1
|
Regunath K, Fomin V, Liu Z, Wang P, Hoque M, Tian B, Rabadan R, Prives C. Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types. Mol Cancer Res 2024; 22:555-571. [PMID: 38393317 DOI: 10.1158/1541-7786.mcr-23-0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/04/2023] [Accepted: 02/21/2024] [Indexed: 02/25/2024]
Abstract
The p53 tumor suppressor protein, a sequence-specific DNA binding transcription factor, regulates the expression of a large number of genes, in response to various forms of cellular stress. Although the protein coding target genes of p53 have been well studied, less is known about its role in regulating long noncoding genes and their functional relevance to cancer. Here we report the genome-wide identification of a large set (>1,000) of long noncoding RNAs (lncRNA), which are putative p53 targets in a colon cancer cell line and in human patient datasets from five different common types of cancer. These lncRNAs have not been annotated by other studies of normal unstressed systems. In the colon cancer cell line, a high proportion of these lncRNAs are uniquely induced by different chemotherapeutic agents that activate p53, whereas others are induced by more than one agent tested. Further, subsets of these lncRNAs independently predict overall and disease-free survival of patients across the five different common cancer types. Interestingly, both genetic alterations and patient survival associated with different lncRNAs are unique to each cancer tested, indicating extraordinary tissue-specific variability in the p53 noncoding response. The newly identified noncoding p53 target genes have allowed us to construct a classifier for tumor diagnosis and prognosis. IMPLICATIONS Our results not only identify myriad p53-regulated long noncoding (lncRNA), they also reveal marked drug-induced, as well as tissue- and tumor-specific heterogeneity in these putative p53 targets and our findings have enabled the construction of robust classifiers for diagnosis and prognosis.
Collapse
Affiliation(s)
- Kausik Regunath
- Department of Biological Sciences, Columbia University, New York, New York
| | - Vitalay Fomin
- Department of Biological Sciences, Columbia University, New York, New York
| | - Zhaoqi Liu
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Pingzhang Wang
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Raul Rabadan
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York
| |
Collapse
|
2
|
Huang Y, Xiong C, Wang C, Deng J, Zuo Z, Wu H, Xiong J, Wu X, Lu H, Hao Q, Zhou X. p53-responsive CMBL reprograms glucose metabolism and suppresses cancer development by destabilizing phosphofructokinase PFKP. Cell Rep 2023; 42:113426. [PMID: 37967006 DOI: 10.1016/j.celrep.2023.113426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/25/2023] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
Aerobic glycolysis is critical for cancer progression and can be exploited in cancer therapy. Here, we report that the human carboxymethylenebutenolidase homolog (carboxymethylenebutenolidase-like [CMBL]) acts as a tumor suppressor by reprogramming glycolysis in colorectal cancer (CRC). The anti-cancer action of CMBL is mediated through its interactions with the E3 ubiquitin ligase TRIM25 and the glycolytic enzyme phosphofructokinase-1 platelet type (PFKP). Ectopic CMBL enhances TRIM25 binding to PFKP, leading to the ubiquitination and proteasomal degradation of PFKP. Interestingly, CMBL is transcriptionally activated by p53 in response to genotoxic stress, and p53 activation represses glycolysis by promoting PFKP degradation. Remarkably, CMBL deficiency, which impairs p53's ability to inhibit glycolysis, makes tumors more sensitive to a combination therapy involving the glycolysis inhibitor 2-deoxyglucose. Taken together, our study demonstrates that CMBL suppresses CRC growth by inhibiting glycolysis and suggests a potential combination strategy for the treatment of CMBL-deficient CRC.
Collapse
Affiliation(s)
- Yingdan Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Lymphoma Medicine (Breast Cancer & Soft Tissue Tumor Medicine), Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430079, China
| | - Chen Xiong
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chunmeng Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jun Deng
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Huijing Wu
- Department of Lymphoma Medicine (Breast Cancer & Soft Tissue Tumor Medicine), Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430079, China
| | - Jianping Xiong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xiaohua Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| |
Collapse
|
3
|
Ott J, Park T. Overview of frequent pattern mining. Genomics Inform 2022; 20:e39. [PMID: 36617647 PMCID: PMC9847378 DOI: 10.5808/gi.22074] [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: 12/12/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Various methods of frequent pattern mining have been applied to genetic problems, specifically, to the combined association of two genotypes (a genotype pattern, or diplotype) at different DNA variants with disease. These methods have the ability to come up with a selection of genotype patterns that are more common in affected than unaffected individuals, and the assessment of statistical significance for these selected patterns poses some unique problems, which are briefly outlined here.
Collapse
Affiliation(s)
- Jurg Ott
- Laboratory of Statistical Genetics, Rockefeller University, New York, NY 10065, USA,Corresponding author E-mail:
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
4
|
Melnik BC, Schmitz G. Milk Exosomal microRNAs: Postnatal Promoters of β Cell Proliferation but Potential Inducers of β Cell De-Differentiation in Adult Life. Int J Mol Sci 2022; 23:ijms231911503. [PMID: 36232796 PMCID: PMC9569743 DOI: 10.3390/ijms231911503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic β cell expansion and functional maturation during the birth-to-weaning period is driven by epigenetic programs primarily triggered by growth factors, hormones, and nutrients provided by human milk. As shown recently, exosomes derived from various origins interact with β cells. This review elucidates the potential role of milk-derived exosomes (MEX) and their microRNAs (miRs) on pancreatic β cell programming during the postnatal period of lactation as well as during continuous cow milk exposure of adult humans to bovine MEX. Mechanistic evidence suggests that MEX miRs stimulate mTORC1/c-MYC-dependent postnatal β cell proliferation and glycolysis, but attenuate β cell differentiation, mitochondrial function, and insulin synthesis and secretion. MEX miR content is negatively affected by maternal obesity, gestational diabetes, psychological stress, caesarean delivery, and is completely absent in infant formula. Weaning-related disappearance of MEX miRs may be the critical event switching β cells from proliferation to TGF-β/AMPK-mediated cell differentiation, whereas continued exposure of adult humans to bovine MEX miRs via intake of pasteurized cow milk may reverse β cell differentiation, promoting β cell de-differentiation. Whereas MEX miR signaling supports postnatal β cell proliferation (diabetes prevention), persistent bovine MEX exposure after the lactation period may de-differentiate β cells back to the postnatal phenotype (diabetes induction).
Collapse
Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany
- Correspondence: ; Tel.: +49-52-4198-8060
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, University of Regensburg, D-93053 Regensburg, Germany
| |
Collapse
|
5
|
Kaller M, Hünten S, Siemens H, Hermeking H. Analysis of the p53/microRNA Network in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:187-228. [DOI: 10.1007/978-3-031-08356-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
6
|
Martinez JD, Mo Q, Xu Y, Qin L, Li Y, Xu J. Common Genomic Aberrations in Mouse and Human Breast Cancers with Concurrent P53 Deficiency and Activated PTEN-PI3K-AKT Pathway. Int J Biol Sci 2022; 18:229-241. [PMID: 34975329 PMCID: PMC8692138 DOI: 10.7150/ijbs.65763] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022] Open
Abstract
Simultaneous P53 loss and activation of the PTEN-restricted PI3K-AKT pathway frequently occur in aggressive breast cancers. P53 loss causes genome instability, while PTEN loss and/or activating mutations of PIK3CA and AKT promote cancer cell proliferation that also increases incidences of genomic aberrations. However, the genomic alterations associated with P53 loss and activated PTEN-PI3K-AKT signaling in breast cancer have not been defined. Spatiotemporally controlled breast cancer models with inactivation of both P53 and Pten in adult mice have not been established for studying genomic alterations. Herein, we deleted both floxed Pten and Tp53 genes in the mammary gland epithelial cells in adult mice using a RCAS virus-mediated Cre-expressing system. These mice developed small tumors in 21 weeks, and poorly differentiated larger tumors in 26 weeks. In these tumors, we identified 360 genes mutated by nonsynonymous point mutations and small insertions and deletions (NSPMs/InDels), 435 genes altered by copy number amplifications (CNAs), and 450 genes inactivated by copy number deletions (CNDs). Importantly, 22.2%, 75.9% and 27.3% of these genes were also altered in human breast tumors with P53 and PTEN losses or P53 loss and activated PI3K-AKT signaling by NSPMs/InDels, CNAs and CNDs, respectively. Therefore, inactivation of P53 and Pten in adult mice causes rapid-growing breast tumors, and these tumors recapitulate a significant number of genetic aberrations in human breast tumors with inactivated P53 and activated PTEN-PI3K-AKT signaling. Further characterization of these commonly altered genes in breast cancer should help to identify novel cancer-driving genes and molecular targets for developing therapeutics.
Collapse
Affiliation(s)
- Jarrod D Martinez
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Qianxing Mo
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Yixiang Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Li Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Yi Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Jianming Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| |
Collapse
|
7
|
Zhou G, Gui X, Qu W. Clinical significance of CCN5 and mutant p53 in primary and recurrent lesions of breast cancer. Am J Transl Res 2021; 13:8433-8437. [PMID: 34377340 PMCID: PMC8340222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE To analyze the expression and significance of CCN5 and mutant p53 proteins in primary and recurrent lesions of breast cancer (BC) patients. METHODS The expression of CCN5 and mutant p53 proteins in 20 normal breast tissues, 60 primary and chest wall recurrent lesions were detected by streptavidin peroxidase conjugated (SP) method. RESULTS The differences in CCN5 and mutant p53 expression is significant among normal breast tissue, primary lesion, and recurrent lesions (Χ2=18.380 and Χ2=30.549, P < 0.05), and the expression of CCN5 protein was higher and the expression of mutant p53 protein was lower in all primary lesions than in recurrent lesions (P < 0.05). CCN5 expression was higher in the group without lymph node metastasis (LNM) than in the group with LNM in BC patients, while mutant p53 protein expression was higher in the group with LNM than in the group without LNM (Χ2=9.775, Χ2=7.102, P < 0.05). There was a negative relationship between CCN5 and mutant p53 protein expression in BC tissues (rp=-0.013, P < 0.001). CONCLUSION CCN5, mutant p53 protein expression may play different regulatory roles in BC recurrence and LNM and have important implications in BC development and prognosis.
Collapse
Affiliation(s)
- Guofeng Zhou
- Department of Pathology, The Third Hospital of Nanchang Nanchang, Jiangxi Province, China
| | - Xingxing Gui
- Department of Pathology, The Third Hospital of Nanchang Nanchang, Jiangxi Province, China
| | - Wei Qu
- Department of Pathology, The Third Hospital of Nanchang Nanchang, Jiangxi Province, China
| |
Collapse
|
8
|
Higgins CE, Tang J, Higgins SP, Gifford CC, Mian BM, Jones DM, Zhang W, Costello A, Conti DJ, Samarakoon R, Higgins PJ. The Genomic Response to TGF-β1 Dictates Failed Repair and Progression of Fibrotic Disease in the Obstructed Kidney. Front Cell Dev Biol 2021; 9:678524. [PMID: 34277620 PMCID: PMC8284093 DOI: 10.3389/fcell.2021.678524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
Tubulointerstitial fibrosis is a common and diagnostic hallmark of a spectrum of chronic renal disorders. While the etiology varies as to the causative nature of the underlying pathology, persistent TGF-β1 signaling drives the relentless progression of renal fibrotic disease. TGF-β1 orchestrates the multifaceted program of kidney fibrogenesis involving proximal tubular dysfunction, failed epithelial recovery or re-differentiation, capillary collapse and subsequent interstitial fibrosis eventually leading to chronic and ultimately end-stage disease. An increasing complement of non-canonical elements function as co-factors in TGF-β1 signaling. p53 is a particularly prominent transcriptional co-regulator of several TGF-β1 fibrotic-response genes by complexing with TGF-β1 receptor-activated SMADs. This cooperative p53/TGF-β1 genomic cluster includes genes involved in cellular proliferative control, survival, apoptosis, senescence, and ECM remodeling. While the molecular basis for this co-dependency remains to be determined, a subset of TGF-β1-regulated genes possess both p53- and SMAD-binding motifs. Increases in p53 expression and phosphorylation, moreover, are evident in various forms of renal injury as well as kidney allograft rejection. Targeted reduction of p53 levels by pharmacologic and genetic approaches attenuates expression of the involved genes and mitigates the fibrotic response confirming a key role for p53 in renal disorders. This review focuses on mechanisms underlying TGF-β1-induced renal fibrosis largely in the context of ureteral obstruction, which mimics the pathophysiology of pediatric unilateral ureteropelvic junction obstruction, and the role of p53 as a transcriptional regulator within the TGF-β1 repertoire of fibrosis-promoting genes.
Collapse
Affiliation(s)
- Craig E. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Jiaqi Tang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Stephen P. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Cody C. Gifford
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Badar M. Mian
- The Urological Institute of Northeastern New York, Albany, NY, United States
- Division of Urology, Department of Surgery, Albany Medical College, Albany, NY, United States
| | - David M. Jones
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, United States
| | - Wenzheng Zhang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Angelica Costello
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - David J. Conti
- Division of Transplantation Surgery, Department of Surgery, Albany Medical College, Albany, NY, United States
| | - Rohan Samarakoon
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Paul J. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
- The Urological Institute of Northeastern New York, Albany, NY, United States
- Division of Urology, Department of Surgery, Albany Medical College, Albany, NY, United States
| |
Collapse
|
9
|
Chang CY, Wang J, Zhao Y, Liu J, Yang X, Yue X, Wang H, Zhou F, Inclan-Rico JM, Ponessa JJ, Xie P, Zhang L, Siracusa MC, Feng Z, Hu W. Tumor suppressor p53 regulates intestinal type 2 immunity. Nat Commun 2021; 12:3371. [PMID: 34099671 PMCID: PMC8184793 DOI: 10.1038/s41467-021-23587-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
The role of p53 in tumor suppression has been extensively studied and well-established. However, the role of p53 in parasitic infections and the intestinal type 2 immunity is unclear. Here, we report that p53 is crucial for intestinal type 2 immunity in response to the infection of parasites, such as Tritrichomonas muris and Nippostrongylus brasiliensis. Mechanistically, p53 plays a critical role in the activation of the tuft cell-IL-25-type 2 innate lymphoid cell circuit, partly via transcriptional regulation of Lrmp in tuft cells. Lrmp modulates Ca2+ influx and IL-25 release, which are critical triggers of type 2 innate lymphoid cell response. Our results thus reveal a previously unrecognized function of p53 in regulating intestinal type 2 immunity to protect against parasitic infections, highlighting the role of p53 as a guardian of immune integrity.
Collapse
Affiliation(s)
- Chun-Yuan Chang
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Jianming Wang
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Yuhan Zhao
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Juan Liu
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Xue Yang
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Xuetian Yue
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Huaying Wang
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Fan Zhou
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Juan M Inclan-Rico
- Department of Medicine, Rutgers New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - John J Ponessa
- Department of Medicine, Rutgers New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Lanjing Zhang
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Pathology, Penn Medicine Princeton Medical Center, Plainsboro, NJ, USA
| | - Mark C Siracusa
- Department of Medicine, Rutgers New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Zhaohui Feng
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
| | - Wenwei Hu
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
| |
Collapse
|
10
|
Hao Q, Chen J, Liao J, Huang Y, Gan Y, Larisch S, Zeng SX, Lu H, Zhou X. p53 induces ARTS to promote mitochondrial apoptosis. Cell Death Dis 2021; 12:204. [PMID: 33627621 PMCID: PMC7904775 DOI: 10.1038/s41419-021-03463-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 11/09/2022]
Abstract
Apoptosis related protein in TGF-β signaling pathway (ARTS) was originally discovered in cells undergoing apoptosis in response to TGF-β, but ARTS also acts downstream of many other apoptotic stimuli. ARTS induces apoptosis by antagonizing the anti-apoptotic proteins XIAP and Bcl-2. Here we identified the pro-apoptotic Sept4/ARTS gene as a p53-responsive target gene. Ectopic p53 and a variety of p53-inducing agents increased both mRNA and protein levels of ARTS, whereas ablation of p53 reduced ARTS expression in response to multiple stress conditions. Also, γ-irradiation induced p53-dependent ARTS expression in mice. Consistently, p53 binds to the responsive DNA element on the ARTS promoter and transcriptionally activated the promoter-driven expression of a luciferase reporter gene. Interestingly, ARTS binds to and sequesters p53 at mitochondria, enhancing the interaction of the latter with Bcl-XL. Ectopic ARTS markedly augments DNA damage stress- or Nutlin-3-triggered apoptosis, while ablation of ARTS preferentially impairs p53-induced apoptosis. Altogether, these findings demonstrate that ARTS collaborates with p53 in mitochondria-engaged apoptosis.
Collapse
Affiliation(s)
- Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jiaxiang Chen
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, China
| | - Junming Liao
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Yingdan Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yu Gan
- Department of Physiology, Medical College of Nanchang University, Nanchang, 330006, China
| | - Sarit Larisch
- Cell Death and Cancer Research Laboratory, Department of Biology, University of Haifa, Haifa, 31905, Israel
| | - Shelya X Zeng
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
11
|
Gong L, Zhang Q, Pan X, Chen S, Yang L, Liu B, Yang W, Yu L, Xiao ZX, Feng XH, Wang H, Yuan ZM, Peng J, Tan WQ, Chen J. p53 Protects Cells from Death at the Heatstroke Threshold Temperature. Cell Rep 2020; 29:3693-3707.e5. [PMID: 31825845 DOI: 10.1016/j.celrep.2019.11.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/12/2019] [Accepted: 11/07/2019] [Indexed: 01/28/2023] Open
Abstract
When the core body temperature is higher than 40°C, life is threatened due to heatstroke. Tumor repressor p53 is required for heat-induced apoptosis at hyperthermia conditions (>41°C). However, its role in sub-heatstroke conditions (≤40°C) remains unclear. Here, we reveal that both zebrafish and human p53 promote survival at 40°C, the heatstroke threshold temperature, by preventing a hyperreactive heat shock response (HSR). At 40°C, both Hsf1 and Hsp90 are activated. Hsf1 upregulates the expression of Hsc70 to trigger Hsc70-mediated protein degradation, whereas Hsp90 stabilizes p53 to repress the expression of Hsf1 and Hsc70, which prevents excessive HSR to maintain cell homeostasis. Under hyperthermia conditions, ATM is activated to phosphorylate p53 at S37, which increases BAX expression to induce apoptosis. Furthermore, growth of p53-deficient tumor xenografts, but not that of their p53+/+ counterparts, was inhibited by 40°C treatment. Our findings may provide a strategy for individualized therapy for p53-deficient cancers.
Collapse
Affiliation(s)
- Lu Gong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Qinghe Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao Pan
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuming Chen
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lina Yang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bin Liu
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, 74 Second Zhonshan Road, Guangzhou 510080, China
| | - Weijun Yang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Luyang Yu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Xin-Hua Feng
- Life Sciences Institute and Innovation Center for Signaling Network, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou 310058, China
| | - Haihe Wang
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, 74 Second Zhonshan Road, Guangzhou 510080, China
| | - Zhi-Min Yuan
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou 310058, China
| | - Wei-Qiang Tan
- Department of Plastic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Hangzhou 310016, China.
| | - Jun Chen
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
12
|
Jakubek P, Cieślewicz J, Bartoszek A. MicroRNAs as novel bioactive components of human breastmilk. POSTEP HIG MED DOSW 2020. [DOI: 10.5604/01.3001.0014.1434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs are short, non-coding oligonucleotides that regulate gene expression at the post-transcriptional level. These small molecules participate in the control of various cellular processes and signalling pathways. Since 2010 microRNAs have been recognized as a new bioactive component of breastmilk, which is an exceptionally rich source of these oligonucleotides. In infants fed with breastmilk, microRNAs are involved in the growth and proper development as well as maturation of the immune system. It has been demonstrated that microRNAs are resistant to harsh conditions during in vitro digestion in simulated gastrointestinal tract of a newborn and, therefore, may be absorbed by the intestinal cells. Protection against RNase activity and low pH is provided by exosomes, which are carriers of microRNAs in skim milk or by fat globules and milk cells. It has been reported that, in contrast to human milk, infant formulas contain only a few microRNAs, which have been derived from other organisms, such as cow or soy. It may be presumed that supplementing infant formulas with microRNAs identical
with those which occur naturally in breastmilk may constitute a new way of designing
artificial substitutes for human breastmilk.
Collapse
Affiliation(s)
- Patrycja Jakubek
- Katedra Chemii, Technologii i Biotechnologii Żywności, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
| | - Joanna Cieślewicz
- Katedra Chemii, Technologii i Biotechnologii Żywności, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
| | - Agnieszka Bartoszek
- Katedra Chemii, Technologii i Biotechnologii Żywności, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
| |
Collapse
|
13
|
P53 and The Immune Response: 40 Years of Exploration-A Plan for the Future. Int J Mol Sci 2020; 21:ijms21020541. [PMID: 31952115 PMCID: PMC7013403 DOI: 10.3390/ijms21020541] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
The p53 field was born from a marriage of the techniques of cancer virus research and immunology. Over the past 40 years, it has followed the path of cancer research. Now cancer treatments are turning to immunotherapy, and there are many hints of the role of the p53 protein in both the regulation of the innate immune system and as an antigen in adaptive immune responses. The p53 gene and protein are part of the innate immune system, and play an important role in infectious diseases, senescence, aging, and the surveillance of repetitive DNA and RNAs. The mutant form of the p53 protein in cancers elicits both a B-cell antibody response (a tumor antigen) and a CD-8 killer T-cell response (a tumor-specific transplantation antigen). The future will take the p53-immune response field of research into cancer immunotherapy, autoimmunity, inflammatory responses, neuro-degeneration, aging, and life span, and the regulation of epigenetic stability and tissue regeneration. The next 40 years will bring the p53 gene and its proteins out of a cancer focus and into an organismic and environmental focus.
Collapse
|
14
|
Zhang YX, Pan WY, Chen J. p53 and its isoforms in DNA double-stranded break repair. J Zhejiang Univ Sci B 2019; 20:457-466. [PMID: 31090271 DOI: 10.1631/jzus.b1900167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA double-stranded break (DSB) is one of the most catastrophic damages of genotoxic insult. Inappropriate repair of DNA DSBs results in the loss of genetic information, mutation, and the generation of harmful genomic rearrangements, which predisposes an organism to immunodeficiency, neurological damage, and cancer. The tumor repressor p53 plays a key role in DNA damage response, and has been found to be mutated in 50% of human cancer. p53, p63, and p73 are three members of the p53 gene family. Recent discoveries have shown that human p53 gene encodes at least 12 isoforms. Different p53 members and isoforms play various roles in orchestrating DNA damage response to maintain genomic integrity. This review briefly explores the functions of p53 and its isoforms in DNA DSB repair.
Collapse
Affiliation(s)
- Yu-Xi Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen-Ya Pan
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jun Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
15
|
Higgins CE, Tang J, Mian BM, Higgins SP, Gifford CC, Conti DJ, Meldrum KK, Samarakoon R, Higgins PJ. TGF-β1-p53 cooperativity regulates a profibrotic genomic program in the kidney: molecular mechanisms and clinical implications. FASEB J 2019; 33:10596-10606. [PMID: 31284746 PMCID: PMC6766640 DOI: 10.1096/fj.201900943r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/10/2019] [Indexed: 12/11/2022]
Abstract
Chronic kidney disease affects >15% of the U.S. population and >850 million individuals worldwide. Fibrosis is the common outcome of many chronic renal disorders and, although the etiology varies (i.e., diabetes, hypertension, ischemia, acute injury, and urologic obstructive disorders), persistently elevated renal TGF-β1 levels result in the relentless progression of fibrotic disease. TGF-β1 orchestrates the multifaceted program of renal fibrogenesis involving proximal tubular dysfunction, failed epithelial recovery and redifferentiation, and subsequent tubulointerstitial fibrosis, eventually leading to chronic renal disease. Recent findings implicate p53 as a cofactor in the TGF-β1-induced signaling pathway and a transcriptional coregulator of several TGF-β1 profibrotic response genes by complexing with receptor-activated SMADs, which are homologous to the small worms (SMA) and Drosophilia mothers against decapentaplegic (MAD) gene families. The cooperative p53-TGF-β1 genomic cluster includes genes involved in cell growth control and extracellular matrix remodeling [e.g., plasminogen activator inhibitor-1 (PAI-1; serine protease inhibitor, clade E, member 1), connective tissue growth factor, and collagen I]. Although the molecular basis for this codependency is unclear, many TGF-β1-responsive genes possess p53 binding motifs. p53 up-regulation and increased p53 phosphorylation; moreover, they are evident in nephrotoxin- and ischemia/reperfusion-induced injury, diabetic nephropathy, ureteral obstructive disease, and kidney allograft rejection. Pharmacologic and genetic approaches that target p53 attenuate expression of the involved genes and mitigate the fibrotic response, confirming a key role for p53 in renal disorders. This review focuses on mechanisms whereby p53 functions as a transcriptional regulator within the TGF-β1 cluster with an emphasis on the potent fibrosis-promoting PAI-1 gene.-Higgins, C. E., Tang, J., Mian, B. M., Higgins, S. P., Gifford, C. C., Conti, D. J., Meldrum, K. K., Samarakoon, R., Higgins, P. J. TGF-β1-p53 cooperativity regulates a profibrotic genomic program in the kidney: molecular mechanisms and clinical implications.
Collapse
Affiliation(s)
- Craig E. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - Jiaqi Tang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - Badar M. Mian
- The Urological Institute of Northeastern New York, Albany, New York, USA
- Division of Urology, Department of Surgery, Albany Medical College, Albany, New York, USA
| | - Stephen P. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - Cody C. Gifford
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - David J. Conti
- Division of Transplantation Surgery, Department of Surgery, Albany Medical College, Albany, New York, USA
| | - Kirstan K. Meldrum
- Division of Pediatric Urology, Central Michigan University, Mount Pleasant, Michigan, USA
| | - Rohan Samarakoon
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - Paul J. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
- The Urological Institute of Northeastern New York, Albany, New York, USA
- Division of Urology, Department of Surgery, Albany Medical College, Albany, New York, USA
| |
Collapse
|
16
|
Hu W, Feng Z. The role of p53 in reproduction, an unexpected function for a tumor suppressor. J Mol Cell Biol 2019; 11:624-627. [PMID: 31310660 PMCID: PMC6735926 DOI: 10.1093/jmcb/mjz072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 01/02/2023] Open
Affiliation(s)
| | - Zhaohui Feng
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08903, USA
| |
Collapse
|
17
|
Voce DJ, Bernal GM, Wu L, Crawley CD, Zhang W, Mansour NM, Cahill KE, Szymura SJ, Uppal A, Raleigh DR, Spretz R, Nunez L, Larsen G, Khodarev NN, Weichselbaum RR, Yamini B. Temozolomide Treatment Induces lncRNA MALAT1 in an NF-κB and p53 Codependent Manner in Glioblastoma. Cancer Res 2019; 79:2536-2548. [PMID: 30940658 DOI: 10.1158/0008-5472.can-18-2170] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/17/2019] [Accepted: 03/28/2019] [Indexed: 01/03/2023]
Abstract
Alkylating chemotherapy is a central component of the management of glioblastoma (GBM). Among the factors that regulate the response to alkylation damage, NF-κB acts to both promote and block cytotoxicity. In this study, we used genome-wide expression analysis in U87 GBM to identify NF-κB-dependent factors altered in response to temozolomide and found the long noncoding RNA (lncRNA) MALAT1 as one of the most significantly upregulated. In addition, we demonstrated that MALAT1 expression was coregulated by p50 (p105) and p53 via novel κB- and p53-binding sites in the proximal MALAT1 coding region. Temozolomide treatment inhibited p50 recruitment to its cognate element as a function of Ser329 phosphorylation while concomitantly increasing p53 recruitment. Moreover, luciferase reporter studies demonstrated that both κB and p53 cis-elements were required for efficient transactivation in response to temozolomide. Depletion of MALAT1 sensitized patient-derived GBM cells to temozolomide cytotoxicity, and in vivo delivery of nanoparticle-encapsulated anti-MALAT1 siRNA increased the efficacy of temozolomide in mice bearing intracranial GBM xenografts. Despite these observations, in situ hybridization of GBM specimens and analysis of publicly available datasets revealed that MALAT1 expression within GBM tissue was not prognostic of overall survival. Together, these findings support MALAT1 as a target for chemosensitization of GBM and identify p50 and p52 as primary regulators of this ncRNA. SIGNIFICANCE: These findings identify NF-κB and p53 as regulators of the lncRNA MALAT1 and suggest MALAT1 as a potential target for the chemosensitization of GBM.
Collapse
Affiliation(s)
- David J Voce
- Department of Neurosurgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Giovanna M Bernal
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois
| | - Longtao Wu
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois
| | - Clayton D Crawley
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois
| | - Wei Zhang
- Department of Preventative Medicine, Northwestern University, Chicago, Illinois
| | - Nassir M Mansour
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois
| | - Kirk E Cahill
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois
| | - Szymon J Szymura
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois
| | - Abhineet Uppal
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois
| | - David R Raleigh
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois
| | | | - Luis Nunez
- LNK Chemsolutions LLC, Lincoln, Nebraska
| | | | - Nikolai N Khodarev
- Department of Radiation and Cellular Oncology, and The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois
| | - Ralph R Weichselbaum
- Department of Radiation and Cellular Oncology, and The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois
| | - Bakhtiar Yamini
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, Illinois.
| |
Collapse
|
18
|
Hafner A, Bulyk ML, Jambhekar A, Lahav G. The multiple mechanisms that regulate p53 activity and cell fate. Nat Rev Mol Cell Biol 2019; 20:199-210. [DOI: 10.1038/s41580-019-0110-x] [Citation(s) in RCA: 452] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
19
|
Liu M, Wang Z, Liu Q, Zhu H, Xu N. Expression of Micro-RNA-492 (MiR-492) in Human Cervical Cancer Cell Lines is Upregulated by Transfection with Wild-Type P53, Irradiation, and 5-Fluorouracil Treatment In Vitro. Med Sci Monit 2018; 24:7750-7758. [PMID: 30374014 PMCID: PMC6354641 DOI: 10.12659/msm.911585] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The status of p53 is critical to the chemoradiosensitivity of cervical cancer cells. Wild-type p53 is essential to orchestrate the cellular response to cytotoxic stimuli. Our previous data illustrated that cervical cancer patients whose specimens overexpressed microR-492 (miR-492) were highly sensitive to concurrent chemoradiation. Although p53 activation has been reported to upregulate miR-492 by a miRNA profiling assay in lung cancer cells, the transcriptional regulation of miR-492 in cervical cancer cells remains poorly understood. Therefore, we aimed to decipher the relationship between p53 and miR-492 in cervical cancer cells. Material/Methods The expression of p53 and miR-492 in cervical cancer cell lines was measured by western blot and real-time PCR. After cells were transfected with wild-type p53 plasmid or were treated by irradiation and 5-fluorouracil (5-FU), the expression changes of p53 as well as miR-492 were examined by western blot and real-time PCR. The putative p53 binding site of miR-492 was first analyzed by bioinformatics tools, then validated by chromatin immunoprecipitation and dual-luciferase reporter assays. Results We found that miR-492 was upregulated in cells with wild-type p53 compared to cells with mutant p53. Transfection of wild-type p53 plasmid or treatments with cytotoxic reagents including irradiation and 5-FU all induced miR-492 overexpression. Bioinformatics analysis and experimental validations further proved p53 interacted with miR-492 promoter directly. Conclusions In cervical cancer cells, p53 activated miR-492 expression transcriptionally.
Collapse
Affiliation(s)
- Mei Liu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Zaozao Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, China (mainland)
| | - Qiao Liu
- Key Laboratory of Experimental Teratology (Ministry of Education), Department of Molecular Medicine and Genetics, School of Basic Medicine Sciences, Shandong University, Jinan, Shandong, China (mainland)
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China (mainland)
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| |
Collapse
|
20
|
Transposons, p53 and Genome Security. Trends Genet 2018; 34:846-855. [PMID: 30195581 DOI: 10.1016/j.tig.2018.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/31/2018] [Accepted: 08/07/2018] [Indexed: 12/16/2022]
Abstract
p53, the most commonly mutated tumor suppressor, is a transcription factor known to regulate proliferation, senescence, and apoptosis. Compelling studies have found that p53 may prevent oncogenesis through effectors that are unrelated to these canonical processes and recent findings have uncovered ancient roles for p53 in the containment of mobile elements. Together, these developments raise the possibility that some p53-driven cancers could result from unrestrained transposons. Here, we explore evidence linking conserved features of p53 biology to the control of transposons. We also show how p53-deficient cells can be exploited to probe the behavior of transposons and illustrate how unrestrained transposons incited by p53 loss might contribute to human malignancies.
Collapse
|
21
|
Zhao H, Wang J, Fang D, Lee O, Chatterton RT, Stearns V, Khan SA, Bulun SE. Adiposity Results in Metabolic and Inflammation Differences in Premenopausal and Postmenopausal Women Consistent with the Difference in Breast Cancer Risk. HORMONES & CANCER 2018; 9:229-239. [PMID: 29546532 PMCID: PMC10355891 DOI: 10.1007/s12672-018-0329-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/05/2018] [Indexed: 11/28/2022]
Abstract
Obesity is associated with increased risk of breast cancer in postmenopausal but not in premenopausal women. Many factors may be responsible for this difference. The aim of this study was to determine the mechanisms by which the genes related to the AMPK pathway, inflammation, and estrogen actions are affected by adiposity in breast tissue with the objective of identifying differences that may explain the different breast cancer risk in premenopausal and postmenopausal women. Random fine needle aspirates (rFNAs) of breast tissue were collected from 57 premenopausal and 55 postmenopausal women and were classified as normal weight, overweight, or obese. Expression levels of 21 target genes were determined using a TaqMan Low Density Array procedure. Breast tissue estradiol levels were measured by a liquid chromatography-tandem mass spectrometry procedure, and serum estradiol and follicle-stimulating hormone (FSH) were measured by a radioimmunoassay and an enzyme-linked immunosorbent assay, respectively. We found that in postmenopausal women, serum and tissue estradiol levels were increased in those who were overweight, and serum FSH levels were decreased in obese status. Interestingly, RPS6KB1, an AMPK downstream-responsive gene for protein synthesis and cell growth, and estrogen receptor α (encoded by the ESR1 gene) and its target gene GATA3 were significantly decreased in rFNA of premenopausal, obese women. In postmenopausal women, RPS6KB1, ESR1, and GATA3 expression remained unchanged in relation to adiposity. However, prostaglandin-endoperoxide synthase 2 (PTGS2), cyclin D1 (CCND1), and another ESR1 target gene, TFF1, were elevated in rFNA of obese postmenopausal women. Thus, as bodyweight increases, gene expression is indicative of increased proliferation in postmenopausal women but decreased proliferation in premenopausal women. Overall, our data reveal a novel process by which obesity promotes the risk of breast cancer in postmenopausal but not premenopausal women.
Collapse
Affiliation(s)
- H Zhao
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Robert H. Lurie Comprehensive Cancer Center, 303 E. Superior Street, Suite 4-121, Chicago, IL, 60611, USA.
| | - J Wang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - D Fang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - O Lee
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - R T Chatterton
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - V Stearns
- Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - S A Khan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - S E Bulun
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| |
Collapse
|
22
|
Wang GX, Tu HC, Dong Y, Skanderup AJ, Wang Y, Takeda S, Ganesan YT, Han S, Liu H, Hsieh JJ, Cheng EH. ΔNp63 Inhibits Oxidative Stress-Induced Cell Death, Including Ferroptosis, and Cooperates with the BCL-2 Family to Promote Clonogenic Survival. Cell Rep 2018; 21:2926-2939. [PMID: 29212036 DOI: 10.1016/j.celrep.2017.11.030] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/08/2017] [Accepted: 11/08/2017] [Indexed: 12/31/2022] Open
Abstract
The BCL-2 family proteins are central regulators of apoptosis. However, cells deficient for BAX and BAK or overexpressing BCL-2 still succumb to oxidative stress upon DNA damage or matrix detachment. Here, we show that ΔNp63α overexpression protects cells from oxidative stress induced by oxidants, DNA damage, anoikis, or ferroptosis-inducing agents. Conversely, ΔNp63α deficiency increases oxidative stress. Mechanistically, ΔNp63α orchestrates redox homeostasis through transcriptional control of glutathione biogenesis, utilization, and regeneration. Analysis of a lung squamous cell carcinoma dataset from The Cancer Genome Atlas (TCGA) reveals that TP63 amplification/overexpression upregulates the glutathione metabolism pathway in primary human tumors. Strikingly, overexpression of ΔNp63α promotes clonogenic survival of p53-/-Bax-/-Bak-/- cells against DNA damage. Furthermore, co-expression of BCL-2 and ΔNp63α confers clonogenic survival against matrix detachment, disrupts the luminal clearance of mammary acini, and promotes cancer metastasis. Our findings highlight the need for a simultaneous blockade of apoptosis and oxidative stress to promote long-term cellular well-being.
Collapse
Affiliation(s)
- Gary X Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Division of Biology & Biomedical Sciences, Washington University, St. Louis, MO 63110, USA
| | - Ho-Chou Tu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yiyu Dong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore, National University of Singapore, 60 Biopolis St., 138672 Singapore, Singapore
| | - Yufeng Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shugaku Takeda
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yogesh Tengarai Ganesan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Song Han
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Han Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James J Hsieh
- Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - Emily H Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.
| |
Collapse
|
23
|
Charni-Natan M, Solomon H, Molchadsky A, Jacob-Berger A, Goldfinger N, Rotter V. Various stress stimuli rewire the profile of liver secretome in a p53-dependent manner. Cell Death Dis 2018; 9:647. [PMID: 29844359 PMCID: PMC5974134 DOI: 10.1038/s41419-018-0697-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/01/2018] [Accepted: 05/07/2018] [Indexed: 12/25/2022]
Abstract
Liver is an important secretory organ that consistently manages various insults in order to retain whole-body homeostasis. Importantly, it was suggested that the tumor-suppressor p53 plays a role in a variety of liver physiological processes and thus it is being regarded as a systemic homeostasis regulator. Using high-throughput mass spectrometric analysis, we identified various p53-dependent liver secretome profiles. This allowed a global view on the role of p53 in maintaining the harmony of liver and whole-body homeostasis. We found that p53 altered the liver secretome differently under various conditions. Under physiological conditions, p53 controls factors that are related mainly to lipid metabolism and injury response. Upon exposure to various types of cancer therapy agents, the hepatic p53 is activated and induces the secretion of proteins related to additional pathways, such as hemostasis, immune response, and cell adhesion. Interestingly, we identified a possible relationship between p53-dependent liver functions and lung tumors. The latter modify differently liver secretome profile toward the secretion of proteins mainly related to cell migration and immune response. The notion that p53 may rewire the liver secretome profile suggests a new non-cell autonomous role of p53 that affect different liver functions and whole organism homeostasis.
Collapse
Affiliation(s)
- Meital Charni-Natan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hilla Solomon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alina Molchadsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Jacob-Berger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Goldfinger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
24
|
Chen X, Guan H, Liu XD, Xie DF, Wang Y, Ma T, Huang B, Zhou PK. p53 positively regulates the expression of cancer stem cell marker CD133 in HCT116 colon cancer cells. Oncol Lett 2018; 16:431-438. [PMID: 29928431 DOI: 10.3892/ol.2018.8619] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 11/16/2017] [Indexed: 02/06/2023] Open
Abstract
Colon cancer stem cells (CSCs), which are highly capable of self-renewal and proliferation, are involved in colon tumorigenesis and response to therapy. CD133 is considered the most robust surface marker for colorectal cancer stem cells. Although the TP53 gene is frequently mutated in colon cancer, it remains not fully understood whether and how tumor protein p53 (p53) is associated with CD133 expression in colon cancer cells. In the present study, the expression of the CSC biomarker CD133 was investigated in terms of p53 status in colorectal carcinoma HCT116 cells. p53 wild-type HCT116 (HCT116 p53+/+) and depleted HCT116 (HCT116 p53-/-) cells were used throughout this study. Cells carrying the CSC biomarkers CD133 and CD44 were examined by flow cytometry. A dual-luciferase reporter assay was employed to further confirm the transcriptional regulation of the CD133 promoter by p53. The results demonstrated that there was a significant difference in the % of CD133-positive cells between the HCT116 p53+/+ cell line (84.84±0.05%) and the HCT116 p53-/- cell line (4.13±0.02%). The mRNA expression levels of CD133 in HCT116 p53+/+ cells were also significantly higher compared with HCT116 p53-/- cells. Knockdown of p53 by specific small interfering RNA greatly reduced the expression of CD133 in HCT116 p53+/+ cells. Transcription factor binding site analysis indicated that there are several p53 binding elements in the CD133 promoter region. A dual-luciferase reporter assay further demonstrated the transcriptional activation of CD133 promoter by p53. In conclusion, these results suggest that p53 positively regulates the expression of CSC marker CD133 in the HCT116 human colon colorectal cancer cell line. p53 may be involved in the initiation and maintenance of colorectal cancer stem cells through regulating the expression of CD133.
Collapse
Affiliation(s)
- Xia Chen
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan 421001, P.R. China.,Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Hua Guan
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Xiao-Dan Liu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Da-Fei Xie
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Yu Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Teng Ma
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| | - Bo Huang
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Ping-Kun Zhou
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan 421001, P.R. China.,Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China
| |
Collapse
|
25
|
Higgins SP, Tang Y, Higgins CE, Mian B, Zhang W, Czekay RP, Samarakoon R, Conti DJ, Higgins PJ. TGF-β1/p53 signaling in renal fibrogenesis. Cell Signal 2017; 43:1-10. [PMID: 29191563 DOI: 10.1016/j.cellsig.2017.11.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 01/04/2023]
Abstract
Fibrotic disorders of the renal, pulmonary, cardiac, and hepatic systems are associated with significant morbidity and mortality. Effective therapies to prevent or curtail the advancement to organ failure, however, remain a major clinical challenge. Chronic kidney disease, in particular, constitutes an increasing medical burden affecting >15% of the US population. Regardless of etiology (diabetes, hypertension, ischemia, acute injury, urologic obstruction), persistently elevated TGF-β1 levels are causatively linked to the activation of profibrotic signaling networks and disease progression. TGF-β1 is the principal driver of renal fibrogenesis, a dynamic pathophysiologic process that involves tubular cell injury/apoptosis, infiltration of inflammatory cells, interstitial fibroblast activation and excess extracellular matrix synthesis/deposition leading to impaired kidney function and, eventually, to chronic and end-stage disease. TGF-β1 activates the ALK5 type I receptor (which phosphorylates SMAD2/3) as well as non-canonical (e.g., src kinase, EGFR, JAK/STAT, p53) pathways that collectively drive the fibrotic genomic program. Such multiplexed signal integration has pathophysiological consequences. Indeed, TGF-β1 stimulates the activation and assembly of p53-SMAD3 complexes required for transcription of the renal fibrotic genes plasminogen activator inhibitor-1, connective tissue growth factor and TGF-β1. Tubular-specific ablation of p53 in mice or pifithrin-α-mediated inactivation of p53 prevents epithelial G2/M arrest, reduces the secretion of fibrotic effectors and attenuates the transition from acute to chronic renal injury, further supporting the involvement of p53 in disease progression. This review focuses on the pathophysiology of TGF-β1-initiated renal fibrogenesis and the role of p53 as a regulator of profibrotic gene expression.
Collapse
Affiliation(s)
- Stephen P Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Yi Tang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Craig E Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Badar Mian
- Department of Surgery, Albany Medical College, Albany, NY 12208, United States; The Urological Institute of Northeastern New York, Albany Medical College, Albany, NY 12208, United States.
| | - Wenzheng Zhang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Ralf-Peter Czekay
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - Rohan Samarakoon
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States.
| | - David J Conti
- Department of Surgery, Albany Medical College, Albany, NY 12208, United States; Division of Transplantation Surgery, Albany Medical College, Albany, NY 12208, United States.
| | - Paul J Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208, United States; Department of Surgery, Albany Medical College, Albany, NY 12208, United States; The Urological Institute of Northeastern New York, Albany Medical College, Albany, NY 12208, United States.
| |
Collapse
|
26
|
Solomon H, Bräuning B, Fainer I, Ben-Nissan G, Rabani S, Goldfinger N, Moscovitz O, Shakked Z, Rotter V, Sharon M. Post-translational regulation of p53 function through 20S proteasome-mediated cleavage. Cell Death Differ 2017; 24:2187-2198. [PMID: 28885617 DOI: 10.1038/cdd.2017.139] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 12/24/2022] Open
Abstract
The tumor suppressor p53 is a transcription factor that regulates the expression of a range of target genes in response to cellular stress. Adding to the complexity of understanding its cellular function is that in addition to the full-length protein, several p53 isoforms are produced in humans, harboring diverse expression patterns and functionalities. One isoform, Δ40p53, which lacks the first transactivation domain including the binding region for the negative regulator MDM2, was shown to be a product of alternative translation initiation. Here we report the discovery of an alternative cellular mechanism for Δ40p53 formation. We show that the 20S proteasome specifically cleaves the full-length protein (FLp53) to generate the Δ40p53 isoform. Moreover, we demonstrate that a dimer of FLp53 interacts with a Δ40p53 dimer, creating a functional hetero-tetramer. Consequently, the co-expression of both isoforms attenuates the transcriptional activity of FLp53 in a dominant negative manner. Finally, we demonstrate that following oxidative stress, at the time when the 20S proteasome becomes the major degradation machinery and FLp53 is activated, the formation of Δ40p53 is enhanced, creating a negative feedback loop that balances FLp53 activation. Overall, our results suggest that Δ40p53 can be generated by a 20S proteasome-mediated post-translational mechanism so as to control p53 function. More generally, the discovery of a specific cleavage function for the 20S proteasome may represent a more general cellular regulatory mechanism to produce proteins with distinct functional properties.
Collapse
Affiliation(s)
- Hilla Solomon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bastian Bräuning
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Stav Rabani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naomi Goldfinger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Oren Moscovitz
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zippora Shakked
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| |
Collapse
|
27
|
Melnik BC. Milk disrupts p53 and DNMT1, the guardians of the genome: implications for acne vulgaris and prostate cancer. Nutr Metab (Lond) 2017; 14:55. [PMID: 28814964 PMCID: PMC5556685 DOI: 10.1186/s12986-017-0212-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/08/2017] [Indexed: 02/06/2023] Open
Abstract
There is accumulating evidence that milk shapes the postnatal metabolic environment of the newborn infant. Based on translational research, this perspective article provides a novel mechanistic link between milk intake and milk miRNA-regulated gene expression of the transcription factor p53 and DNA methyltransferase 1 (DNMT1), two guardians of the human genome, that control transcriptional activity, cell survival, and apoptosis. Major miRNAs of milk, especially miRNA-125b, directly target TP53 and complex p53-dependent gene regulatory networks. TP53 regulates the expression of key genes involved in cell homeostasis such as FOXO1, PTEN, SESN1, SESN2, AR, IGF1R, BAK1, BIRC5, and TNFSF10. Nuclear interaction of p53 with DNMT1 controls gene silencing. The most abundant miRNA of milk and milk fat, miRNA-148a, directly targets DNMT1. Reduced DNMT1 expression further attenuates the activity of histone deacetylase 1 (HDAC1) involved in the regulation of chromatin structure and access to transcription. The presented milk-mediated miRNA-p53-DNMT1 pathway exemplified at the promoter regulation of survivin (BIRC5) provides a novel explanation for the epidemiological association between milk consumption and acne vulgaris and prostate cancer. Notably, p53- and DNMT1-targeting miRNAs of bovine and human milk survive pasteurization and share identical seed sequences, which theoretically allows the interaction of bovine miRNAs with the human genome. Persistent intake of milk-derived miRNAs that attenuate p53- and DNMT1 signaling of the human milk consumer may thus present an overlooked risk factor promoting acne vulgaris, prostate cancer, and other p53/DNMT1-related Western diseases. Therefore, bioactive miRNAs of commercial milk should be eliminated from the human food chain.
Collapse
Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, Am Finkenhügel 7a, D-49076 Osnabrück, Germany
| |
Collapse
|
28
|
An alternative microRNA-mediated post-transcriptional regulation of GADD45A by p53 in human non-small-cell lung cancer cells. Sci Rep 2017; 7:7153. [PMID: 28769054 PMCID: PMC5541050 DOI: 10.1038/s41598-017-07332-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/28/2017] [Indexed: 01/30/2023] Open
Abstract
GADD45A (growth arrest and DNA damage inducible alpha), a stress response gene induced by genotoxic and nongenotoxic stresses, is implicated in various key processes, including the control of cell cycle checkpoints and DNA repair. The expression of GADD45A is directly regulated by numerous transcription factors, with p53 being the most representative. Moreover, post-transcriptional regulation also plays a role in GADD45A expression. However, little is known about the regulatory effects of microRNAs (miRNAs) on GADD45A expression. As a potential tumour suppressor, miR-138 has pleiotropic biological functions in various cancers. We have previously reported p53-mediated activation of miR-138 in human non-small-cell lung cancer (NSCLC) cells. In this study, we found that miR-138 specifically targeted AGO2, which affects the stability and maturation of miR-130b. Decreased expression of miR-130b promoted the expression of GADD45A and resulted in the G2/M phase arrest and proliferation inhibition in human NSCLC cells. Our results suggested that p53 could alternatively upregulate GADD45A in human NSCLC cells through a post-transcriptional pathway in which miR-138 is involved.
Collapse
|
29
|
Chen G, Zhou T, Li Y, Yu Z, Sun L. p53 target miR-29c-3p suppresses colon cancer cell invasion and migration through inhibition of PHLDB2. Biochem Biophys Res Commun 2017; 487:90-95. [PMID: 28392396 DOI: 10.1016/j.bbrc.2017.04.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 04/06/2017] [Indexed: 12/28/2022]
Abstract
miR-29c-3p is a potential tumor suppressor microRNA that is reportedly downregulated in several types of human cancers, but its role in colon cancer remains to be elucidated. Meanwhile, TP53, one of the most important tumor suppressors, is highly mutated in colon cancer. In the attempt to connect p53 and miR-29c-3p, we found that the upstream of miR-29c-3p gene contains a functional p53 consensus responsive element that is driven by p53 transcriptional factor activity, suggesting miR-29c-3p as a direct p53 target gene. Through online software prediction and in vivo validation, we demonstrated that Pleckstrin Homology Like Domain Family Member 2 (PHLDB2) is a valid miR-29c-3p target gene. Analysis of human cancer databases available from PROGgeneV2 showed that higher expression of PHLDB2 is associated with shorter overall survival and metastasis-free survival of colon cancer patients. Further, suppression of colon cancer cell invasion and migration by miR-29c-3p was significantly attenuated in the presence of ectopic PHLDB2, indicating PHLDB2 is a critical downstream target of miR-29c-3p. Collectively, our findings present the first to elucidate that miR-29c is a direct p53 target gene, and also identify PHLDB2 as an important miR-29c target gene involved in colon cancer metastasis.
Collapse
Affiliation(s)
- Geng Chen
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, 130021, China; Department of Gastroenterology, The First Hospital of Jilin University, Changchun, 130021, China
| | - Tong Zhou
- Department of Endocrinology, The First Hospital of Jilin University, Changchun, 130021, China
| | - Yang Li
- Department of Respiration, The First Hospital of Jilin University, Changchun, 130021, China
| | - Zhenxiang Yu
- Department of Respiration, The First Hospital of Jilin University, Changchun, 130021, China
| | - Liankun Sun
- Department of Pathophysiology, Basic College of Medicine, Jilin University, Changchun, 130021, China.
| |
Collapse
|
30
|
Abstract
This perspective will focus on the physiological impact of wild-type and mutant p53 activities. In particular, the tissue-specific nature of activation of p53 targets and their subsequent effects on cell behavior will be discussed. Because mutations in p53 are common in human cancers, the regulation and physiological consequences of mutant p53 proteins will also be discussed.
Collapse
|
31
|
Epigenetic inactivation of the p53-induced long noncoding RNA TP53 target 1 in human cancer. Proc Natl Acad Sci U S A 2016; 113:E7535-E7544. [PMID: 27821766 DOI: 10.1073/pnas.1608585113] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are important regulators of cellular homeostasis. However, their contribution to the cancer phenotype still needs to be established. Herein, we have identified a p53-induced lncRNA, TP53TG1, that undergoes cancer-specific promoter hypermethylation-associated silencing. In vitro and in vivo assays identify a tumor-suppressor activity for TP53TG1 and a role in the p53 response to DNA damage. Importantly, we show that TP53TG1 binds to the multifaceted DNA/RNA binding protein YBX1 to prevent its nuclear localization and thus the YBX1-mediated activation of oncogenes. TP53TG1 epigenetic inactivation in cancer cells releases the transcriptional repression of YBX1-targeted growth-promoting genes and creates a chemoresistant tumor. TP53TG1 hypermethylation in primary tumors is shown to be associated with poor outcome. The epigenetic loss of TP53TG1 therefore represents an altered event in an lncRNA that is linked to classical tumoral pathways, such as p53 signaling, but is also connected to regulatory networks of the cancer cell.
Collapse
|
32
|
Identification of p53-target genes in Danio rerio. Sci Rep 2016; 6:32474. [PMID: 27581768 PMCID: PMC5007497 DOI: 10.1038/srep32474] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/08/2016] [Indexed: 11/22/2022] Open
Abstract
To orchestrate the genomic response to cellular stress signals, p53 recognizes and binds to DNA containing specific and well-characterized p53-responsive elements (REs). Differences in RE sequences can strongly affect the p53 transactivation capacity and occur even between closely related species. Therefore, the identification and characterization of a species-specific p53 Binding sistes (BS) consensus sequence and of the associated target genes may help to provide new insights into the evolution of the p53 regulatory networks across different species. Although p53 functions were studied in a wide range of species, little is known about the p53-mediated transcriptional signature in Danio rerio. Here, we designed and biochemically validated a computational approach to identify novel p53 target genes in Danio rerio genome. Screening all the Danio rerio genome by pattern-matching-based analysis, we found p53 RE-like patterns proximal to 979 annotated Danio rerio genes. Prioritization analysis identified a subset of 134 candidate pattern-related genes, 31 of which have been investigated in further biochemical assays. Our study identified runx1, axin1, traf4a, hspa8, col4a5, necab2, and dnajc9 genes as novel direct p53 targets and 12 additional p53-controlled genes in Danio rerio genome. The proposed combinatorial approach resulted to be highly sensitive and robust for identifying new p53 target genes also in additional animal species.
Collapse
|
33
|
Baudot AD, Crighton D, O'Prey J, Somers J, Sierra Gonzalez P, Ryan KM. p53 directly regulates the glycosidase FUCA1 to promote chemotherapy-induced cell death. Cell Cycle 2016; 15:2299-308. [PMID: 27315169 PMCID: PMC5004703 DOI: 10.1080/15384101.2016.1191714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/11/2016] [Accepted: 05/14/2016] [Indexed: 12/16/2022] Open
Abstract
p53 is a central factor in tumor suppression as exemplified by its frequent loss in human cancer. p53 exerts its tumor suppressive effects in multiple ways, but the ability to invoke the eradication of damaged cells by programmed cell death is considered a key factor. The ways in which p53 promotes cell death can involve direct activation or engagement of the cell death machinery, or can be via indirect mechanisms, for example though regulation of ER stress and autophagy. We present here another level of control in p53-mediated tumor suppression by showing that p53 activates the glycosidase, FUCA1, a modulator of N-linked glycosylation. We show that p53 transcriptionally activates FUCA1 and that p53 modulates fucosidase activity via FUCA1 up-regulation. Importantly, we also report that chemotherapeutic drugs induce FUCA1 and fucosidase activity in a p53-dependent manner. In this context, while we found that over-expression of FUCA1 does not induce cell death, RNAi-mediated knockdown of endogenous FUCA1 significantly attenuates p53-dependent, chemotherapy-induced apoptotic death. In summary, these findings add an additional component to p53s tumor suppressive response and highlight another mechanism by which the tumor suppressor controls programmed cell death that could potentially be exploited for cancer therapy.
Collapse
Affiliation(s)
- Alice D. Baudot
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, Scotland, UK
| | - Diane Crighton
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, Scotland, UK
| | - Jim O'Prey
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, Scotland, UK
| | - Joanna Somers
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, Scotland, UK
| | | | - Kevin M. Ryan
- Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, Scotland, UK
| |
Collapse
|
34
|
Cao B, Wang K, Liao JM, Zhou X, Liao P, Zeng SX, He M, Chen L, He Y, Li W, Lu H. Inactivation of oncogenic cAMP-specific phosphodiesterase 4D by miR-139-5p in response to p53 activation. eLife 2016; 5. [PMID: 27383270 PMCID: PMC4959878 DOI: 10.7554/elife.15978] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/29/2016] [Indexed: 12/13/2022] Open
Abstract
Increasing evidence highlights the important roles of microRNAs in mediating p53’s tumor suppression functions. Here, we report miR-139-5p as another new p53 microRNA target. p53 induced the transcription of miR-139-5p, which in turn suppressed the protein levels of phosphodiesterase 4D (PDE4D), an oncogenic protein involved in multiple tumor promoting processes. Knockdown of p53 reversed these effects. Also, overexpression of miR-139-5p decreased PDE4D levels and increased cellular cAMP levels, leading to BIM-mediated cell growth arrest. Furthermore, our analysis of human colorectal tumor specimens revealed significant inverse correlation between the expression of miR-139-5p and that of PDE4D. Finally, overexpression of miR-139-5p suppressed the growth of xenograft tumors, accompanied by decrease in PDE4D and increase in BIM. These results demonstrate that p53 inactivates oncogenic PDE4D by inducing the expression of miR-139-5p. DOI:http://dx.doi.org/10.7554/eLife.15978.001 The human body is kept mostly free from tumors by the actions of so-called tumor suppressor genes. One such gene encodes a protein called p53, which prevents tumors from growing by regulating the activity of many other genes that either inhibit cell growth or cause cells to die. For example, p53 regulates genes that encode short molecules called microRNAs, which in turn suppress the activity of other target genes. Although a number of microRNAs have been reported as p53-regulated genes, there are still more to find. Discovering these genes would in turn help researchers to better understand exactly how p53 acts to suppress the growth of tumors, and to treat cancers caused by mutations in this tumor suppressor gene. Cao, Wang et al. now discover a new microRNA – called miR-139-5p – as one that is activated by p53 in human cells. Colon tumors produce much lower levels of this microRNA than normal tissues, while the cancer cells with a higher level of miR-139-5p grow slower than do the cancer cells with less miR-139-5p. Further experiments showed that this is because miR-139-5p can suppress the production of a protein called PDE4D, which is often highly expressed in human cancers. The suppression of PDE4D by this microRNA results in an increase in the levels of a protein that can cause cancer cells to die. Cao, Wang et al. suggest that miR-139-5p and PDE4D form part of a signaling pathway that plays an important role in suppressing the growth of colon cancer cells. Since microRNAs often have more than one target, future studies could explore if miR-139-5p regulates the production of other cancer-related proteins as well. DOI:http://dx.doi.org/10.7554/eLife.15978.002
Collapse
Affiliation(s)
- Bo Cao
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, United States
| | - Kebing Wang
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jun-Ming Liao
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, United States
| | - Xiang Zhou
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, United States
| | - Peng Liao
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, United States
| | - Shelya X Zeng
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, United States
| | - Meifang He
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lianzhou Chen
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yulong He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wen Li
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, United States
| |
Collapse
|
35
|
Monteith JA, Mellert H, Sammons MA, Kuswanto LA, Sykes SM, Resnick-Silverman L, Manfredi JJ, Berger SL, McMahon SB. A rare DNA contact mutation in cancer confers p53 gain-of-function and tumor cell survival via TNFAIP8 induction. Mol Oncol 2016; 10:1207-20. [PMID: 27341992 DOI: 10.1016/j.molonc.2016.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 01/15/2023] Open
Abstract
The p53 tumor suppressor gene encodes a sequence-specific transcription factor. Mutations in the coding sequence of p53 occur frequently in human cancer and often result in single amino acid substitutions (missense mutations) in the DNA binding domain (DBD), blocking normal tumor suppressive functions. In addition to the loss of canonical functions, some missense mutations in p53 confer gain-of-function (GOF) activities to tumor cells. While many missense mutations in p53 cluster at six "hotspot" amino acids, the majority of mutations in human cancer occur elsewhere in the DBD and at a much lower frequency. We report here that mutations at K120, a non-hotspot DNA contact residue, confer p53 with the previously unrecognized ability to bind and activate the transcription of the pro-survival TNFAIP8 gene. Mutant K120 p53 binds the TNFAIP8 locus at a cryptic p53 response element that is not occupied by wild-type p53. Furthermore, induction of TNFAIP8 is critical for the evasion of apoptosis by tumor cells expressing the K120R variant of p53. These findings identify induction of pro-survival targets as a mechanism of gain-of-function activity for mutant p53 and will likely broaden our understanding of this phenomenon beyond the limited number of GOF activities currently reported for hotspot mutants.
Collapse
Affiliation(s)
- Jessica A Monteith
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th Street, Philadelphia, PA 19107, United States.
| | - Hestia Mellert
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th Street, Philadelphia, PA 19107, United States.
| | - Morgan A Sammons
- Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, 9-125 Smilow Center for Translational Research, Philadelphia, PA 19104, United States.
| | - Laudita A Kuswanto
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th Street, Philadelphia, PA 19107, United States; University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, United States.
| | - Stephen M Sykes
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th Street, Philadelphia, PA 19107, United States; Medical Genetics and Molecular Biology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, United States.
| | - Lois Resnick-Silverman
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - James J Manfredi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Shelley L Berger
- Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, 9-125 Smilow Center for Translational Research, Philadelphia, PA 19104, United States.
| | - Steven B McMahon
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th Street, Philadelphia, PA 19107, United States.
| |
Collapse
|
36
|
Chan C, Thurnherr T, Wang J, Gallart-Palau X, Sze SK, Rozen S, Lee CG. Global re-wiring of p53 transcription regulation by the hepatitis B virus X protein. Mol Oncol 2016; 10:1183-95. [PMID: 27302019 DOI: 10.1016/j.molonc.2016.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The tumour suppressor p53 is a central player in transcription regulation and cell fate determination. By interacting with p53 and altering its sequence-specific binding to the response elements, the hepatitis B virus X protein (HBx) was reported to re-direct p53 regulation of some genes. RESULTS Coupling massively parallel deep sequencing with p53 chromatin immunoprecipitation, we demonstrate that HBx modulates global p53 site selection and that this was strongly influenced by altered interaction with transcription co-factors/co-regulators as well as post-translational modifications. Specifically, HBx attenuated p53-TBP-RB1 transcription complex recruitment and interaction and this was associated with hyper-phosphorylation of p53 at serine 315 by HBx. Concurrently, HBx enhanced p53 DNA occupancy to other response elements either alone by displacing specific transcription factors such as CEBPB and NFkB1, or in complex with distinct interacting co-factors Sp1, JUN and E2F1. Importantly, re-wiring of p53 transcription regulation by HBx was linked to the deregulation of genes involved in cell proliferation and death, suggesting a role of HBx in errant cell fate determination mediated by altered p53 site selection of target genes. CONCLUSIONS Our study thus presents first evidence of global modes of p53 transcription alteration by HBx and provides new insights to understand and potentially curtail the viral oncoprotein.
Collapse
Affiliation(s)
- Cheryl Chan
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 169610, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore; Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Jingbo Wang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Steve Rozen
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Caroline G Lee
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 169610, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore; Duke-NUS Graduate Medical School, Singapore 169857, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| |
Collapse
|
37
|
Li J, Xia W, Su X, Qin X, Chen Y, Li S, Dong J, Ding H, Li H, Huang A, Ge X, Hou L, Wang C, Sun L, Bai C, Shen X, Fang T, Liu Y, Zhang Y, Zhang H, Zhang H, Shao N. Species-specific mutual regulation of p53 and miR-138 between human, rat and mouse. Sci Rep 2016; 6:26187. [PMID: 27183959 PMCID: PMC4869026 DOI: 10.1038/srep26187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/27/2016] [Indexed: 12/31/2022] Open
Abstract
In recent years, p53 was identified to regulate the expression of many miRNAs and was also regulated by miRNAs. In this paper, we found that miR-138 showed a pronounced increase after p53 activation in human non-small cell lung cancer (NSCLC) cells, which is mediated by p53 binding sites in the promoter region of its host gene, but this did not happen with rat and mouse cells. More interestingly, we found that p53 could be also regulated by miR-138 in mouse and rat cells, but not in the human NSCLC cells. Our results suggest the existence of species-specific differences of the regulations of miRNA against its targets and the regulations of miRNA itself by other proteins.
Collapse
Affiliation(s)
- Jie Li
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Wei Xia
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xueting Su
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xingliang Qin
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Ying Chen
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Shaohua Li
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jie Dong
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Hongmei Ding
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Hui Li
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Aixue Huang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xingfeng Ge
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Lvbin Hou
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Chaonan Wang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Leqiao Sun
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Chenjun Bai
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xuelian Shen
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Tao Fang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Yuanlin Liu
- Department of Cell Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Yi Zhang
- Department of Cell Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Hongru Zhang
- Otorhinolaryngological department, Haidian Section of Peking University third Hospital, Beijing 100080, China
| | - Hongwen Zhang
- Department of Interventional Radiology, General Hospital of Fuzhou, Fuzhou, China
| | - Ningsheng Shao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Beijing 100850, China
| |
Collapse
|
38
|
Levine AJ, Ting DT, Greenbaum BD. P53 and the defenses against genome instability caused by transposons and repetitive elements. Bioessays 2016; 38:508-13. [PMID: 27172878 PMCID: PMC5031199 DOI: 10.1002/bies.201600031] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The recent publication by Wylie et al. is reviewed, demonstrating that the p53 protein regulates the movement of transposons. While this work presents genetic evidence for a piRNA‐mediated p53 interaction with transposons in Drosophila and zebrafish, it is herein placed in the context of a decade or so of additional work that demonstrated a role for p53 in regulating transposons and other repetitive elements. The line of thought in those studies began with the observation that transposons damage DNA and p53 regulates DNA damage. The presence of transposon movement can increase the rate of evolution in the germ line and alter genes involved in signal transduction pathways. Transposition can also play an important role in cancers where the p53 gene function is often mutated. This is particularly interesting as recent work has shown that de‐repression of repetitive elements in cancer has important consequences for the immune system and tumor microenvironment.
Collapse
Affiliation(s)
- Arnold J Levine
- Institute for Advanced Study, School of Natural Sciences, The Simons Center for Systems Biology, Princeton, NJ, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Benjamin D Greenbaum
- Department of Medicine, Hematology, and Medical Oncology, and Pathology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
39
|
Laptenko O, Shiff I, Freed-Pastor W, Zupnick A, Mattia M, Freulich E, Shamir I, Kadouri N, Kahan T, Manfredi J, Simon I, Prives C. The p53 C terminus controls site-specific DNA binding and promotes structural changes within the central DNA binding domain. Mol Cell 2016; 57:1034-1046. [PMID: 25794615 DOI: 10.1016/j.molcel.2015.02.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/23/2014] [Accepted: 02/06/2015] [Indexed: 11/19/2022]
Abstract
DNA binding by numerous transcription factors including the p53 tumor suppressor protein constitutes a vital early step in transcriptional activation. While the role of the central core DNA binding domain (DBD) of p53 in site-specific DNA binding has been established, the contribution of the sequence-independent C-terminal domain (CTD) is still not well understood. We investigated the DNA-binding properties of a series of p53 CTD variants using a combination of in vitro biochemical analyses and in vivo binding experiments. Our results provide several unanticipated and interconnected findings. First, the CTD enables DNA binding in a sequence-dependent manner that is drastically altered by either its modification or deletion. Second, dependence on the CTD correlates with the extent to which the p53 binding site deviates from the canonical consensus sequence. Third, the CTD enables stable formation of p53-DNA complexes to divergent binding sites via DNA-induced conformational changes within the DBD itself.
Collapse
Affiliation(s)
- Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Idit Shiff
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel
| | - Will Freed-Pastor
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Andrew Zupnick
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Melissa Mattia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ella Freulich
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Inbal Shamir
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel
| | - Noam Kadouri
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel
| | - Tamar Kahan
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel
| | - James Manfredi
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Hebrew University Medical School, IMRIC, Jerusalem 91120, Israel.
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| |
Collapse
|
40
|
Liao JM, Cao B, Deng J, Zhou X, Strong M, Zeng S, Xiong J, Flemington E, Lu H. TFIIS.h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene. Sci Rep 2016; 6:23542. [PMID: 27005522 PMCID: PMC4804275 DOI: 10.1038/srep23542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/03/2016] [Indexed: 11/09/2022] Open
Abstract
Tumor suppressor p53 transcriptionally regulates hundreds of genes involved in various cellular functions. However, the detailed mechanisms underlying the selection of p53 targets in response to different stresses are still elusive. Here, we identify TFIIS.h, a transcription elongation factor, as a new transcriptional target of p53, and also show that it can enhance the efficiency of transcription elongation of apoptosis-associated bax gene, but not cell cycle-associated p21 (CDKN1A) gene. TFIIS.h is revealed as a p53 target through microarray analysis of RNAs extracted from cells treated with or without inauhzin (INZ), a p53 activator, and further confirmed by RT-q-PCR, western blot, luciferase reporter, and ChIP assays. Interestingly, knocking down TFIIS.h impairs, but overexpressing TFIIS.h promotes, induction of bax, but not other p53 targets including p21, by p53 activation. In addition, overexpression of TFIIS.h induces cell death in a bax- dependent fashion. These findings reveal a mechanism by which p53 utilizes TFIIS.h to selectively promote the transcriptional elongation of the bax gene, upsurging cell death in response to severe DNA damage.
Collapse
Affiliation(s)
- Jun-Ming Liao
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Bo Cao
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Jun Deng
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA.,Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Xiang Zhou
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Michael Strong
- Department of Pathology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Shelya Zeng
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Jianping Xiong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Erik Flemington
- Department of Pathology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Hua Lu
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| |
Collapse
|
41
|
Yeo SY, Itahana Y, Guo AK, Han R, Iwamoto K, Nguyen HT, Bao Y, Kleiber K, Wu YJ, Bay BH, Voorhoeve M, Itahana K. Transglutaminase 2 contributes to a TP53-induced autophagy program to prevent oncogenic transformation. eLife 2016; 5:e07101. [PMID: 26956429 PMCID: PMC4798945 DOI: 10.7554/elife.07101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 01/13/2016] [Indexed: 12/19/2022] Open
Abstract
Genetic alterations which impair the function of the TP53 signaling pathway in TP53 wild-type human tumors remain elusive. To identify new components of this pathway, we performed a screen for genes whose loss-of-function debilitated TP53 signaling and enabled oncogenic transformation of human mammary epithelial cells. We identified transglutaminase 2 (TGM2) as a putative tumor suppressor in the TP53 pathway. TGM2 suppressed colony formation in soft agar and tumor formation in a xenograft mouse model. The depletion of growth supplements induced both TGM2 expression and autophagy in a TP53-dependent manner, and TGM2 promoted autophagic flux by enhancing autophagic protein degradation and autolysosome clearance. Reduced expression of both CDKN1A, which regulates the cell cycle downstream of TP53, and TGM2 synergized to promote oncogenic transformation. Our findings suggest that TGM2-mediated autophagy and CDKN1A-mediated cell cycle arrest are two important barriers in the TP53 pathway that prevent oncogenic transformation. DOI:http://dx.doi.org/10.7554/eLife.07101.001 Cancers grow from rogue cells that manage to defy the strict rules that normally stop a cell from dividing when it should not. Each cell contains many proteins that are responsible for implementing these rules, and thus help to prevent tumors from forming. One of these proteins – p53 (which is also called TP53) – plays a central role in this process. Information about many processes within and around a cell filters through the p53 protein, before being passed on to a range of different proteins. The proteins that are alerted by p53 are commonly referred to as its 'downstream effectors', and it is these proteins that stop cells from dividing too much. For example, the protein p21 (also called CDKN1A) – which is the best understood of p53’s downstream effectors – hinders the machinery that causes cells to divide. Other p53 effectors can cause cells to kill themselves to prevent cancer growth. However, recent experiments with mice predicted that there may be other p53’s effectors that are important too. Yeo, Itahana et al. have now depleted the proteins that potentially work in p53’s network, one by one, in human cells called mammary epithelial cells, to test if these cells can become cancerous in the laboratory. The experiments showed that another downstream effector protein of p53 – an enzyme called transglutaminase 2 – contributes to prevent these mammary epithelial cells from becoming cancerous. Transglutaminase 2 promotes a process known as autophagy, which recycles damaged and old components of the cell, and therefore normally helps to keep cells healthy. Yeo, Itahana et al. also demonstrated that the effects of both p21 and transglutaminase 2 are critical to stop human mammary epithelial cells grown in the laboratory from dividing too much and from forming tumors when injected into mice. These experiments provide a deeper understanding of how most cells manage to remain healthy rather than becoming cancerous and reveal a potential new target for the early detection of cancer. Further investigations could now explore whether therapies could re-activate this enzyme to prevent or treat cancer. DOI:http://dx.doi.org/10.7554/eLife.07101.002
Collapse
Affiliation(s)
- Shi Yun Yeo
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Yoko Itahana
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Alvin Kunyao Guo
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Rachel Han
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Kozue Iwamoto
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Hung Thanh Nguyen
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Yi Bao
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Kai Kleiber
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Ya Jun Wu
- Department of Anatomy, Yong Loo Lin School of Medicine, National University Health System, , Singapore
| | - Boon Huat Bay
- Department of Anatomy, Yong Loo Lin School of Medicine, National University Health System, , Singapore
| | - Mathijs Voorhoeve
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| | - Koji Itahana
- Cancer & Stem Cell Biology Program, Duke-NUS Medical School, , Singapore
| |
Collapse
|
42
|
Mukhopadhyay UK, Cass J, Raptis L, Craig AW, Bourdeau V, Varma S, SenGupta S, Elliott BE, Ferbeyre G. STAT5A is regulated by DNA damage via the tumor suppressor p53. Cytokine 2016; 82:70-9. [PMID: 26876578 DOI: 10.1016/j.cyto.2016.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/21/2016] [Accepted: 01/23/2016] [Indexed: 11/18/2022]
Abstract
Here we report that the STAT5A transcription factor is a direct p53 transcriptional target gene. STAT5A is well expressed in p53 wild type cells but not in p53-null cells. Inhibition of p53 reduces STAT5A expression. DNA damaging agents such as doxorubicin also induced STAT5A expression in a p53 dependent manner. Two p53 binding sites were mapped in the STAT5A gene and named PBS1 and PBS2; these sites were sufficient to confer p53 responsiveness in a luciferase reporter gene. Chromatin immunoprecipitation experiments revealed that PBS2 has constitutive p53 bound to it, while p53 binding to PBS1 required DNA damage. In normal human breast lobules, weak p53 staining correlated with regions of intense STAT5A staining. Interestingly, in a cohort of triple negative breast tumor tissues there was little correlation between regions of p53 and STAT5A staining, likely reflecting a high frequency of p53 mutations that stabilize the protein in these tumors. We thus reveal an unexpected connection between cytokine signaling and p53.
Collapse
Affiliation(s)
- Utpal K Mukhopadhyay
- Division of Cancer Biology and Genetics, Queen's University, Cancer Research Institute, Kingston, Ontario K7L 3N6, Canada
| | - Jamaica Cass
- Division of Cancer Biology and Genetics, Queen's University, Cancer Research Institute, Kingston, Ontario K7L 3N6, Canada
| | - Leda Raptis
- Division of Cancer Biology and Genetics, Queen's University, Cancer Research Institute, Kingston, Ontario K7L 3N6, Canada
| | - Andrew W Craig
- Department of Biochemistry, Queens University, Kingston, Ontario, Canada
| | - Véronique Bourdeau
- Université de Montréal, Département de biochimie, Montréal, Québec H3C 3J7, Canada
| | - Sonal Varma
- Division of Cancer Biology and Genetics, Queen's University, Cancer Research Institute, Kingston, Ontario K7L 3N6, Canada
| | - Sandip SenGupta
- Division of Cancer Biology and Genetics, Queen's University, Cancer Research Institute, Kingston, Ontario K7L 3N6, Canada
| | - Bruce E Elliott
- Division of Cancer Biology and Genetics, Queen's University, Cancer Research Institute, Kingston, Ontario K7L 3N6, Canada.
| | - Gerardo Ferbeyre
- Université de Montréal, Département de biochimie, Montréal, Québec H3C 3J7, Canada.
| |
Collapse
|
43
|
p53 regulates the mevalonate pathway in human glioblastoma multiforme. Cell Death Dis 2015; 6:e1909. [PMID: 26469958 PMCID: PMC4632304 DOI: 10.1038/cddis.2015.279] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 08/04/2015] [Accepted: 08/09/2015] [Indexed: 11/30/2022]
Abstract
The mevalonate (MVA) pathway is an important metabolic pathway implicated in multiple aspects of tumorigenesis. In this study, we provided evidence that p53 induces the expression of a group of enzymes of the MVA pathway including 3′-hydroxy-3′-methylglutaryl-coenzyme A reductase, MVA kinase, farnesyl diphosphate synthase and farnesyl diphosphate farnesyl transferase 1, in the human glioblastoma multiforme cell line, U343 cells, and in normal human astrocytes, NHAs. Genetic and pharmacologic perturbation of p53 directly influences the expression of these genes. Furthermore, p53 is recruited to the gene promoters in designated p53-responsive elements, thereby increasing their transcription. Such effect was abolished by site-directed mutagenesis in the p53-responsive element of promoter of the genes. These findings highlight another aspect of p53 functions unrelated to tumor suppression and suggest p53 as a novel regulator of the MVA pathway providing insight into the role of this pathway in cancer progression.
Collapse
|
44
|
Novel p53 target genes secreted by the liver are involved in non-cell-autonomous regulation. Cell Death Differ 2015; 23:509-20. [PMID: 26358154 PMCID: PMC5072444 DOI: 10.1038/cdd.2015.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 07/01/2015] [Accepted: 07/28/2015] [Indexed: 12/24/2022] Open
Abstract
The tumor-suppressor p53 is a transcription factor that prevents cancer development and is involved in regulation of various physiological processes. This is mediated both by induction of cell cycle arrest and apoptosis and by controlling the expression of a plethora of target genes, including secreted proteins. It has been demonstrated that p53 may exert its effect in non-cell-autonomous manner by modulating the expression of genes that encode for secreted factors. In this study, we utilized our microarray data to identify and characterize novel p53 target genes expressed in human liver cells and associated with steroid hormones processing and transfer. We identified the steroid hormones binding factors, sex hormone-binding globulin (SHBG), corticosteroid-binding globulin (CBG) and cytochrome P450 family 21 subfamily A polypeptide 2, as novel p53 target genes. Their expression and secretion was increased following p53 activation in various hepatic cells. We observed that p53 wild-type mice exhibited higher levels of CBG compared with their p53 null counterparts. We demonstrated that the induction of the steroid hormones binding factors can be mediated by binding to specific p53 responsive elements within their promoters. In addition, utilizing conditioned medium experiments we have shown that p53-dependent induction of SHBG secretion from liver cells enhances apoptosis of breast cancer cells. Moreover, depletion of SHBG abolished the induction of breast cancer cells death. The newly identified p53 target genes suggest a novel non-cell-autonomous tumor-suppressive regulation mediated by p53 that is central for maintaining organism homeostasis.
Collapse
|
45
|
Tebaldi T, Zaccara S, Alessandrini F, Bisio A, Ciribilli Y, Inga A. Whole-genome cartography of p53 response elements ranked on transactivation potential. BMC Genomics 2015; 16:464. [PMID: 26081755 PMCID: PMC4470028 DOI: 10.1186/s12864-015-1643-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 05/20/2015] [Indexed: 11/18/2022] Open
Abstract
Background Many recent studies using ChIP-seq approaches cross-referenced to trascriptome data and also to potentially unbiased in vitro DNA binding selection experiments are detailing with increasing precision the p53-directed gene regulatory network that, nevertheless, is still expanding. However, most experiments have been conducted in established cell lines subjected to specific p53-inducing stimuli, both factors potentially biasing the results. Results We developed p53retriever, a pattern search algorithm that maps p53 response elements (REs) and ranks them according to predicted transactivation potentials in five classes. Besides canonical, full site REs, we developed specific pattern searches for non-canonical half sites and 3/4 sites and show that they can mediate p53-dependent responsiveness of associated coding sequences. Using ENCODE data, we also mapped p53 REs in about 44,000 distant enhancers and identified a 16-fold enrichment for high activity REs within those sites in the comparison with genomic regions near transcriptional start sites (TSS). Predictions from our pattern search were cross-referenced to ChIP-seq, ChIP-exo, expression, and various literature data sources. Based on the mapping of predicted functional REs near TSS, we examined expression changes of thirteen genes as a function of different p53-inducing conditions, providing further evidence for PDE2A, GAS6, E2F7, APOBEC3H, KCTD1, TRIM32, DICER, HRAS, KITLG and TGFA p53-dependent regulation, while MAP2K3, DNAJA1 and potentially YAP1 were identified as new direct p53 target genes. Conclusions We provide a comprehensive annotation of canonical and non-canonical p53 REs in the human genome, ranked on predicted transactivation potential. We also establish or corroborate direct p53 transcriptional control of thirteen genes. The entire list of identified and functionally classified p53 REs near all UCSC-annotated genes and within ENCODE mapped enhancer elements is provided. Our approach is distinct from, and complementary to, existing methods designed to identify p53 response elements. p53retriever is available as an R package at: http://tomateba.github.io/p53retriever. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1643-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Toma Tebaldi
- Centre for Integrative Biology (CIBIO), University of Trento, via delle Regole 101, 38123, Mattarello, TN, Italy.
| | - Sara Zaccara
- Centre for Integrative Biology (CIBIO), University of Trento, via delle Regole 101, 38123, Mattarello, TN, Italy.
| | - Federica Alessandrini
- Centre for Integrative Biology (CIBIO), University of Trento, via delle Regole 101, 38123, Mattarello, TN, Italy.
| | - Alessandra Bisio
- Centre for Integrative Biology (CIBIO), University of Trento, via delle Regole 101, 38123, Mattarello, TN, Italy.
| | - Yari Ciribilli
- Centre for Integrative Biology (CIBIO), University of Trento, via delle Regole 101, 38123, Mattarello, TN, Italy.
| | - Alberto Inga
- Centre for Integrative Biology (CIBIO), University of Trento, via delle Regole 101, 38123, Mattarello, TN, Italy.
| |
Collapse
|
46
|
Hull R, Oosthuysen B, Cajee UF, Mokgohloa L, Nweke E, Antunes RJ, Coetzer THT, Ntwasa M. The Drosophila retinoblastoma binding protein 6 family member has two isoforms and is potentially involved in embryonic patterning. Int J Mol Sci 2015; 16:10242-66. [PMID: 25955646 PMCID: PMC4463644 DOI: 10.3390/ijms160510242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/13/2015] [Indexed: 12/16/2022] Open
Abstract
The human retinoblastoma binding protein 6 (RBBP6) is implicated in esophageal, lung, hepatocellular and colon cancers. Furthermore, RBBP6 was identified as a strong marker for colon cancer prognosis and as a predisposing factor in familial myeloproliferative neoplasms. Functionally, the mammalian protein interacts with p53 and enhances the activity of Mdm2, the prototypical negative regulator of p53. However, since RBBP6 (known as PACT in mice) exists in multiple isoforms and pact-/- mice exhibit a more severe phenotype than mdm2-/- mutants, it must possess some Mdm2-independent functions. The function of the invertebrate homologue is poorly understood. This is complicated by the absence of the Mdm2 gene in both Drosophila and Caenorhabditis elegans. We have experimentally identified the promoter region of Snama, the Drosophila homologue, analyzed potential transcription factor binding sites and confirmed the existence of an additional isoform. Using band shift and co-immunoprecipitation assays combined with mass spectrometry, we found evidence that this gene may be regulated by, amongst others, DREF, which regulates hundreds of genes related to cell proliferation. The potential transcription factors for Snama fall into distinct functional groups, including anteroposterior embryonic patterning and nucleic acid metabolism. Significantly, previous work in mice shows that pact-/- induces an anteroposterior phenotype in embryos when rescued by simultaneous deletion of p53. Taken together, these observations indicate the significance of RBBP6 proteins in carcinogenesis and in developmental defects.
Collapse
Affiliation(s)
- Rodney Hull
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Brent Oosthuysen
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Umar-Faruq Cajee
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Lehlogonolo Mokgohloa
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Ekene Nweke
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Ricardo Jorge Antunes
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| | - Theresa H T Coetzer
- School of Life Sciences, University of KwaZulu-Natal (Pietermaritzburg campus); 3209 Scottsville, South Africa.
| | - Monde Ntwasa
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa Private Bag 3, WITS-2050 Johannesburg, South Africa.
| |
Collapse
|
47
|
Gong L, Gong H, Pan X, Chang C, Ou Z, Ye S, Yin L, Yang L, Tao T, Zhang Z, Liu C, Lane DP, Peng J, Chen J. p53 isoform Δ113p53/Δ133p53 promotes DNA double-strand break repair to protect cell from death and senescence in response to DNA damage. Cell Res 2015; 25:351-69. [PMID: 25698579 DOI: 10.1038/cr.2015.22] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/06/2014] [Accepted: 11/10/2014] [Indexed: 02/07/2023] Open
Abstract
The inhibitory role of p53 in DNA double-strand break (DSB) repair seems contradictory to its tumor-suppressing property. The p53 isoform Δ113p53/Δ133p53 is a p53 target gene that antagonizes p53 apoptotic activity. However, information on its functions in DNA damage repair is lacking. Here we report that Δ113p53 expression is strongly induced by γ-irradiation, but not by UV-irradiation or heat shock treatment. Strikingly, Δ113p53 promotes DNA DSB repair pathways, including homologous recombination, non-homologous end joining and single-strand annealing. To study the biological significance of Δ113p53 in promoting DNA DSB repair, we generated a zebrafish Δ113p53(M/M) mutant via the transcription activator-like effector nuclease technique and found that the mutant is more sensitive to γ-irradiation. The human ortholog, Δ133p53, is also only induced by γ-irradiation and functions to promote DNA DSB repair. Δ133p53-knockdown cells were arrested at the G2 phase at the later stage in response to γ-irradiation due to a high level of unrepaired DNA DSBs, which finally led to cell senescence. Furthermore, Δ113p53/Δ133p53 promotes DNA DSB repair via upregulating the transcription of repair genes rad51, lig4 and rad52 by binding to a novel type of p53-responsive element in their promoters. Our results demonstrate that Δ113p53/Δ133p53 is an evolutionally conserved pro-survival factor for DNA damage stress by preventing apoptosis and promoting DNA DSB repair to inhibit cell senescence. Our data also suggest that the induction of Δ133p53 expression in normal cells or tissues provides an important tolerance marker for cancer patients to radiotherapy.
Collapse
Affiliation(s)
- Lu Gong
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences
| | - Hongjian Gong
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences
| | - Xiao Pan
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences
| | - Changqing Chang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong 510650, China
| | - Zhao Ou
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences
| | - Shengfan Ye
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences
| | - Le Yin
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences
| | - Lina Yang
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences
| | - Ting Tao
- College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, Zhenjiang 310058, China
| | - Zhenhai Zhang
- National Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, and Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Cong Liu
- Developmental and Stem Cell Institute, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - David P Lane
- Biomedical Research Council, Agency for Science and Technology Research, Singapore
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, Zhenjiang 310058, China
| | - Jun Chen
- Key laboratory for Molecular Animal Nutrition, Ministry of Education, Innovation Center for Signaling Network, College of Life Sciences
| |
Collapse
|
48
|
Botcheva K. p53 binding to human genome: crowd control navigation in chromatin context. Front Genet 2014; 5:447. [PMID: 25566329 PMCID: PMC4273661 DOI: 10.3389/fgene.2014.00447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/05/2014] [Indexed: 11/22/2022] Open
Abstract
p53 is the most studied human protein because of its role in maintaining genomic stability. Binding to genomic targets is essential for transcription-dependent p53 tumor suppression, but how p53 selects targets remains unclear. Here, the impact of chromatin context on p53 genome-wide binding and targets selection is discussed. It is proposed that p53 genomic binding serves not only to regulate transcription, but to sense epigenomic changes threatening the genomic integrity. The problem of p53 navigating the human genome is discussed with respect to the degenerate p53 binding motif. This discussion relates to the fundamental problem of DNA binding factors navigating large genomes in search for cognate binding sites.
Collapse
Affiliation(s)
- Krassimira Botcheva
- Cell and Molecular Biology Department, Life Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA, USA
| |
Collapse
|
49
|
Cell context dependent p53 genome-wide binding patterns and enrichment at repeats. PLoS One 2014; 9:e113492. [PMID: 25415302 PMCID: PMC4240582 DOI: 10.1371/journal.pone.0113492] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/23/2014] [Indexed: 12/02/2022] Open
Abstract
The p53 ability to elicit stress specific and cell type specific responses is well recognized, but how that specificity is established remains to be defined. Whether upon activation p53 binds to its genomic targets in a cell type and stress type dependent manner is still an open question. Here we show that the p53 binding to the human genome is selective and cell context-dependent. We mapped the genomic binding sites for the endogenous wild type p53 protein in the human cancer cell line HCT116 and compared them to those we previously determined in the normal cell line IMR90. We report distinct p53 genome-wide binding landscapes in two different cell lines, analyzed under the same treatment and experimental conditions, using the same ChIP-seq approach. This is evidence for cell context dependent p53 genomic binding. The observed differences affect the p53 binding sites distribution with respect to major genomic and epigenomic elements (promoter regions, CpG islands and repeats). We correlated the high-confidence p53 ChIP-seq peaks positions with the annotated human repeats (UCSC Human Genome Browser) and observed both common and cell line specific trends. In HCT116, the p53 binding was specifically enriched at LINE repeats, compared to IMR90 cells. The p53 genome-wide binding patterns in HCT116 and IMR90 likely reflect the different epigenetic landscapes in these two cell lines, resulting from cancer-associated changes (accumulated in HCT116) superimposed on tissue specific differences (HCT116 has epithelial, while IMR90 has mesenchymal origin). Our data support the model for p53 binding to the human genome in a highly selective manner, mobilizing distinct sets of genes, contributing to distinct pathways.
Collapse
|
50
|
Chung JH, Larsen AR, Chen E, Bunz F. A PTCH1 homolog transcriptionally activated by p53 suppresses Hedgehog signaling. J Biol Chem 2014; 289:33020-31. [PMID: 25296753 DOI: 10.1074/jbc.m114.597203] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The p53-mediated responses to DNA damage and the Hedgehog (Hh) signaling pathway are each recurrently dysregulated in many types of human cancer. Here we describe PTCH53, a p53 target gene that is homologous to the tumor suppressor gene PTCH1 and can function as a repressor of Hh pathway activation. PTCH53 (previously designated PTCHD4) was highly responsive to p53 in vitro and was among a small number of genes that were consistently expressed at reduced levels in diverse TP53 mutant cell lines and human tumors. Increased expression of PTCH53 inhibited canonical Hh signaling by the G protein-coupled receptor SMO. PTCH53 thus delineates a novel, inducible pathway by which p53 can repress tumorigenic Hh signals.
Collapse
Affiliation(s)
- Jon H Chung
- From the Department of Radiation Oncology and Molecular Radiation Sciences, The Kimmel Cancer Center at Johns Hopkins, Baltimore, Maryland 21231
| | - Andrew R Larsen
- From the Department of Radiation Oncology and Molecular Radiation Sciences, The Kimmel Cancer Center at Johns Hopkins, Baltimore, Maryland 21231
| | - Evan Chen
- From the Department of Radiation Oncology and Molecular Radiation Sciences, The Kimmel Cancer Center at Johns Hopkins, Baltimore, Maryland 21231
| | - Fred Bunz
- From the Department of Radiation Oncology and Molecular Radiation Sciences, The Kimmel Cancer Center at Johns Hopkins, Baltimore, Maryland 21231
| |
Collapse
|