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Liu Z, Han S, Luo Y, Zhao Z, Ni L, Chai L, Tang H. PERP May Affect the Prognosis of Lung Adenocarcinoma by Inhibiting Apoptosis. Cancer Manag Res 2024; 16:199-214. [PMID: 38525370 PMCID: PMC10961073 DOI: 10.2147/cmar.s443490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
Background PERP, a member of the peripheral myelin protein gene family, is a new therapeutic target in cancer. The relationships between PERP and immune cell infiltration in lung cancer have not been studied. Therefore, the role of PERP in the tumour microenvironment (TME) of lung cancer needs to be further explored. Methods In this study, we explored the association between PERP expression and clinical characteristics by analysing data from the TCGA database. Cox regression and Kaplan‒Meier methods were used to investigate the relationship between the expression of PERP and overall survival in patients with lung adenocarcinoma (LUAD). The relationship between PERP expression and the degree of infiltration of specific immune cell subsets in LUAD was evaluated using the TIMER database and GEPIA. We also performed GO enrichment analysis and KEGG enrichment analysis to reveal genes coexpressed with PERP using the Coexpedia database. Finally, we verified the expression and function of PERP in LUAD tissues and the A549 cell line by RT‒PCR, Western blot, CCK-8, IHC, and wound healing assays. The mouse model was used to study the in vivo effects of PERP. Results According to our results, PERP expression was significantly higher in LUAD tissues and associated with the clinical characteristics of the disease. Survival was independently associated with PERP in LUAD patients. We further verified that PERP might regulate B-cell infiltration in LUAD to affect the prognosis of LUAD. To identify PERP-related signalling pathways in LUAD, we performed a genome-aggregation analysis (GSEA) between low and high PERP expression datasets. LUAD cells express higher levels of PERP than paracarcinoma cells, and PERP inhibits the proliferation and metastasis of A549 cells through apoptosis. Conclusion PERP may affect the prognosis of lung adenocarcinoma by inhibiting apoptosis and is associated with immune cell infiltration.
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Affiliation(s)
- Zhongxiang Liu
- Department of Pulmonary and Critical Care Medicine, the Yancheng Clinical College of Xuzhou Medical University, The First People’s Hospital of Yancheng, the First Affiliated Hospital of Jiangsu Vocational College of Medicine, Yancheng, 224000, People’s Republic of China
| | - Shuhua Han
- Department of Respiratory and Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, People’s Republic of China
| | - Yuhong Luo
- College of Life Science and Technology, Guangxi University, Nanning, 530004, People’s Republic of China
| | - Zhangyan Zhao
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, People’s Republic of China
| | - Lingyu Ni
- China School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210046, People’s Republic of China
| | - Linlin Chai
- Department of Pathology, The Yancheng Clinical College of Xuzhou Medical University, The First People’s Hospital of Yancheng, The First Affiliated Hospital of Jiangsu Vocational College of Medicine, Yancheng, 224000, People’s Republic of China
| | - Haicheng Tang
- Department of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, People’s Republic of China
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Wick KD, Fang X, Maishan M, Matsumoto S, Spottiswoode N, Sarma A, Simoneau C, Khakoo M, Langelier C, Calfee CS, Gotts JE, Matthay MA. Impact of e-cigarette aerosol on primary human alveolar epithelial type 2 cells. Am J Physiol Lung Cell Mol Physiol 2022; 323:L152-L164. [PMID: 35670478 PMCID: PMC9559034 DOI: 10.1152/ajplung.00503.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022] Open
Abstract
Electronic cigarettes (e-cigarettes) are designed to simulate combustible cigarette smoking and to aid in smoking cessation. Although the number of e-cigarette users has been increasing, the potential health impacts and biological effects of e-cigarettes are still not fully understood. Previous research has focused on the biological effects of e-cigarettes on lung cancer cell lines and distal airway epithelial cells; however, there have been few published studies on the effect of e-cigarettes on primary lung alveolar epithelial cells. The primary purpose of this study was to investigate the direct effect of e-cigarette aerosol on primary human lung alveolar epithelial type 2 (AT2) cells, both alone and in the presence of viral infection. The Melo-3 atomizer caused direct AT2 cell toxicity, whereas the more popular Juul pod's aerosol did not have a detectable cytotoxic effect on AT2 cells. Juul nicotine aerosol also did not increase short-term susceptibility to viral infection. However, 3 days of exposure upregulated genes central to the generation of reactive oxygen species, lipid peroxidation, and carcinogen metabolism and downregulated key innate immune system genes related to cytokine and chemokine signaling. These findings have implications for the potentially injurious impact of long-term use of popular low-power e-cigarette pods on the human alveolar epithelium. Gene expression data might be an important endpoint for evaluating the potential harmful effects of vaping devices that do not cause overt toxicity.
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Affiliation(s)
- Katherine D Wick
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Xiaohui Fang
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Mazharul Maishan
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Shotaro Matsumoto
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Natasha Spottiswoode
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California
| | - Aartik Sarma
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, San Francisco, California
| | - Camille Simoneau
- Gladstone Institutes, University of California, San Francisco, California
| | - Manisha Khakoo
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Chaz Langelier
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California
- Chan Zuckerberg Biohub, San Francisco, California
| | - Carolyn S Calfee
- Cardiovascular Research Institute, University of California, San Francisco, California
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, San Francisco, California
| | - Jeffrey E Gotts
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Michael A Matthay
- Cardiovascular Research Institute, University of California, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
- Department of Anesthesia, University of California, San Francisco, California
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Establishment of a prognostic model of ten transcription factors in gastric cancer. Genomics 2021; 113:4075-4087. [PMID: 34688795 DOI: 10.1016/j.ygeno.2021.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 09/23/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Transcription factors (TFs) play an important role in tumors. We integrated and analyzed 13 GPL570 platform gastric cancer (GC) microarrays, identified 10 independent prognostic TFs, and constructed a GC prognostic model. Using GSE26942 as the verification set, the Kaplan-Meier curve showed that the signature distinguish the survival rate of GC patients (P < 0.01), and the AUC values are 0.746 and 0.630, respectively. Compared with the clinicopathological characteristics, the signature is an independent prognostic factor (P < 0.05). A nomogram was established based on the model, and the five-year calibration curve verified that the prediction of the nomogram was almost consistent with the actual survival rate, C-index of 0.747 indicated a moderate prognostic ability. The analysis of target genes of 10 TFs showed that they are closely related to the progression of GC. External database and rt-PCR showed that the RNA and protein expression of TFs are consistent with our analysis.
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Downregulated mRNA Expression of ZNF385B Is an Independent Predictor of Breast Cancer. Int J Genomics 2021; 2021:4301802. [PMID: 33614780 PMCID: PMC7876827 DOI: 10.1155/2021/4301802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/13/2020] [Accepted: 01/07/2021] [Indexed: 11/17/2022] Open
Abstract
Background ZNF385B, a zinc finger protein, has been known as a potential biomarker in some neurological and hematological studies recently. Although numerous studies have demonstrated the potential function of zinc finger proteins in tumor progression, the effects of ZNF385B in breast cancer (BC) are less studied. Methods The Oncomine database and “ESurv” tool were used to explore the differential expression of ZNF385B in pan-cancer. Furthermore, data of patients with BC were downloaded from The Cancer Genome Atlas (TCGA). The receiver operating characteristic (ROC) curve of ZNF385B expression was established to explore the diagnostic value of ZNF385B and to obtain the cut-off value of high or low ZNF385B expression in BC. The chi-square test as well as Fisher exact test was used for identification of the relationships between clinical features and ZNF385B expression. Furthermore, the effects of ZNF385B on BC patients' survival were evaluated by the Kaplan-Meier and Cox regression. Data from the Gene Expression Omnibus (GEO) database were employed to validate the results of TCGA. Protein expression of ZNF385B in BC patient specimens was detected by immunohistochemistry (IHC) staining. Results ZNF385B expression was downregulated in most types of cancer including BC. Low ZNF385B expression was related with survival status, overall survival (OS), and recurrence of BC. ZNF385B had modest diagnostic value, which is indicated by the area under the ROC curve (AUC = 0.671). Patients with lower ZNF385B expression had shorter OS and RFS (relapse-free survival). It had been demonstrated that low ZNF385B expression represented independent prognostic value for OS and RFS by multivariate survival analysis. The similar results were verified by datasets from the GEO database as well. The protein expression of ZNF385B was decreased in patients' samples compared with adjacent tissues by IHC. Conclusions Low ZNF385B expression was an independent predictor for worse prognosis of BC patients.
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Roberts O, Paraoan L. PERP-ing into diverse mechanisms of cancer pathogenesis: Regulation and role of the p53/p63 effector PERP. Biochim Biophys Acta Rev Cancer 2020; 1874:188393. [PMID: 32679166 DOI: 10.1016/j.bbcan.2020.188393] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/11/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022]
Abstract
The tetraspan plasma membrane protein PERP (p53 apoptosis effector related to PMP22) is a lesser-known transcriptional target of p53 and p63. A member of the PMP22/GAS3/EMP membrane protein family, PERP was originally identified as a p53 target specifically trans-activated during apoptosis, but not during cell-cycle arrest. Several studies have since shown downregulation of PERP expression in numerous cancers, suggesting that PERP is a tumour suppressor protein. This review focusses on the important advances made in elucidating the mechanisms regulating PERP expression and its function as a tumour suppressor in diverse human cancers, including breast cancer and squamous cell carcinoma. Investigating PERP's role in clinically-aggressive uveal melanoma has revealed that PERP engages a positive-feedback loop with p53 to regulate its own expression, and that p63 is required beside p53 to achieve pro-apoptotic levels of PERP in this cancer. Furthermore, the recent discovery of the apoptosis-mediating interaction of PERP with SERCA2b at the plasma membrane-endoplasmic reticulum interface demonstrates a novel mechanism of PERP stabilisation, and how PERP can mediate Ca2+ signalling to facilitate apoptosis. The multi-faceted role of PERP in cancer, involving well-documented functions in mediating apoptosis and cell-cell adhesion is discussed, alongside PERP's emerging roles in epithelial-mesenchymal transition, and PERP crosstalk with inflammation signalling pathways, and other signalling pathways. The potential for restoring PERP expression as a means of cancer therapy is also considered.
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Affiliation(s)
- Owain Roberts
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Luminita Paraoan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom.
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Li Z, Chen B, Dong W, Xu W, Song M, Fang M, Guo J, Xu Y. Epigenetic activation of PERP transcription by MKL1 contributes to ROS-induced apoptosis in skeletal muscle cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30177-9. [PMID: 30056131 DOI: 10.1016/j.bbagrm.2018.07.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/19/2018] [Accepted: 07/24/2018] [Indexed: 12/25/2022]
Abstract
Excessive reactive oxygen species (ROS) causes irreparable damages to cells and commit cells to programmed cell death or apoptosis. A panel of well-documented pro-apoptotic genes, including p53 apoptosis effector related to PMP-22 (PERP), are up-regulated and collectively mediate ROS induced apoptosis. The epigenetic mechanism whereby ROS stimulates PERP transcription, however, lacks in-depth characterization. Here we report that the transcriptional modulator megakaryocytic leukemia 1 (MKL1) is activated by H2O2 treatment in skeletal muscle cells (C2C12). Small interfering RNA (siRNA) mediated silencing or small-molecule compound (CCG-1423) mediated inhibition of MKL1 attenuated H2O2 induced apoptosis of C2C12 cells. Over-expression of MKL1 potentiated trans-activation of PERP whereas MKL1 ablation/inhibition abrogated the induction of PERP by H2O2 in C2C12 cells. Mechanistically, MKL1 interacted with and was recruited to the PERP promoter by the transcription factor E2F1. Once bound to the PERP promoter, MKL1 engaged the histone demethylase KDM3A to modulate the chromatin structure surrounding the PERP promoter thereby leading to PERP trans-activation. Depletion of either E2F1 or KDM3A blocked the induction of PERP by H2O2. In conclusion, our data illustrate a novel epigenetic pathway that links PERP transcription to ROS-induced apoptosis in skeletal muscle cells.
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Affiliation(s)
- Zilong Li
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China; Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Baoyu Chen
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Wenhui Dong
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Wenping Xu
- Department of Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Mingzi Song
- Department of Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Mingming Fang
- Department of Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Junli Guo
- Cardiovascular Disease and Research Institute, Affiliated Hospital of Hainan Medical College, Haikou, Hainan, China.
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China; Institute of Biomedical Research, Liaocheng University, Liaocheng, China.
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7
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Bell AH, DeMonte F, Raza SM, Rhines LD, Tatsui CE, Prieto VG, Fuller GN, Bell D. Transcriptome comparison identifies potential biomarkers of spine and skull base chordomas. Virchows Arch 2017; 472:489-497. [PMID: 28844110 DOI: 10.1007/s00428-017-2224-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/08/2017] [Accepted: 08/20/2017] [Indexed: 10/19/2022]
Abstract
Chordomas are rare, slowly growing, locally aggressive bone neoplasms that arise from embryonic remnants of the notochord, showing dual epithelial-mesenchymal differentiation. The high plasticity probably is the main reason for the high variety in phenotypes of chordoma, from its high heterogeneity on a cellular level to its subtype variations depending on tissue location, with its potential to develop from an inactive quiescent form to an aggressive cancer with extreme adaptability and resistance to drugs and other treatments. Gene expression profiles of formalin-fixed, paraffin-embedded skull chordoma, spine chordoma, and normal tissue specimens were generated and compared. Using strict criteria, we identified 222 differentially expressed transcripts unique to skull base chordoma, 261 unique to spine chordoma, and 192 common to both chordoma subtypes. Further analysis of these three groups of transcripts allowed the selection of three subsets of highly differentially expressed genes as potential biomarkers, disease drivers, and therapeutic targets in both chordoma subtypes. Immunohistochemistry revealed LMX1A to be dominant in skull base chordoma, SALL3 to be unique to spine chordoma, and T to be common to both chordoma subtypes. In both chordoma subtypes, the genes with the highest expression were predominantly development-related genes, mostly transcription factors. Our findings indicate that these developmental genes play important oncogenic roles in chordoma, mainly causing high plasticity and resistance to therapy in both these cancer subtypes but also determining their differentiation status and proliferation activity, pointing to features expected of heterogeneous stem cell-like tissues with similarities to their notochord origins.
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Affiliation(s)
- Achim H Bell
- Pathology Department, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.,Pathology Research Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Franco DeMonte
- Head and Neck Surgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Neurosurgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaan M Raza
- Head and Neck Surgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Neurosurgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laurence D Rhines
- Neurosurgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Claudio E Tatsui
- Neurosurgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Victor G Prieto
- Pathology Department, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Gregory N Fuller
- Pathology Department, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Diana Bell
- Pathology Department, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA. .,Head and Neck Surgery Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Ishibashi T, Yaguchi A, Terada K, Ueno-Yokohata H, Tomita O, Iijima K, Kobayashi K, Okita H, Fujimura J, Ohki K, Shimizu T, Kiyokawa N. Ph-like ALL-related novel fusion kinase ATF7IP-PDGFRB exhibits high sensitivity to tyrosine kinase inhibitors in murine cells. Exp Hematol 2015; 44:177-88.e5. [PMID: 26703895 DOI: 10.1016/j.exphem.2015.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 11/27/2022]
Abstract
ATF7IP-PDGFRB is a novel PDGFRB-related fusion gene identified in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with a signature similar to that of Ph1 ALL, so-called Ph-like ALL. When we introduced ATF7IP-PDGFRB, murine Ba/F3 cells acquired the ability to proliferate in an interleukin (IL)-3-independent manner. On the contrary, the expression of wild-type PDGFRB is not sufficient to acquire the ability for IL-3-independent proliferation in Ba/F3 cells. The introduction of ATF7IP-PDGFRB also induces a typical gene expression profile for Ph1-ALL in Ba/F3 cells. A series of biochemical and cell biological experiments revealed the constitutive activation of ATF7IP-PDGFRB as well as downstream signaling molecules, including AKT and MAPK. Although the phosphoinositide 3-kinase inhibitor led to cell death in both cells into which ATF7IP-PDGFRB had been introduced and IL-3-maintained Mock cells, MEK inhibitor selectively led to cell death into which ATF7IP-PDGFRB had been introduced. The introduction of tyrosine to phenylalanine mutations at binding sites of adaptor molecules important in the MAPK pathway located in the PDGFRB portion abolished ATF7IP-PDGFRB-mediated cell transformation, suggesting that MAPK-mediated signals are critical in ATF7IP-PDGFRB-mediated cell transformation. On treatment with tyrosine kinase inhibitors, ATF7IP-PDGFRB-expressing, but not Mock, Ba/F3 cells underwent rapid apoptosis accompanied by reduced phosphorylation of MAPK. Importantly, the sensitivity of ATF7IP-PDGFRB-expressing Ba/F3 cells to imatinib is significantly higher than that of BCR-ABL1-transformed Ba/F3 cells, as assessed by the IC50. Taken together, ATF7IP-PDGFRB has transforming potential via the constitutive activation of MAPK and participates in the pathogenesis of Ph-like ALL. Our observations suggest the therapeutic importance of tyrosine kinase inhibitors and possibly MEK inhibitor for a subset of BCP-ALL harboring PDGFRB-related fusion kinases.
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Affiliation(s)
- Takeshi Ishibashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan; Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Akinori Yaguchi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan; Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Kazuki Terada
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Hitomi Ueno-Yokohata
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Osamu Tomita
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan; Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Kazutoshi Iijima
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan; Department of Industrial Chemistry, Faculty of Engineering, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Kenichiro Kobayashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Hajime Okita
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Junya Fujimura
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo, Japan.
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Znf385C mediates a novel p53-dependent transcriptional switch to control timing of facial bone formation. Dev Biol 2015; 400:23-32. [DOI: 10.1016/j.ydbio.2015.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 01/12/2015] [Indexed: 11/18/2022]
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10
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Lake RJ, Boetefuer EL, Tsai PF, Jeong J, Choi I, Won KJ, Fan HY. The sequence-specific transcription factor c-Jun targets Cockayne syndrome protein B to regulate transcription and chromatin structure. PLoS Genet 2014; 10:e1004284. [PMID: 24743307 PMCID: PMC3990521 DOI: 10.1371/journal.pgen.1004284] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/20/2014] [Indexed: 11/19/2022] Open
Abstract
Cockayne syndrome is an inherited premature aging disease associated with numerous developmental and neurological defects, and mutations in the gene encoding the CSB protein account for the majority of Cockayne syndrome cases. Accumulating evidence suggests that CSB functions in transcription regulation, in addition to its roles in DNA repair, and those defects in this transcriptional activity might contribute to the clinical features of Cockayne syndrome. Transcription profiling studies have so far uncovered CSB-dependent effects on gene expression; however, the direct targets of CSB's transcriptional activity remain largely unknown. In this paper, we report the first comprehensive analysis of CSB genomic occupancy during replicative cell growth. We found that CSB occupancy sites display a high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, we found that CSB occupancy is enriched at sites containing the TPA-response element. Consistent with this binding site preference, we show that CSB and the transcription factor c-Jun can be found in the same protein-DNA complex, suggesting that c-Jun can target CSB to specific genomic regions. In support of this notion, we observed decreased CSB occupancy of TPA-response elements when c-Jun levels were diminished. By modulating CSB abundance, we found that CSB can influence the expression of nearby genes and impact nucleosome positioning in the vicinity of its binding site. These results indicate that CSB can be targeted to specific genomic loci by sequence-specific transcription factors to regulate transcription and local chromatin structure. Additionally, comparison of CSB occupancy sites with the MSigDB Pathways database suggests that CSB might function in peroxisome proliferation, EGF receptor transactivation, G protein signaling and NF-κB activation, shedding new light on the possible causes and mechanisms of Cockayne syndrome. Cockayne syndrome is a devastating inherited disease, in which patients appear to age prematurely, have sun sensitivity and suffer from profound neurological and developmental defects. Mutations in the CSB gene account for the majority of Cockayne syndrome cases. CSB is an ATP-dependent chromatin remodeler, and these proteins can use energy from ATP-hydrolysis to alter contacts between DNA and histones of a nucleosome, the basic units of chromatin structure. CSB functions in DNA repair, but accumulating evidence reveals that CSB also functions in transcription regulation. Here, we determined the genomic localization of CSB to identify its gene targets and found that CSB occupancy displays high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, CSB is enriched at genomic regions containing the binding site for the c-Jun transcription factor, and we found that these two proteins interact, uncovering a new targeting mechanism for CSB. We also demonstrate that CSB can influence gene expression in the vicinity of its binding sites and alter local chromatin structure. Together, this study supports the hypothesis that defects in the regulation of gene expression and chromatin structure by CSB might contribute to the diverse clinical features of Cockayne syndrome.
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Affiliation(s)
- Robert J. Lake
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Erica L. Boetefuer
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Biology Graduate Program, Graduate School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Pei-Fang Tsai
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jieun Jeong
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Inchan Choi
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kyoung-Jae Won
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hua-Ying Fan
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Tomita O, Iijima K, Ishibashi T, Osumi T, Kobayashi K, Okita H, Saito M, Mori T, Shimizu T, Kiyokawa N. Sensitivity of SNX2-ABL1 toward tyrosine kinase inhibitors distinct from that of BCR-ABL1. Leuk Res 2014; 38:361-70. [DOI: 10.1016/j.leukres.2013.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 11/20/2013] [Accepted: 11/23/2013] [Indexed: 12/21/2022]
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Gao S, Hsieh CL, Zhou J, Shemshedini L. Zinc Finger 280B regulates sGCα1 and p53 in prostate cancer cells. PLoS One 2013; 8:e78766. [PMID: 24236047 PMCID: PMC3827277 DOI: 10.1371/journal.pone.0078766] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/23/2013] [Indexed: 11/29/2022] Open
Abstract
The Zinc Finger (ZNF) 280B protein was identified as an unexpected target of an shRNA designed for sGCα1. Further analysis showed that these two proteins are connected in another way, with 280B up-regulation of sGCα1 expression. Knock-down and over-expression experiments showed that 280B serves pro-growth and pro-survival functions in prostate cancer. Surprisingly however, these pro-cancer functions of 280B are not mediated by sGCα1, which itself has similar functions in prostate cancer, but by down-regulated p53. The p53 protein is a second target of 280B in prostate cancer, but unlike sGCα1, p53 is down-regulated by 280B. 280B induces p53 nuclear export, leading to subsequent proteasomal degradation. The protein responsible for p53 regulation by 280B is Mdm2, the E3 ubiquitin ligase that promotes p53 degradation by inducing its nuclear export. We show here that 280B up-regulates expression of Mdm2 in prostate cancer cells, and this regulation is via the Mdm2 promoter. To demonstrate an in vivo relevance to this interaction, expression studies show that 280B protein levels are up-regulated in prostate cancer and these levels correspond to reduced levels of p53. Thus, by enhancing the expression of Mdm2, the uncharacterized 280B protein provides a novel mechanism of p53 suppression in prostate cancer.
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Affiliation(s)
- Shuai Gao
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Chen-Lin Hsieh
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Jun Zhou
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Lirim Shemshedini
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
- * E-mail:
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