1
|
Benedetti R, Di Crosta M, D’Orazi G, Cirone M. Post-Translational Modifications (PTMs) of mutp53 and Epigenetic Changes Induced by mutp53. BIOLOGY 2024; 13:508. [PMID: 39056701 PMCID: PMC11273943 DOI: 10.3390/biology13070508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
Wild-type (wt) p53 and mutant forms (mutp53) play a key but opposite role in carcinogenesis. wtP53 acts as an oncosuppressor, preventing oncogenic transformation, while mutp53, which loses this property, may instead favor this process. This suggests that a better understanding of the mechanisms activating wtp53 while inhibiting mutp53 may help to design more effective anti-cancer treatments. In this review, we examine possible PTMs with which both wt- and mutp53 can be decorated and discuss how their manipulation could represent a possible strategy to control the stability and function of these proteins, focusing in particular on mutp53. The impact of ubiquitination, phosphorylation, acetylation, and methylation of p53, in the context of several solid and hematologic cancers, will be discussed. Finally, we will describe some of the recent studies reporting that wt- and mutp53 may influence the expression and activity of enzymes responsible for epigenetic changes such as acetylation, methylation, and microRNA regulation and the possible consequences of such changes.
Collapse
Affiliation(s)
- Rossella Benedetti
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| | - Michele Di Crosta
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| | - Gabriella D’Orazi
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. D’Annunzio”, 66013 Chieti, Italy
| | - Mara Cirone
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; (R.B.); (M.D.C.)
| |
Collapse
|
2
|
Begolli R, Chatziangelou M, Samiotaki M, Goutas A, Barda S, Goutzourelas N, Kevrekidis DP, Malea P, Trachana V, Liu M, Lin X, Kollatos N, Stagos D, Giakountis A. Transcriptome and proteome analysis reveals the anti-cancer properties of Hypnea musciformis marine macroalga extract in liver and intestinal cancer cells. Hum Genomics 2023; 17:71. [PMID: 37525271 PMCID: PMC10388463 DOI: 10.1186/s40246-023-00517-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Marine seaweeds are considered as a rich source of health-promoting compounds by the food and pharmaceutical industry. Hypnea musciformis is a marine red macroalga (seaweed) that is widely distributed throughout the world, including the Mediterranean Sea. It is known to contain various bioactive compounds, including sulfated polysaccharides, flavonoids, and phlorotannins. Recent studies have investigated the potential anticancer effects of extracts from H. musciformis demonstrating their cytotoxic effects on various cancer cell lines. The anticancer effects of these extracts are thought to be due to the presence of bioactive compounds, particularly sulfated polysaccharides, which have been shown to have anticancer and immunomodulatory effects. However, further studies are needed to fully understand the molecular mechanisms that underlie their anticancer effects and to determine their potential as therapeutic agents for cancer treatment. METHODS H. musciformis was collected from the Aegean Sea (Greece) and used for extract preparation. Transcriptome and proteome analysis was performed in liver and colon cancer human cell lines following treatment with H. musciformis seaweed extracts to characterize its anticancer effect in detail at the molecular level and to link transcriptome and proteome responses to the observed phenotypes in cancer cells. RESULTS We have identified that treatment with the seaweed extract triggers a p53-mediated response at the transcriptional and protein level in liver cancer cells, in contrast to colon cancer cells in which the effects are more associated with metabolic changes. Furthermore, we show that in treated HepG2 liver cancer cells, p53 interacts with the chromatin of several target genes and facilitates their upregulation possibly through the recruitment of the p300 co-activator. CONCLUSIONS Overall, the available evidence suggests that extracts from H. musciformis have the potential to serve as a source of anticancer agents in liver cancer cells mainly through activation of a p53-mediated anti-tumor response that is linked to inhibition of cellular proliferation and induction of cell death.
Collapse
Affiliation(s)
- Rodiola Begolli
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Myrto Chatziangelou
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | | | - Andreas Goutas
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Sofia Barda
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Nikolaos Goutzourelas
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Dimitrios Phaedon Kevrekidis
- Laboratory of Forensic Medicine and Toxicology, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Paraskevi Malea
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Varvara Trachana
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Ming Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Xiukun Lin
- College of Marine Sciences, Beibu Gulf University, 12 Binhai Rd, Qinzhou, 535011, Guangxi, China
| | - Nikolaos Kollatos
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Dimitrios Stagos
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece.
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece.
| |
Collapse
|
3
|
Gioukaki C, Georgiou A, Gkaralea LE, Kroupis C, Lazaris AC, Alamanis C, Thomopoulou GE. Unravelling the Role of P300 and TMPRSS2 in Prostate Cancer: A Literature Review. Int J Mol Sci 2023; 24:11299. [PMID: 37511059 PMCID: PMC10379122 DOI: 10.3390/ijms241411299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/26/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Prostate cancer is one of the most common malignant diseases in men, and it contributes significantly to the increased mortality rate in men worldwide. This study aimed to review the roles of p300 and TMPRSS2 (transmembrane protease, serine 2) in the AR (androgen receptor) pathway as they are closely related to the development and progression of prostate cancer. This paper represents a library-based study conducted by selecting the most suitable, up-to-date scientific published articles from online journals. We focused on articles that use similar techniques, particularly those that use prostate cancer cell lines and immunohistochemical staining to study the molecular impact of p300 and TMPRSS2 in prostate cancer specimens. The TMPRSS2:ERG fusion is considered relevant to prostate cancer, but its association with the development and progression as well as its clinical significance have not been fully elucidated. On the other hand, high p300 levels in prostate cancer biopsies predict larger tumor volumes, extraprostatic extension of disease, and seminal vesicle involvement at prostatectomy, and may be associated with prostate cancer progression after surgery. The inhibition of p300 has been shown to reduce the proliferation of prostate cancer cells with TMPRSS2:ETS (E26 transformation-specific) fusions, and combining p300 inhibitors with other targeted therapies may increase their efficacy. Overall, the interplay between the p300 and TMPRSS2 pathways is an active area of research.
Collapse
Affiliation(s)
- Charitomeni Gioukaki
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Alexandros Georgiou
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | - Christos Kroupis
- Department of Clinical Biochemistry, Attikon University Hospital, National and Kapodistrian University of Athens, 12461 Athens, Greece
| | - Andreas C Lazaris
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christos Alamanis
- 1st Urology Department, Laiko Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Georgia Eleni Thomopoulou
- Cytopathology Department, Attikon University Hospital, National and Kapodistrian University of Athens, 12461 Athens, Greece
| |
Collapse
|
4
|
Gandhi S, Bhushan A, Shukla U, Pundir A, Singh S, Srivastava T. Downregulation of lncRNA SNHG1 in hypoxia and stem cells is associated with poor disease prognosis in gliomas. Cell Cycle 2023; 22:1135-1153. [PMID: 36945177 PMCID: PMC10081076 DOI: 10.1080/15384101.2023.2191411] [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: 11/01/2022] [Revised: 02/15/2023] [Accepted: 03/12/2023] [Indexed: 03/23/2023] Open
Abstract
Gliomas are brain tumors associated with high morbidity, relapse and lethality despite improvement in therapeutic regimes. The hypoxic tumor microenvironment is a key feature associated with such poor outcomes in gliomas. The Hypoxia Inducible Factor (HIF) family of transcription factors are master regulators of cellular proliferation, high metabolic rates and angiogenesis via aberrant expression of downstream genes. Recent studies have implicated long non-coding RNAs (lncRNAs) as potential prognostic and diagnostic biomarkers. In this study, identification of hypoxia regulated lncRNA with a bioinformatic pipeline consisting of a newly developed tool "GenOx" was utilized for the identification of Hypoxia Response Element (HRE) and Hypoxia Ancillary Sequence (HAS) motifs in the promoter regions of lncRNAs. This was coupled with molecular, functional and interactome-based analyses of these hypoxia-relevant lncRNAs in primary tumors and cell-line models. We report on the identification of novel hypoxia regulated lncRNAs SNHG12, CASC7 and MF12-AS1. A strong association of RNA splicing mechanisms was observed with enriched lncRNAs. Several lncRNAs have emerged as prognostic biomarkers, of which TP53TG1 and SNHG1 were identified as highly relevant lncRNAs in glioma progression and validated in hypoxia cultured cells. Significantly, we determined that SNHG1 expression in tumor (vs. normal) is different from glioma stem cells, GSC (vs. tumors) and in hypoxia (vs. normoxia), positioning downregulation of SNHG1 to be associated with worsened prognosis.
Collapse
Affiliation(s)
- Sanchit Gandhi
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Ashish Bhushan
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Unmesh Shukla
- Institute of Informatics and Communication, University of Delhi South Campus, New Delhi, India
| | - Amit Pundir
- Department of Electronics, Maharaja Agrasen College, University of Delhi, Delhi, India
| | - Sanjeev Singh
- Institute of Informatics and Communication, University of Delhi South Campus, New Delhi, India
| | - Tapasya Srivastava
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| |
Collapse
|
5
|
Azemin WA, Alias N, Ali AM, Shamsir MS. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. J Biomol Struct Dyn 2023; 41:1141-1167. [PMID: 34935583 DOI: 10.1080/07391102.2021.2017349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor of Growth (ING) family members are also shown to directly interact with p53 and promote cell cycle arrest, senescence, apoptosis and participate in DNA replication and DNA damage responses to suppress the tumour initiation and progression. However, the interrelation between INGs and HepTH1-5 remains unknown. Therefore, this study aims to identify the mechanism and their protein interactions using in silico approaches. The finding revealed that HepTH1-5 and its ligands had interacted mostly on hotspot residues of ING proteins which involved in histone modifications via acetylation, phosphorylation, and methylation. This proves that HepTH1-5 might implicate in an apoptosis signalling pathway and preserve the protein structure and function of INGs by reducing the perturbation of histone binding upon oxidative stress response. This study would provide theoretical guidance for the design and experimental studies to decipher the role of HepTH1-5 as a potential therapeutic agent for cancer therapy. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Wan-Atirah Azemin
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia.,Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Nadiawati Alias
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| |
Collapse
|
6
|
Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
Collapse
|
7
|
Guharoy M, Lazar T, Macossay-Castillo M, Tompa P. Degron masking outlines degronons, co-degrading functional modules in the proteome. Commun Biol 2022; 5:445. [PMID: 35545699 PMCID: PMC9095673 DOI: 10.1038/s42003-022-03391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/22/2022] [Indexed: 11/28/2022] Open
Abstract
Effective organization of proteins into functional modules (networks, pathways) requires systems-level coordination between transcription, translation and degradation. Whereas the cooperation between transcription and translation was extensively studied, the cooperative degradation regulation of protein complexes and pathways has not been systematically assessed. Here we comprehensively analyzed degron masking, a major mechanism by which cellular systems coordinate degron recognition and protein degradation. For over 200 substrates with characterized degrons (E3 ligase targeting motifs, ubiquitination sites and disordered proteasomal entry sequences), we demonstrate that degrons extensively overlap with protein-protein interaction sites. Analysis of binding site information and protein abundance comparisons show that regulatory partners effectively outcompete E3 ligases, masking degrons from the ubiquitination machinery. Protein abundance variations between normal and cancer cells highlight the dynamics of degron masking components. Finally, integrative analysis of gene co-expression, half-life correlations and functional relationships between interacting proteins point towards higher-order, co-regulated degradation modules (‘degronons’) in the proteome. Systematic bioinformatics analysis of cooperative degradation of protein complexes indicates that degrons extensively overlap with protein-protein interaction sites, hiding degrons from ubiquitination machinery and suggesting the existence of co-degrading functional modules in the proteome.
Collapse
Affiliation(s)
- Mainak Guharoy
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium. .,VIB Bioinformatics Core, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Mauricio Macossay-Castillo
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium. .,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117, Budapest, Hungary.
| |
Collapse
|
8
|
Activation of ABCC Genes by Cisplatin Depends on the CoREST Occurrence at Their Promoters in A549 and MDA-MB-231 Cell Lines. Cancers (Basel) 2022; 14:cancers14040894. [PMID: 35205642 PMCID: PMC8870433 DOI: 10.3390/cancers14040894] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Cisplatin resistance is a common issue that affects patients with a variety of cancers who are treated with this drug. In this research, we present a novel epigenetic mechanism that controls the expression of ABC-family transporters, which are involved in multidrug resistance. We report that the CoREST complex may be a key factor that determines the transcription of ABC transporters in non-small cell lung and triple-negative breast cancer cells (A549 and MDA-MB-231, respectively) treated with cisplatin. By occupying gene promoters, this multi-subunit repressor prevents both an EP300-dependent increase in ABCC transcription induced by the alkylating drug and gene overexpression in cisplatin-resistant phenotypes. Moreover, the CoREST-free promoter of ABCC10 responds to cisplatin with EP300-mediated gene activation, which is only possible in p53-proficient cells. Abstract Although cisplatin-based therapies are common among anticancer approaches, they are often associated with the development of cancer drug resistance. This phenomenon is, among others, caused by the overexpression of ATP-binding cassette, membrane-anchored transporters (ABC proteins), which utilize ATP to remove, e.g., chemotherapeutics from intracellular compartments. To test the possible molecular basis of increased expression of ABCC subfamily members in a cisplatin therapy mimicking model, we generated two cisplatin-resistant cell lines derived from non-small cell lung cancer cells (A549) and triple-negative breast cancer cells (MDA-MB-231). Analysis of data for A549 cells deposited in UCSC Genome Browser provided evidence on the negative interdependence between the occurrence of the CoREST complex at the gene promoters and the overexpression of ABCC genes in cisplatin-resistant lung cancer cells. Pharmacological inhibition of CoREST enzymatic subunits—LSD1 and HDACs—restored gene responsiveness to cisplatin. Overexpression of CoREST-free ABCC10 in cisplatin-resistant phenotypes was caused by the activity of EP300 that was enriched at the ABCC10 promoter in drug-treated cells. Cisplatin-induced and EP300-dependent transcriptional activation of ABCC10 was only possible in the presence of p53. In summary, the CoREST complex prevents the overexpression of some multidrug resistance proteins from the ABCC subfamily in cancer cells exposed to cisplatin. p53-mediated activation of some ABCC genes by EP300 occurs once their promoters are devoid of the CoREST complex.
Collapse
|
9
|
Singh S, Senapati P, Kundu TK. Metabolic Regulation of Lysine Acetylation: Implications in Cancer. Subcell Biochem 2022; 100:393-426. [PMID: 36301501 DOI: 10.1007/978-3-031-07634-3_12] [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] [Indexed: 06/16/2023]
Abstract
Lysine acetylation is the second most well-studied post-translational modification after phosphorylation. While phosphorylation regulates signaling cascades, one of the most significant roles of acetylation is regulation of chromatin structure. Acetyl-coenzyme A (acetyl-CoA) serves as the acetyl group donor for acetylation reactions mediated by lysine acetyltransferases (KATs). On the other hand, NAD+ serves as the cofactor for lysine deacetylases (KDACs). Both acetyl-CoA and NAD+ are metabolites integral to energy metabolism, and therefore, their metabolic flux can regulate the activity of KATs and KDACs impacting the epigenome. In this chapter, we review our current understanding of how metabolic pathways regulate lysine acetylation in normal and cancer cells.
Collapse
Affiliation(s)
- Siddharth Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Parijat Senapati
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
- Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India.
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India.
| |
Collapse
|
10
|
Karr JP, Ferrie JJ, Tjian R, Darzacq X. The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer-promoter communication. Genes Dev 2022; 36:7-16. [PMID: 34969825 PMCID: PMC8763055 DOI: 10.1101/gad.349160.121] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
How distal cis-regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle-one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer-promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.
Collapse
Affiliation(s)
- Jonathan P Karr
- University of California at Berkeley, Berkeley, California 94720, USA
| | - John J Ferrie
- University of California at Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Robert Tjian
- University of California at Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Xavier Darzacq
- University of California at Berkeley, Berkeley, California 94720, USA
| |
Collapse
|
11
|
The oncogenicity of tumor-derived mutant p53 is enhanced by the recruitment of PLK3. Nat Commun 2021; 12:704. [PMID: 33514736 PMCID: PMC7846773 DOI: 10.1038/s41467-021-20928-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 12/21/2020] [Indexed: 01/10/2023] Open
Abstract
p53 mutations with single amino acid changes in cancer often lead to dominant oncogenic changes. Here, we have developed a mouse model of gain-of-function (GOF) p53-driven lung cancer utilizing conditionally active LSL p53-R172H and LSL K-Ras-G12D knock-in alleles that can be activated by Cre in lung club cells. Mutation of the p53 transactivation domain (TAD) (p53-L25Q/W26S/R172H) eliminating significant transactivation activity resulted in loss of tumorigenicity, demonstrating that transactivation mediated by or dependent on TAD is required for oncogenicity by GOF p53. GOF p53 TAD mutations significantly reduce phosphorylation of nearby p53 serine 20 (S20), which is a target for PLK3 phosphorylation. Knocking out PLK3 attenuated S20 phosphorylation along with transactivation and oncogenicity by GOF p53, indicating that GOF p53 exploits PLK3 to trigger its transactivation capability and exert oncogenic functions. Our data show a mechanistic involvement of PLK3 in mutant p53 pathway of oncogenesis. The mechanisms of how gain-of-function (GOF) mutant p53 drives carcinogenesis are unclear. Here, the authors show that a GOF mutant p53 requires its transactivation capability to induce mouse lung tumors and this is dependent on PLK3 phosphorylation of GOF mutant p53.
Collapse
|
12
|
Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
Collapse
Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
13
|
Yang Y, Li W, Wei B, Wu K, Liu D, Zhu D, Zhang C, Wen F, Fan Y, Zhao S. MicroRNA let-7i Inhibits Histone Lysine Demethylase KDM5B to Halt Esophageal Cancer Progression. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:846-861. [PMID: 33230480 PMCID: PMC7658493 DOI: 10.1016/j.omtn.2020.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/11/2020] [Indexed: 11/25/2022]
Abstract
Recent studies have suggested that microRNA let-7i is a tumor suppressor in human cancers, including esophageal cancer, but its underlying mechanism is not yet fully understood. We investigated the role and mechanisms of let-7i in the progression of esophageal cancer. We first showed that let-7i was downregulated in esophageal cancer tissues and cells and then linked its low expression to cancer progression. Bioinformatic analysis predicted KDM5B as a target gene of let-7i, which was confirmed by a dual-luciferase reporter assay. Loss- and gain-of function approaches were adopted to examine the interactions of let-7i, KDM5B, SOX17, and GREB1 in vitro and in vivo. Overexpression of let-7i suppressed esophageal cancer cell proliferation and invasion and promoted apoptosis. Mechanistic investigation showed that let-7i targeted and inhibited KDM5B expression, whereas KDM5B enhanced H3K4me3 at the SOX17 promoter region. Overexpression of let-7i suppressed the expression of GREB1 in esophageal cancer cells by regulating the KDM5B/SOX17 axis in vivo and in vitro. Taken together, our findings reveal the tumor-suppressive properties of let-7i in esophageal cancer in association with an apparent KDM5B-dependent SOX17/GREB1 axis. This study offers a potential prognostic marker and therapeutic target for esophageal cancer.
Collapse
Affiliation(s)
- Yang Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Wenhua Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Bochong Wei
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Kai Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Donglei Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Dengyan Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Chunyang Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Fengbiao Wen
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Yuxia Fan
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| | - Song Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450015, P.R. China
| |
Collapse
|
14
|
Sikder S, Kaypee S, Kundu TK. Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease. J Biosci 2020. [DOI: 10.1007/s12038-019-9974-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
15
|
Sikder S, Kaypee S, Kundu TK. Regulation of epigenetic state by non-histone chromatin proteins and transcription factors: Implications in disease. J Biosci 2020; 45:15. [PMID: 31965993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Besides the fundamental components of the chromatin, DNA and octameric histone, the non-histone chromatin proteins and non-coding RNA play a critical role in the organization of functional chromatin domains. The non-histone chromatin proteins therefore regulate the transcriptional outcome in both physiological and pathophysiological state as well. They also help to maintain the epigenetic state of the genome indirectly. Several transcription factors and histone interacting factors also contribute in the maintenance of the epigenetic states, especially acetylation by the induction of autoacetylation ability of p300/CBP. Alterations of KAT activity have been found to be causally related to disease manifestation, and thus could be potential therapeutic target.
Collapse
Affiliation(s)
- Sweta Sikder
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560 064, India
| | | | | |
Collapse
|
16
|
Singh S, Kumar M, Kumar S, Sen S, Upadhyay P, Bhattacharjee S, M N, Tomar VS, Roy S, Dutt A, Kundu TK. The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis. J Biol Chem 2019; 294:14081-14095. [PMID: 31366730 PMCID: PMC6755804 DOI: 10.1074/jbc.ra118.007265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 06/21/2019] [Indexed: 02/05/2023] Open
Abstract
TP53 is the most frequently mutated tumor suppressor gene in many cancers, yet biochemical characterization of several of its reported mutations with probable biological significance have not been accomplished enough. Specifically, missense mutations in TP53 can contribute to tumorigenesis through gain-of-function of biochemical and biological properties that stimulate tumor growth. Here, we identified a relatively rare mutation leading to a proline to leucine substitution (P152L) in TP53 at the very end of its DNA-binding domain (DBD) in a sample from an Indian oral cancer patient. Although the P152Lp53 DBD alone bound to DNA, the full-length protein completely lacked binding ability at its cognate DNA motifs. Interestingly, P152Lp53 could efficiently tetramerize, and the mutation had only a limited impact on the structure and stability of full-length p53. Significantly, when we expressed this variant in a TP53-null cell line, it induced cell motility, proliferation, and invasion compared with a vector-only control. Also, enhanced tumorigenic potential was observed when P152Lp53-expressing cells were xenografted into nude mice. Investigating the effects of P152Lp53 expression on cellular pathways, we found that it is associated with up-regulation of several pathways, including cell-cell and cell-extracellular matrix signaling, epidermal growth factor receptor signaling, and Rho-GTPase signaling, commonly active in tumorigenesis and metastasis. Taken together, our findings provide a detailed account of the biochemical and cellular alterations associated with the cancer-associated P152Lp53 variant and establish it as a gain-of-function TP53 variant.
Collapse
Affiliation(s)
- Siddharth Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Manoj Kumar
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | | | - Shrinka Sen
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - Sayan Bhattacharjee
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Naveen M
- BioCOS Life Sciences Pvt. Ltd., Bengaluru, India
| | - Vivek Singh Tomar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Amit Dutt
- Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| |
Collapse
|
17
|
Ghosh R, Kaypee S, Shasmal M, Kundu TK, Roy S, Sengupta J. Tumor Suppressor p53-Mediated Structural Reorganization of the Transcriptional Coactivator p300. Biochemistry 2019; 58:3434-3443. [DOI: 10.1021/acs.biochem.9b00333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raka Ghosh
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | | | - Tapas K. Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| |
Collapse
|