omics data provided valuable molecular insights into the molecular mechanisms of SLE.
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Affiliation(s)
- Ting-You Wang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yan Zhang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jiangshan Jane Shen
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China; Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, China
| | - Mengbiao Guo
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
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195
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Lee S, Karas PJ, Hadley CC, Bayley V JC, Khan AB, Jalali A, Sweeney AD, Klisch TJ, Patel AJ. The Role of Merlin/NF2 Loss in Meningioma Biology. Cancers (Basel) 2019; 11:E1633. [PMID: 31652973 PMCID: PMC6893739 DOI: 10.3390/cancers11111633] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/17/2019] [Accepted: 10/19/2019] [Indexed: 02/06/2023] Open
Abstract
Mutations in the neurofibromin 2 (NF2) gene were among the first genetic alterations implicated in meningioma tumorigenesis, based on analysis of neurofibromatosis type 2 (NF2) patients who not only develop vestibular schwannomas but later have a high incidence of meningiomas. The NF2 gene product, merlin, is a tumor suppressor that is thought to link the actin cytoskeleton with plasma membrane proteins and mediate contact-dependent inhibition of proliferation. However, the early recognition of the crucial role of NF2 mutations in the pathogenesis of the majority of meningiomas has not yet translated into useful clinical insights, due to the complexity of merlin's many interacting partners and signaling pathways. Next-generation sequencing studies and increasingly sophisticated NF2-deletion-based in vitro and in vivo models have helped elucidate the consequences of merlin loss in meningioma pathogenesis. In this review, we seek to summarize recent findings and provide future directions toward potential therapeutics for this tumor.
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Affiliation(s)
- Sungho Lee
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Patrick J Karas
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Caroline C Hadley
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
| | - James C Bayley V
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
| | - A Basit Khan
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Alex D Sweeney
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tiemo J Klisch
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
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196
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Rotelli MD, Bolling AM, Killion AW, Weinberg AJ, Dixon MJ, Calvi BR. An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue. G3 (BETHESDA, MD.) 2019; 9:3087-3100. [PMID: 31387856 PMCID: PMC6778782 DOI: 10.1534/g3.119.400581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/31/2019] [Indexed: 12/23/2022]
Abstract
Cell division and tissue growth must be coordinated with development. Defects in these processes are the basis for a number of diseases, including developmental malformations and cancer. We have conducted an unbiased RNAi screen for genes that are required for growth in the Drosophila wing, using GAL4-inducible short hairpin RNA (shRNA) fly strains made by the Drosophila RNAi Screening Center. shRNA expression down the center of the larval wing disc using dpp-GAL4, and the central region of the adult wing was then scored for tissue growth and wing hair morphology. Out of 4,753 shRNA crosses that survived to adulthood, 18 had impaired wing growth. FlyBase and the new Alliance of Genome Resources knowledgebases were used to determine the known or predicted functions of these genes and the association of their human orthologs with disease. The function of eight of the genes identified has not been previously defined in Drosophila The genes identified included those with known or predicted functions in cell cycle, chromosome segregation, morphogenesis, metabolism, steroid processing, transcription, and translation. All but one of the genes are similar to those in humans, and many are associated with disease. Knockdown of lin-52, a subunit of the Myb-MuvB transcription factor, or βNACtes6, a gene involved in protein folding and trafficking, resulted in a switch from cell proliferation to an endoreplication growth program through which wing tissue grew by an increase in cell size (hypertrophy). It is anticipated that further analysis of the genes that we have identified will reveal new mechanisms that regulate tissue growth during development.
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Affiliation(s)
- Michael D Rotelli
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Anna M Bolling
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Andrew W Killion
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | | | - Michael J Dixon
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405 and
- Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202
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197
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Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors. Proc Natl Acad Sci U S A 2019; 116:21715-21726. [PMID: 31591222 DOI: 10.1073/pnas.1912858116] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Meningiomas account for one-third of all primary brain tumors. Although typically benign, about 20% of meningiomas are aggressive, and despite the rigor of the current histopathological classification system there remains considerable uncertainty in predicting tumor behavior. Here, we analyzed 160 tumors from all 3 World Health Organization (WHO) grades (I through III) using clinical, gene expression, and sequencing data. Unsupervised clustering analysis identified 3 molecular types (A, B, and C) that reliably predicted recurrence. These groups did not directly correlate with the WHO grading system, which classifies more than half of the tumors in the most aggressive molecular type as benign. Transcriptional and biochemical analyses revealed that aggressive meningiomas involve loss of the repressor function of the DREAM complex, which results in cell-cycle activation; only tumors in this category tend to recur after full resection. These findings should improve our ability to predict recurrence and develop targeted treatments for these clinically challenging tumors.
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198
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Han SK, Torii KU. Linking cell cycle to stomatal differentiation. CURRENT OPINION IN PLANT BIOLOGY 2019; 51:66-73. [PMID: 31075538 DOI: 10.1016/j.pbi.2019.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 05/20/2023]
Abstract
Stomatal differentiation manifests via several rounds of asymmetric cell division and a single symmetric cell division: the former, formative divisions amplify the number of epidermal cells, and the latter is essential for creating a functional guard cell pair. These cell division patterns are coordinated with progressive fate specification and cell-state transitional steps, which rely on the transcriptional regulation by a set of cell type-specific basic helix loop helix (bHLH) transcription factors. It has been proposed that the mechanisms underlying cell-fate decision and cell cycle progression are interconnected in a wide range of developmental processes. This review highlights the recent findings on how cell cycle regulators are transcriptionally regulated and contributing to each step of stomatal lineage progression.
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Affiliation(s)
- Soon-Ki Han
- Institute of Transformative BioMolecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Keiko U Torii
- Institute of Transformative BioMolecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan; Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, WA 98195, USA.
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199
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Ma Y, McKay DJ, Buttitta L. Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells. PLoS Biol 2019; 17:e3000378. [PMID: 31479438 PMCID: PMC6743789 DOI: 10.1371/journal.pbio.3000378] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 09/13/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
During terminal differentiation, most cells exit the cell cycle and enter into a prolonged or permanent G0 in which they are refractory to mitogenic signals. Entry into G0 is usually initiated through the repression of cell cycle gene expression by formation of a transcriptional repressor complex called dimerization partner (DP), retinoblastoma (RB)-like, E2F and MuvB (DREAM). However, when DREAM repressive function is compromised during terminal differentiation, additional unknown mechanisms act to stably repress cycling and ensure robust cell cycle exit. Here, we provide evidence that developmentally programmed, temporal changes in chromatin accessibility at a small subset of critical cell cycle genes act to enforce cell cycle exit during terminal differentiation in the Drosophila melanogaster wing. We show that during terminal differentiation, chromatin closes at a set of pupal wing enhancers for the key rate-limiting cell cycle regulators Cyclin E (cycE), E2F transcription factor 1 (e2f1), and string (stg). This closing coincides with wing cells entering a robust postmitotic state that is strongly refractory to cell cycle reactivation, and the regions that close contain known binding sites for effectors of mitogenic signaling pathways such as Yorkie and Notch. When cell cycle exit is genetically disrupted, chromatin accessibility at cell cycle genes remains unaffected, and the closing of distal enhancers at cycE, e2f1, and stg proceeds independent of the cell cycling status. Instead, disruption of cell cycle exit leads to changes in accessibility and expression of a subset of hormone-induced transcription factors involved in the progression of terminal differentiation. Our results uncover a mechanism that acts as a cell cycle–independent timer to limit the response to mitogenic signaling and aberrant cycling in terminally differentiating tissues. In addition, we provide a new molecular description of the cross talk between cell cycle exit and terminal differentiation during metamorphosis. The longer a cell remains in G0, the more refractory it becomes to re-entering the cell cycle. This study shows that in terminally differentiated cells in vivo, regulatory elements at genes encoding just three key cell cycle regulators (cycE, e2f1 and stg) become inaccessible, limiting their aberrant activation and maintaining a prolonged, robust G0.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Daniel J McKay
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Laura Buttitta
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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200
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Laaniste L, Srivastava PK, Stylianou J, Syed N, Cases-Cunillera S, Shkura K, Zeng Q, Rackham OJL, Langley SR, Delahaye-Duriez A, O'Neill K, Williams M, Becker A, Roncaroli F, Petretto E, Johnson MR. Integrated systems-genetic analyses reveal a network target for delaying glioma progression. Ann Clin Transl Neurol 2019; 6:1616-1638. [PMID: 31420939 PMCID: PMC6764637 DOI: 10.1002/acn3.50850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022] Open
Abstract
Objective To identify a convergent, multitarget proliferation characteristic for astrocytoma transformation that could be targeted for therapy discovery. Methods Using an integrated functional genomics approach, we prioritized networks associated with astrocytoma progression using the following criteria: differential co‐expression between grade II and grade III IDH1‐mutated and 1p/19q euploid astrocytomas, preferential enrichment for genetic risk to cancer, association with patient survival and sample‐level genomic features. Drugs targeting the identified multitarget network characteristic for astrocytoma transformation were computationally predicted using drug transcriptional perturbation data and validated using primary human astrocytoma cells. Results A single network, M2, consisting of 177 genes, was associated with glioma progression on the basis of the above criteria. Functionally, M2 encoded physically interacting proteins regulating cell cycle processes and analysis of genome‐wide gene‐regulatory interactions using mutual information and DNA–protein interactions revealed the known regulators of cell cycle processes FoxM1, B‐Myb, and E2F2 as key regulators of M2. These results suggest functional disruption of M2 via gene mutation or altered expression as a convergent pathway regulating astrocytoma transformation. By considering M2 as a multitarget drug target regulating astrocytoma transformation, we identified several drugs that are predicted to restore M2 expression in anaplastic astrocytoma toward its low‐grade profile and of these, we validated the known antiproliferative drug resveratrol as down‐regulating multiple nodes of M2 including at nanomolar concentrations achievable in human cerebrospinal fluid by oral dosing. Interpretation Our results identify M2 as a multitarget network characteristic for astrocytoma progression and encourage M2‐based drug screening to identify new compounds for preventing glioma transformation.
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Affiliation(s)
- Liisi Laaniste
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Julianna Stylianou
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Nelofer Syed
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Qingyu Zeng
- John Fulcher Neuro-oncology Laboratory, Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | | | - Sarah R Langley
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.,Duke-NUS Medical School, Singapore
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK.,PROTECT, INSERM, Université Paris Diderot, Sorbonne Paris Cité, France
| | - Kevin O'Neill
- Department of Neurosurgery, Imperial College Healthcare NHS Trust, London, UK
| | - Matthew Williams
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Albert Becker
- Department of Neuropathology, University of Bonn Medical Centre, Bonn, Germany
| | - Federico Roncaroli
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Enrico Petretto
- Duke-NUS Medical School, Singapore.,MRC London Institute of Medical Sciences (LMS), Imperial College London, London, UK
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
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