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Borlak J, Ciribilli Y, Bisio A, Selvaraj S, Inga A, Oh JH, Spanel R. The Abl1 tyrosine kinase is a key player in doxorubicin-induced cardiomyopathy and its p53/p73 cell death mediated signaling differs in atrial and ventricular cardiomyocytes. J Transl Med 2024; 22:845. [PMID: 39285385 PMCID: PMC11403941 DOI: 10.1186/s12967-024-05623-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/16/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND Doxorubicin is an important anticancer drug, however, elicits dose-dependently cardiomyopathy. Given its mode of action, i.e. topoisomerase inhibition and DNA damage, we investigated genetic events associated with cardiomyopathy and searched for mechanism-based possibilities to alleviate cardiotoxicity. We treated rats at clinically relevant doses of doxorubicin. Histopathology and transmission electron microscopy (TEM) defined cardiac lesions, and transcriptomics unveiled cardiomyopathy-associated gene regulations. Genomic-footprints revealed critical components of Abl1-p53-signaling, and EMSA-assays evidenced Abl1 DNA-binding activity. Gene reporter assays confirmed Abl1 activity on p53-targets while immunohistochemistry/immunofluorescence microscopy demonstrated Abl1, p53&p73 signaling. RESULTS Doxorubicin treatment caused dose-dependently toxic cardiomyopathy, and TEM evidenced damaged mitochondria and myofibrillar disarray. Surviving cardiomyocytes repressed Parkin-1 and Bnip3-mediated mitophagy, stimulated dynamin-1-like dependent mitochondrial fission and induced anti-apoptotic Bag1 signaling. Thus, we observed induced mitochondrial biogenesis. Transcriptomics discovered heterogeneity in cellular responses with minimal overlap between treatments, and the data are highly suggestive for distinct cardiomyocyte (sub)populations which differed in their resilience and reparative capacity. Genome-wide footprints revealed Abl1 and p53 enriched binding sites in doxorubicin-regulated genes, and we confirmed Abl1 DNA-binding activity in EMSA-assays. Extraordinarily, Abl1 signaling differed in the heart with highly significant regulations of Abl1, p53 and p73 in atrial cardiomyocytes. Conversely, in ventricular cardiomyocytes, Abl1 solely-modulated p53-signaling that was BAX transcription-independent. Gene reporter assays established Abl1 cofactor activity for the p53-reporter PG13-luc, and ectopic Abl1 expression stimulated p53-mediated apoptosis. CONCLUSIONS The tyrosine kinase Abl1 is of critical importance in doxorubicin induced cardiomyopathy, and we propose its inhibition as means to diminish risk of cardiotoxicity.
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Affiliation(s)
- Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - Yari Ciribilli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandra Bisio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Saravanakumar Selvaraj
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Alberto Inga
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jung-Hwa Oh
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, Republic of Korea
| | - Reinhard Spanel
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
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2
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Grossi S, Berno E, Chiofalo P, Chiaravalli AM, Cinquetti R, Bruno A, Palano MT, Gallazzi M, La Rosa S, Sessa F, Acquati F, Campomenosi P. Proline Dehydrogenase (PRODH) Is Expressed in Lung Adenocarcinoma and Modulates Cell Survival and 3D Growth by Inducing Cellular Senescence. Int J Mol Sci 2024; 25:714. [PMID: 38255788 PMCID: PMC10815008 DOI: 10.3390/ijms25020714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
The identification of markers for early diagnosis, prognosis, and improvement of therapeutic options represents an unmet clinical need to increase survival in Non-Small Cell Lung Cancer (NSCLC), a neoplasm still characterized by very high incidence and mortality. Here, we investigated whether proline dehydrogenase (PRODH), a mitochondrial flavoenzyme catalyzing the key step in proline degradation, played a role in NSCLC tumorigenesis. PRODH expression was investigated by immunohistochemistry; digital PCR, quantitative PCR, immunoblotting, measurement of reactive oxygen species (ROS), and functional cellular assays were carried out. PRODH expression was found in the majority of lung adenocarcinomas (ADCs). Patients with PRODH-positive tumors had better cancer-free specific and overall survival compared to those with negative tumors. Ectopic modulation of PRODH expression in NCI-H1299 and the other tested lung ADC cell lines decreased cell survival. Moreover, cell proliferation curves showed delayed growth in NCI-H1299, Calu-6 and A549 cell lines when PRODH-expressing clones were compared to control clones. The 3D growth in soft agar was also impaired in the presence of PRODH. PRODH increased reactive oxygen species production and induced cellular senescence in the NCI-H1299 cell line. This study supports a role of PRODH in decreasing survival and growth of lung ADC cells by inducing cellular senescence.
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Affiliation(s)
- Sarah Grossi
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
| | - Elena Berno
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
| | - Priscilla Chiofalo
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
| | - Anna Maria Chiaravalli
- Unità di Anatomia Patologica, Ospedale di Circolo e Fondazione Macchi, Via O. Rossi 9, 21100 Varese, Italy; (A.M.C.); (S.L.R.); (F.S.)
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Raffaella Cinquetti
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
| | - Antonino Bruno
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
- Laboratorio di Immunità Innata, Unità di Patologia Molecolare, Biochimica, e Immunologia, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Via Fantoli 16/15, 20138 Milan, Italy; (M.T.P.); (M.G.)
- Centro di Ricerca per l’Invecchiamento di Successo (CRIS), Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Maria Teresa Palano
- Laboratorio di Immunità Innata, Unità di Patologia Molecolare, Biochimica, e Immunologia, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Via Fantoli 16/15, 20138 Milan, Italy; (M.T.P.); (M.G.)
| | - Matteo Gallazzi
- Laboratorio di Immunità Innata, Unità di Patologia Molecolare, Biochimica, e Immunologia, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Via Fantoli 16/15, 20138 Milan, Italy; (M.T.P.); (M.G.)
| | - Stefano La Rosa
- Unità di Anatomia Patologica, Ospedale di Circolo e Fondazione Macchi, Via O. Rossi 9, 21100 Varese, Italy; (A.M.C.); (S.L.R.); (F.S.)
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università degli Studi dell’Insubria, 21100 Varese, Italy
- Dipartimento di Medicina e Innovazione Tecnologica, DIMIT, Università degli Studi dell’Insubria, Via Guicciardini 9, 21100 Varese, Italy
| | - Fausto Sessa
- Unità di Anatomia Patologica, Ospedale di Circolo e Fondazione Macchi, Via O. Rossi 9, 21100 Varese, Italy; (A.M.C.); (S.L.R.); (F.S.)
- Dipartimento di Medicina e Innovazione Tecnologica, DIMIT, Università degli Studi dell’Insubria, Via Guicciardini 9, 21100 Varese, Italy
| | - Francesco Acquati
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
- Centro di Ricerca per l’Invecchiamento di Successo (CRIS), Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Paola Campomenosi
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
- Centro di Ricerca per l’Invecchiamento di Successo (CRIS), Università degli Studi dell’Insubria, 21100 Varese, Italy
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3
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Vojsovič M, Kratochvilová L, Valková N, Šislerová L, El Rashed Z, Menichini P, Inga A, Monti P, Brázda V. Transactivation by partial function P53 family mutants is increased by the presence of G-quadruplexes at a promoter site. Biochimie 2024; 216:14-23. [PMID: 37838351 DOI: 10.1016/j.biochi.2023.09.026] [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: 07/19/2023] [Revised: 09/04/2023] [Accepted: 09/27/2023] [Indexed: 10/16/2023]
Abstract
The effect of mutations in the P53 family of transcription factors on their biological functions, including partial or complete loss of transcriptional activity, has been confirmed several times. At present, P53 family proteins showing partial loss of activity appear to be promising potential candidates for the development of novel therapeutic strategies which could restore their transcriptional activity. In this context, it is important to employ tools to precisely monitor their activity; in relation to this, non-canonical DNA secondary structures in promoters including G-quadruplexes (G4s) were shown to influence the activity of transcription factors. Here, we used a defined yeast assay to evaluate the impact of differently modeled G4 forming sequences on a panel of partial function P53 family mutant proteins. Specifically, a 22-mer G4 prone sequence (derived from the KSHV virus) and five derivatives that progressively mutate characteristic guanine stretches were placed upstream of a minimal promoter, adjacent to a P53 response element in otherwise isogenic yeast luciferase reporter strains. The transactivation ability of cancer-associated P53 (TA-P53α: A161T, R213L, N235S, V272L, R282W, R283C, R337C, R337H, and G360V) or Ectodermal Dyplasia syndromes-related P63 mutant proteins (ΔN-P63α: G134D, G134V and inR155) were tested. Our results show that the presence of G4 forming sequences can increase the transactivation ability of partial function P53 family proteins. These observations are pointing to the importance of DNA structural characteristics for accurate classification of P53 family proteins functionality in the context of the wide variety of TP53 and TP63 germline and somatic mutations.
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Affiliation(s)
- Matúš Vojsovič
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic; Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200, Brno, Czech Republic.
| | - Libuše Kratochvilová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic; Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200, Brno, Czech Republic.
| | - Natália Valková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic.
| | - Lucie Šislerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic; Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200, Brno, Czech Republic.
| | - Zeinab El Rashed
- Gene Expression Regulation, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
| | - Paola Menichini
- Mutagenesis and Cancer Prevention, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy.
| | - Paola Monti
- Mutagenesis and Cancer Prevention, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic; Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200, Brno, Czech Republic.
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4
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Kratochvilová L, Vojsovič M, Valková N, Šislerová L, El Rashed Z, Inga A, Monti P, Brázda V. The presence of a G-quadruplex prone sequence upstream of a minimal promoter increases transcriptional activity in the yeast Saccharomyces cerevisiae. Biosci Rep 2023; 43:BSR20231348. [PMID: 38112096 PMCID: PMC10730334 DOI: 10.1042/bsr20231348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 12/20/2023] Open
Abstract
Non-canonical secondary structures in DNA are increasingly being revealed as critical players in DNA metabolism, including modulating the accessibility and activity of promoters. These structures comprise the so-called G-quadruplexes (G4s) that are formed from sequences rich in guanine bases. Using a well-defined transcriptional reporter system, we sought to systematically investigate the impact of the presence of G4 structures on transcription in yeast Saccharomyces cerevisiae. To this aim, different G4 prone sequences were modeled to vary the chance of intramolecular G4 formation, analyzed in vitro by Thioflavin T binding test and circular dichroism and then placed at the yeast ADE2 locus on chromosome XV, downstream and adjacent to a P53 response element (RE) and upstream from a minimal CYC1 promoter and Luciferase 1 (LUC1) reporter gene in isogenic strains. While the minimal CYC1 promoter provides basal reporter activity, the P53 RE enables LUC1 transactivation under the control of P53 family proteins expressed under the inducible GAL1 promoter. Thus, the impact of the different G4 prone sequences on both basal and P53 family protein-dependent expression was measured after shifting cells onto galactose containing medium. The results showed that the presence of G4 prone sequences upstream of a yeast minimal promoter increased its basal activity proportionally to their potential to form intramolecular G4 structures; consequently, this feature, when present near the target binding site of P53 family transcription factors, can be exploited to regulate the transcriptional activity of P53, P63 and P73 proteins.
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Affiliation(s)
- Libuše Kratochvilová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200 Brno, Czech Republic
| | - Matúš Vojsovič
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200 Brno, Czech Republic
| | - Natália Valková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Lucie Šislerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200 Brno, Czech Republic
| | - Zeinab El Rashed
- Gene Expression Regulation SSD, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Paola Monti
- Mutagenesis and Cancer Prevention UO, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 61200 Brno, Czech Republic
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5
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Meškytė EM, Pezzè L, Bartolomei L, Forcato M, Bocci IA, Bertalot G, Barbareschi M, Oliveira-Ferrer L, Bisio A, Bicciato S, Baltriukienė D, Ciribilli Y. ETV7 reduces inflammatory responses in breast cancer cells by repressing the TNFR1/NF-κB axis. Cell Death Dis 2023; 14:263. [PMID: 37041130 PMCID: PMC10089821 DOI: 10.1038/s41419-023-05718-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 04/13/2023]
Abstract
The transcription factor ETV7 is an oncoprotein that is up-regulated in all breast cancer (BC) types. We have recently demonstrated that ETV7 promoted breast cancer progression by increasing cancer cell proliferation and stemness and was also involved in the development of chemo- and radio-resistance. However, the roles of ETV7 in breast cancer inflammation have yet to be studied. Gene ontology analysis previously performed on BC cells stably over-expressing ETV7 demonstrated that ETV7 was involved in the suppression of innate immune and inflammatory responses. To better decipher the involvement of ETV7 in these signaling pathways, in this study, we identified TNFRSF1A, encoding for the main receptor of TNF-α, TNFR1, as one of the genes down-regulated by ETV7. We demonstrated that ETV7 directly binds to the intron I of this gene, and we showed that the ETV7-mediated down-regulation of TNFRSF1A reduced the activation of NF-κB signaling. Furthermore, in this study, we unveiled a potential crosstalk between ETV7 and STAT3, another master regulator of inflammation. While it is known that STAT3 directly up-regulates the expression of TNFRSF1A, here we demonstrated that ETV7 reduces the ability of STAT3 to bind to the TNFRSF1A gene via a competitive mechanism, recruiting repressive chromatin remodelers, which results in the repression of its transcription. The inverse correlation between ETV7 and TNFRSF1A was confirmed also in different cohorts of BC patients. These results suggest that ETV7 can reduce the inflammatory responses in breast cancer through the down-regulation of TNFRSF1A.
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Affiliation(s)
- Erna Marija Meškytė
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Laura Pezzè
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Alia Therapeutics, s.r.l., Trento, Italy
| | - Laura Bartolomei
- Laboratory of Radiobiology, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Irene Adelaide Bocci
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institut für Zellbiologie, Universitätsklinikum Essen, Essen, Germany
| | - Giovanni Bertalot
- Unità Operativa Multizonale di Anatomia Patologica, APSS, Trento, Italy
- Centre for Medical Sciences (CISMed), University of Trento, Trento, Italy
| | - Mattia Barbareschi
- Unità Operativa Multizonale di Anatomia Patologica, APSS, Trento, Italy
- Centre for Medical Sciences (CISMed), University of Trento, Trento, Italy
| | | | - Alessandra Bisio
- Laboratory of Radiobiology, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daiva Baltriukienė
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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6
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Tadijan A, Precazzini F, Hanžić N, Radić M, Gavioli N, Vlašić I, Ozretić P, Pinto L, Škreblin L, Barban G, Slade N, Ciribilli Y. Altered Expression of Shorter p53 Family Isoforms Can Impact Melanoma Aggressiveness. Cancers (Basel) 2021; 13:cancers13205231. [PMID: 34680379 PMCID: PMC8533715 DOI: 10.3390/cancers13205231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 02/05/2023] Open
Abstract
Cutaneous melanoma is the most aggressive form of skin cancer. Despite the significant advances in the management of melanoma in recent decades, it still represents a challenge for clinicians. The TP53 gene, the guardian of the genome, which is altered in more than 50% of human cancers, is rarely mutated in melanoma. More recently, researchers started to appreciate the importance of shorter p53 isoforms as potential modifiers of the p53-dependent responses. We analyzed the expression of p53 and p73 isoforms both at the RNA and protein level in a panel of melanoma-derived cell lines with different TP53 and BRAF status, in normal conditions or upon treatment with common anti-cancer DNA damaging agents or targeted therapy. Using lentiviral vectors, we also generated stable clones of H1299 p53 null cells over-expressing the less characterized isoforms Δ160p53α, Δ160p53β, and Δ160p53γ. Further, we obtained two melanoma-derived cell lines resistant to BRAF inhibitor vemurafenib. We observed that melanoma cell lines expressed a wide array of p53 and p73 isoforms, with Δ160p53α as the most variable one. We demonstrated for the first time that Δ160p53α, and to a lesser extent Δ160p53β, can be recruited on chromatin, and that Δ160p53γ can localize in perinuclear foci; moreover, all Δ160p53 isoforms can stimulate proliferation and in vitro migration. Lastly, vemurafenib-resistant melanoma cells showed an altered expression of p53 and p73 isoforms, namely an increased expression of potentially pro-oncogenic Δ40p53β and a decrease in tumor-suppressive TAp73β. We therefore propose that p53 family isoforms can play a role in melanoma cells' aggressiveness.
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Affiliation(s)
- Ana Tadijan
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Francesca Precazzini
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
- Laboratory of RNA Biology and Biotechnology, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy
| | - Nikolina Hanžić
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Martina Radić
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Nicolò Gavioli
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
| | - Ignacija Vlašić
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Lia Pinto
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
| | - Lidija Škreblin
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
| | - Giulia Barban
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
| | - Neda Slade
- Laboratory for Protein Dynamics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (A.T.); (N.H.); (M.R.); (I.V.); (L.Š.)
- Correspondence: (N.S.); (Y.C.)
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123 Povo, TN, Italy; (F.P.); (N.G.); (L.P.); (G.B.)
- Correspondence: (N.S.); (Y.C.)
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7
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ETV7 regulates breast cancer stem-like cell features by repressing IFN-response genes. Cell Death Dis 2021; 12:742. [PMID: 34315857 PMCID: PMC8316333 DOI: 10.1038/s41419-021-04005-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022]
Abstract
Cancer stem cells (CSCs) represent a population of cells within the tumor able to drive tumorigenesis and known to be highly resistant to conventional chemotherapy and radiotherapy. In this work, we show a new role for ETV7, a transcriptional repressor member of the ETS family, in promoting breast cancer stem-like cells plasticity and resistance to chemo- and radiotherapy in breast cancer (BC) cells. We observed that MCF7 and T47D BC-derived cells stably over-expressing ETV7 showed reduced sensitivity to the chemotherapeutic drug 5-fluorouracil and to radiotherapy, accompanied by an adaptive proliferative behavior observed in different culture conditions. We further noticed that alteration of ETV7 expression could significantly affect the population of breast CSCs, measured by CD44+/CD24low cell population and mammosphere formation efficiency. By transcriptome profiling, we identified a signature of Interferon-responsive genes significantly repressed in cells over-expressing ETV7, which could be responsible for the increase in the breast CSCs population, as this could be partially reverted by the treatment with IFN-β. Lastly, we show that the expression of the IFN-responsive genes repressed by ETV7 could have prognostic value in breast cancer, as low expression of these genes was associated with a worse prognosis. Therefore, we propose a novel role for ETV7 in breast cancer stem cells’ plasticity and associated resistance to conventional chemotherapy and radiotherapy, which involves the repression of a group of IFN-responsive genes, potentially reversible upon IFN-β treatment. We, therefore, suggest that an in-depth investigation of this mechanism could lead to novel breast CSCs targeted therapies and to the improvement of combinatorial regimens, possibly involving the therapeutic use of IFN-β, with the aim of avoiding resistance development and relapse in breast cancer.
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Evaluating the Influence of a G-Quadruplex Prone Sequence on the Transactivation Potential by Wild-Type and/or Mutant P53 Family Proteins through a Yeast-Based Functional Assay. Genes (Basel) 2021; 12:genes12020277. [PMID: 33672023 PMCID: PMC7919268 DOI: 10.3390/genes12020277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
P53, P63, and P73 proteins belong to the P53 family of transcription factors, sharing a common gene organization that, from the P1 and P2 promoters, produces two groups of mRNAs encoding proteins with different N-terminal regions; moreover, alternative splicing events at C-terminus further contribute to the generation of multiple isoforms. P53 family proteins can influence a plethora of cellular pathways mainly through the direct binding to specific DNA sequences known as response elements (REs), and the transactivation of the corresponding target genes. However, the transcriptional activation by P53 family members can be regulated at multiple levels, including the DNA topology at responsive promoters. Here, by using a yeast-based functional assay, we evaluated the influence that a G-quadruplex (G4) prone sequence adjacent to the p53 RE derived from the apoptotic PUMA target gene can exert on the transactivation potential of full-length and N-terminal truncated P53 family α isoforms (wild-type and mutant). Our results show that the presence of a G4 prone sequence upstream or downstream of the P53 RE leads to significant changes in the relative activity of P53 family proteins, emphasizing the potential role of structural DNA features as modifiers of P53 family functions at target promoter sites.
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9
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P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development. Biosci Rep 2020; 39:221381. [PMID: 31789342 PMCID: PMC6914664 DOI: 10.1042/bsr20192114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/15/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022] Open
Abstract
TP63 is a member of the TP53 gene family, sharing a common gene structure that produces two groups of mRNAs' encoding proteins with different N-terminal regions (ΔN and TA isoforms); both transcripts are also subjected to alternative splicing mechanisms at C-terminus, generating a variety of isoforms. p63 is a master regulator of epidermal development and homoeostasis as well as an important player in tumorigenesis and cancer progression with both oncogenic and tumour suppressive roles. A number of studies have aimed at the identification of p63 target genes, allowing the dissection of the molecular pathways orchestrated by the different isoforms. In the present study we investigated in more detail the p63 responsiveness of the WDFY2 (WD repeat and FYVE domain containing 2) gene, encoding for an endosomal protein identified as a binding partner of the PI-3K/AKT signalling pathway. We showed that overexpression of different p63 isoforms was able to induce WDFY2 expression in TP53-null cells. The p63-dependent transcriptional activation was associated with specific response elements (REs) that have been identified by a bioinformatics tool and validated by yeast- and mammal-based assays. Interestingly, to confirm that WDFY2 belongs to the p63 network of cancer regulation, we analysed the impact of WDFY2 alterations, by showing its frequent deletion in different types of tumours and suggesting its expression level as a prognostic biomarker. Lastly, we identified a chromosomal translocation involving the WDFY2 locus in a patient affected by a rare congenital limb anomaly, indicating WDFY2 as a possible susceptibility gene placed downstream p63 in the network of limb development.
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10
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Kuo TC, Huang KY, Yang SC, Wu S, Chung WC, Chang YL, Hong TM, Wang SP, Chen HY, Hsiao TH, Yang PC. Monocarboxylate Transporter 4 Is a Therapeutic Target in Non-small Cell Lung Cancer with Aerobic Glycolysis Preference. Mol Ther Oncolytics 2020; 18:189-201. [PMID: 32695876 PMCID: PMC7364124 DOI: 10.1016/j.omto.2020.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Targeting metabolic reprogramming is an emerging strategy in cancer therapy. However, clinical attempts to target metabolic reprogramming have been proved to be challenging, with metabolic heterogeneity of cancer being one of many reasons that causes treatment failure. Here, we stratified non-small cell lung cancer (NSCLC) cells, mainly lung adenocarcinoma, based on their metabolic phenotypes and demonstrated that the aerobic glycolysis-preference NSCLC cell subtype was resistant to the OXPHOS-targeting inhibitors. We identified that monocarboxylate transporter 4 (MCT4), a lactate transporter, was highly expressed in the aerobic glycolysis-preference subtype with function supporting the proliferation of these cells. Glucose could induce the expression of MCT4 in these cells through a ΔNp63α and Sp1-dependent pathway. Next, we showed that knockdown of MCT4 increased intracellular lactate concentration and induced a reactive oxygen species (ROS)-dependent cellular apoptosis in the aerobic glycolysis-preference NSCLC cell subtype. By scanning a panel of monoclonal antibodies with MCT4 neutralizing activity, we further identified a MCT4 immunoglobulin M (IgM) monoclonal antibody showing capable anti-proliferation efficacy on the aerobic glycolysis-preference NSCLC cell subtype. Our findings indicate that the metabolic heterogeneity is a critical factor for NSCLC therapy and manipulating the expression or function of MCT4 can be an effective strategy in targeting the aerobic glycolysis-preference NSCLC cell subtype.
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Affiliation(s)
- Ting-Chun Kuo
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Kuo-Yen Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 33303, Taiwan
| | - Shuenn-Chen Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Sean Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Wei-Chia Chung
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yih-Leong Chang
- Department of Pathology and Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Tse-Ming Hong
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shu-Ping Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
- PhD Program in Microbial Genomics, National Chung Hsing University, Taichung 40227, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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11
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Nassiri I, Inga A, Meškytė EM, Alessandrini F, Ciribilli Y, Priami C. Regulatory Crosstalk of Doxorubicin, Estradiol and TNFα Combined Treatment in Breast Cancer-derived Cell Lines. Sci Rep 2019; 9:15172. [PMID: 31645610 PMCID: PMC6811586 DOI: 10.1038/s41598-019-51349-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 09/28/2019] [Indexed: 11/10/2022] Open
Abstract
We present a new model of ESR1 network regulation based on analysis of Doxorubicin, Estradiol, and TNFα combination treatment in MCF-7. We used Doxorubicin as a therapeutic agent, TNFα as marker and mediator of an inflammatory microenvironment and 17β-Estradiol (E2) as an agonist of Estrogen Receptors, known predisposing factor for hormone-driven breast cancer, whose pharmacological inhibition reduces the risk of breast cancer recurrence. Based on the results of transcriptomics analysis, we found 71 differentially expressed genes that are specific for the combination treatment with Doxorubicin + Estradiol + TNFα in comparison with single or double treatments. The responsiveness to the triple treatment was examined for seven genes by qPCR, of which six were validated, and then extended to four additional cell lines differing for p53 and/or ER status. The results of differential regulation enrichment analysis highlight the role of the ESR1 network that included 36 of 71 specific differentially expressed genes. We propose that the combined activation of p53 and NF-kB transcription factors significantly influences ligand-dependent, ER-driven transcriptional responses, also of the ESR1 gene itself. These results provide a model of coordinated interaction of TFs to explain the Doxorubicin, E2 and TNFα induced repression mechanisms.
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Affiliation(s)
- Isar Nassiri
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, TN, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Erna Marija Meškytė
- Laboratory of Molecular Cancer Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy.,Department of Biological Models, Life Sciences Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Federica Alessandrini
- Laboratory of Molecular Cancer Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, TN, Italy. .,Dipartimento di Informatica, Università di Pisa, Pisa, Italy.
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12
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Alessandrini F, Pezzè L, Menendez D, Resnick MA, Ciribilli Y. ETV7-Mediated DNAJC15 Repression Leads to Doxorubicin Resistance in Breast Cancer Cells. Neoplasia 2018; 20:857-870. [PMID: 30025229 PMCID: PMC6077117 DOI: 10.1016/j.neo.2018.06.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 12/20/2022]
Abstract
Breast cancer treatment often includes Doxorubicin as adjuvant as well as neoadjuvant chemotherapy. Despite its cytotoxicity, cells can develop drug resistance to Doxorubicin. Uncovering pathways and mechanisms involved in drug resistance is an urgent and critical aim for breast cancer research oriented to improve treatment efficacy. Here we show that Doxorubicin and other chemotherapeutic drugs induce the expression of ETV7, a transcriptional repressor member of ETS family of transcription factors. The ETV7 expression led to DNAJC15 down-regulation, a co-chaperone protein whose low expression was previously associated with drug resistance in breast and ovarian cancer. There was a corresponding reduction in Doxorubicin sensitivity of MCF7 and MDA-MB-231 breast cancer cells. We identified the binding site for ETV7 within DNAJC15 promoter and we also found that DNA methylation may be a factor in ETV7-mediated DNAJC15 transcriptional repression. These findings of an inverse correlation between ETV7 and DNAJC15 expression in MCF7 cells in terms of Doxorubicin resistance, correlated well with treatment responses of breast cancer patients with recurrent disease, based on our analyses of reported genome-wide expression arrays. Moreover, we demonstrated that ETV7-mediated Doxorubicin-resistance involves increased Doxorubicin efflux via nuclear pumps, which could be rescued in part by DNAJC15 up-regulation. With this study, we propose a novel role for ETV7 in breast cancer, and we identify DNAJC15 as a new target gene responsible for ETV7-mediated Doxorubicin-resistance. A better understanding of the opposing impacts of Doxorubicin could improve the design of combinatorial adjuvant regimens with the aim of avoiding resistance and relapse.
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Affiliation(s)
- Federica Alessandrini
- Laboratory of Molecular Cancer Genetics, Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo (TN), Italy.
| | - Laura Pezzè
- Laboratory of Molecular Cancer Genetics, Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo (TN), Italy
| | - Daniel Menendez
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIHES), NIH, Research Triangle Park, NC 27709, USA
| | - Michael A Resnick
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIHES), NIH, Research Triangle Park, NC 27709, USA
| | - Yari Ciribilli
- Laboratory of Molecular Cancer Genetics, Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo (TN), Italy.
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13
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Billant O, Léon A, Le Guellec S, Friocourt G, Blondel M, Voisset C. The dominant-negative interplay between p53, p63 and p73: A family affair. Oncotarget 2018; 7:69549-69564. [PMID: 27589690 PMCID: PMC5342497 DOI: 10.18632/oncotarget.11774] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/10/2016] [Indexed: 12/15/2022] Open
Abstract
The tumor suppression activity of p53 is frequently impaired in cancers even when a wild-type copy of the gene is still present, suggesting that a dominant-negative effect is exerted by some of p53 mutants and isoforms. p63 and p73, which are related to p53, have also been reported to be subjected to a similar loss of function, suggesting that a dominant-negative interplay might happen between p53, p63 and p73. However, to which extent p53 hotspot mutants and isoforms of p53, p63 and p73 are able to interfere with the tumor suppressive activity of their siblings as well as the underlying mechanisms remain undeciphered. Using yeast, we showed that a dominant-negative effect is widely spread within the p53/p63/p73 family as all p53 loss-of-function hotspot mutants and several of the isoforms of p53 and p73 tested exhibit a dominant-negative potential. In addition, we found that this dominant-negative effect over p53 wild-type is based on tetramer poisoning through the formation of inactive hetero-tetramers and does not rely on a prion-like mechanism contrary to what has been previously suggested. We also showed that mutant p53-R175H gains the ability to inhibit p63 and p73 activity by a mechanism that is only partially based on tetramerization.
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Affiliation(s)
- Olivier Billant
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Alice Léon
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Solenn Le Guellec
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Gaëlle Friocourt
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Marc Blondel
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
| | - Cécile Voisset
- Inserm UMR 1078, Université de Bretagne Occidentale, Faculté de Médecine et des Sciences de la Santé, Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France
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14
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Abstract
Since its discovery in 1979, p53 has been on the forefront of cancer research. It is considered a master gene of cancer suppression and is found mutated in around 50% of all human tumors. In addition, the progressive identification of p53-related transcription factors p63 and p73 as well as their multiple isoforms have added further layers of complexity to an already dense network. Among the numerous models used to unravel the p53 family mysteries, S. cerevisiae has been particularly useful. This seemingly naive model allows the expression of a functional human p53 and thus the assessment of p53 intrinsic transcriptional activity. The aim of this article is to review the various contributions that the budding yeast has made to the understanding of p53, p63 and p73 biology and to envision new possible directions for yeast-based assays in the field of cancer as well as other p53-family-related diseases.
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15
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Sharma V, Monti P, Fronza G, Inga A. Human transcription factors in yeast: the fruitful examples of P53 and NF-кB. FEMS Yeast Res 2016; 16:fow083. [PMID: 27683095 DOI: 10.1093/femsyr/fow083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2016] [Indexed: 12/31/2022] Open
Abstract
The observation that human transcription factors (TFs) can function when expressed in yeast cells has stimulated the development of various functional assays to investigate (i) the role of binding site sequences (herein referred to as response elements, REs) in transactivation specificity, (ii) the impact of polymorphic nucleotide variants on transactivation potential, (iii) the functional consequences of mutations in TFs and (iv) the impact of cofactors or small molecules. These approaches have found applications in basic as well as applied research, including the identification and the characterisation of mutant TF alleles from clinical samples. The ease of genome editing of yeast cells and the availability of regulated systems for ectopic protein expression enabled the development of quantitative reporter systems, integrated at a chosen chromosomal locus in isogenic yeast strains that differ only at the level of a specific RE targeted by a TF or for the expression of distinct TF alleles. In many cases, these assays were proven predictive of results in higher eukaryotes. The potential to work in small volume formats and the availability of yeast strains with modified chemical uptake have enhanced the scalability of these approaches. Next to well-established one-, two-, three-hybrid assays, the functional assays with non-chimeric human TFs enrich the palette of opportunities for functional characterisation. We review ∼25 years of research on human sequence-specific TFs expressed in yeast, with an emphasis on the P53 and NF-кB family of proteins, highlighting outcomes, advantages, challenges and limitations of these heterologous assays.
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Affiliation(s)
- Vasundhara Sharma
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
| | - Paola Monti
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Gilberto Fronza
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Alberto Inga
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
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16
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He Z, Agostini M, Liu H, Melino G, Simon HU. p73 regulates basal and starvation-induced liver metabolism in vivo. Oncotarget 2016; 6:33178-90. [PMID: 26375672 PMCID: PMC4741757 DOI: 10.18632/oncotarget.5090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/26/2015] [Indexed: 12/30/2022] Open
Abstract
As a member of the p53 gene family, p73 regulates cell cycle arrest, apoptosis, neurogenesis, immunity and inflammation. Recently, p73 has been shown to transcriptionally regulate selective metabolic enzymes, such as cytochrome c oxidase subunit IV isoform 1, glucose 6-phosphate dehydrogenase and glutaminase-2, resulting in significant effects on metabolism, including hepatocellular lipid metabolism, glutathione homeostasis and the pentose phosphate pathway. In order to further investigate the metabolic effect of p73, here, we compared the global metabolic profile of livers from p73 knockout and wild-type mice under both control and starvation conditions. Our results show that the depletion of all p73 isoforms cause altered lysine metabolism and glycolysis, distinct patterns for glutathione synthesis and Krebs cycle, as well as an elevated pentose phosphate pathway and abnormal lipid accumulation. These results indicate that p73 regulates basal and starvation-induced fuel metabolism in the liver, a finding that is likely to be highly relevant for metabolism-associated disorders, such as diabetes and cancer.
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Affiliation(s)
- Zhaoyue He
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Massimiliano Agostini
- Medical Research Council, Toxicology Unit, Leicester, United Kingdom.,Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | - He Liu
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Gerry Melino
- Medical Research Council, Toxicology Unit, Leicester, United Kingdom.,Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland
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17
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Sharma V, Jordan JJ, Ciribilli Y, Resnick MA, Bisio A, Inga A. Quantitative Analysis of NF-κB Transactivation Specificity Using a Yeast-Based Functional Assay. PLoS One 2015; 10:e0130170. [PMID: 26147604 PMCID: PMC4493129 DOI: 10.1371/journal.pone.0130170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/18/2015] [Indexed: 11/18/2022] Open
Abstract
The NF-κB transcription factor family plays a central role in innate immunity and inflammation processes and is frequently dysregulated in cancer. We developed an NF-κB functional assay in yeast to investigate the following issues: transactivation specificity of NF-κB proteins acting as homodimers or heterodimers; correlation between transactivation capacity and in vitro DNA binding measurements; impact of co-expressed interacting proteins or of small molecule inhibitors on NF-κB-dependent transactivation. Full-length p65 and p50 cDNAs were cloned into centromeric expression vectors under inducible GAL1 promoter in order to vary their expression levels. Since p50 lacks a transactivation domain (TAD), a chimeric construct containing the TAD derived from p65 was also generated (p50TAD) to address its binding and transactivation potential. The p50TAD and p65 had distinct transactivation specificities towards seventeen different κB response elements (κB-REs) where single nucleotide changes could greatly impact transactivation. For four κB-REs, results in yeast were predictive of transactivation potential measured in the human MCF7 cell lines treated with the NF-κB activator TNFα. Transactivation results in yeast correlated only partially with in vitro measured DNA binding affinities, suggesting that features other than strength of interaction with naked DNA affect transactivation, although factors such as chromatin context are kept constant in our isogenic yeast assay. The small molecules BAY11-7082 and ethyl-pyruvate as well as expressed IkBα protein acted as NF-κB inhibitors in yeast, more strongly towards p65. Thus, the yeast-based system can recapitulate NF-κB features found in human cells, thereby providing opportunities to address various NF-κB functions, interactions and chemical modulators.
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Affiliation(s)
- Vasundhara Sharma
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jennifer J. Jordan
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yari Ciribilli
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michael A. Resnick
- Chromosome Stability Group; National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Alessandra Bisio
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
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18
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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.
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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.
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19
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Lion M, Raimondi I, Donati S, Jousson O, Ciribilli Y, Inga A. Evolution of p53 transactivation specificity through the lens of a yeast-based functional assay. PLoS One 2015; 10:e0116177. [PMID: 25668429 PMCID: PMC4323202 DOI: 10.1371/journal.pone.0116177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 10/16/2014] [Indexed: 11/18/2022] Open
Abstract
Co-evolution of transcription factors (TFs) with their respective cis-regulatory network enhances functional diversity in the course of evolution. We present a new approach to investigate transactivation capacity of sequence-specific TFs in evolutionary studies. Saccharomyces cerevisiae was used as an in vivo test tube and p53 proteins derived from human and five commonly used animal models were chosen as proof of concept. p53 is a highly conserved master regulator of environmental stress responses. Previous reports indicated conserved p53 DNA binding specificity in vitro, even for evolutionary distant species. We used isogenic yeast strains where p53-dependent transactivation was measured towards chromosomally integrated p53 response elements (REs). Ten REs were chosen to sample a wide range of DNA binding affinity and transactivation capacity for human p53 and proteins were expressed at two levels using an inducible expression system. We showed that the assay is amenable to study thermo-sensitivity of frog p53, and that chimeric constructs containing an ectopic transactivation domain could be rapidly developed to enhance the activity of proteins, such as fruit fly p53, that are poorly effective in engaging the yeast transcriptional machinery. Changes in the profile of relative transactivation towards the ten REs were measured for each p53 protein and compared to the profile obtained with human p53. These results, which are largely independent from relative p53 protein levels, revealed widespread evolutionary divergence of p53 transactivation specificity, even between human and mouse p53. Fruit fly and human p53 exhibited the largest discrimination among REs while zebrafish p53 was the least selective.
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Affiliation(s)
- Mattia Lion
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Ivan Raimondi
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Stefano Donati
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Olivier Jousson
- Laboratory of Microbial Genomics, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Yari Ciribilli
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, Mattarello, Trento, Italy
- * E-mail:
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20
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Adámik M, Bažantová P, Navrátilová L, Polášková A, Pečinka P, Holaňová L, Tichý V, Brázdová M. Impact of cadmium, cobalt and nickel on sequence-specific DNA binding of p63 and p73 in vitro and in cells. Biochem Biophys Res Commun 2014; 456:29-34. [PMID: 25446071 DOI: 10.1016/j.bbrc.2014.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 11/30/2022]
Abstract
Site-specific DNA recognition and binding activity belong to common attributes of all three members of tumor suppressor p53 family proteins: p53, p63 and p73. It was previously shown that heavy metals can affect p53 conformation, sequence-specific binding and suppress p53 response to DNA damage. Here we report for the first time that cadmium, nickel and cobalt, which have already been shown to disturb various DNA repair mechanisms, can also influence p63 and p73 sequence-specific DNA binding activity and transactivation of p53 family target genes. Based on results of electrophoretic mobility shift assay and luciferase reporter assay, we conclude that cadmium inhibits sequence-specific binding of all three core domains to p53 consensus sequences and abolishes transactivation of several promoters (e.g. BAX and MDM2) by 50μM concentrations. In the presence of specific DNA, all p53 family core domains were partially protected against loss of DNA binding activity due to cadmium treatment. Effective cadmium concentration to abolish DNA-protein interactions was about two times higher for p63 and p73 proteins than for p53. Furthermore, we detected partial reversibility of cadmium inhibition for all p53 family members by EDTA. DTT was able to reverse cadmium inhibition only for p53 and p73. Nickel and cobalt abolished DNA-p53 interaction at sub-millimolar concentrations while inhibition of p63 and p73 DNA binding was observed at millimolar concentrations. In summary, cadmium strongly inhibits p53, p63 and p73 DNA binding in vitro and in cells in comparison to nickel and cobalt. The role of cadmium inhibition of p53 tumor suppressor family in carcinogenesis is discussed.
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Affiliation(s)
- Matej Adámik
- Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavla Bažantová
- Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 701 03 Ostrava, Czech Republic
| | - Lucie Navrátilová
- Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Alena Polášková
- Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Pečinka
- Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 701 03 Ostrava, Czech Republic
| | - Lucie Holaňová
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého 1/3, 61242 Brno, Czech Republic
| | - Vlastimil Tichý
- Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic; Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého 1/3, 61242 Brno, Czech Republic.
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21
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Studying p53 family proteins in yeast: induction of autophagic cell death and modulation by interactors and small molecules. Exp Cell Res 2014; 330:164-77. [PMID: 25265062 DOI: 10.1016/j.yexcr.2014.09.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/19/2014] [Accepted: 09/20/2014] [Indexed: 01/08/2023]
Abstract
In this work, the yeast Saccharomyces cerevisiae was used to individually study human p53, p63 (full length and truncated forms) and p73. Using this cell system, the effect of these proteins on cell proliferation and death, and the influence of MDM2 and MDMX on their activities were analyzed. When expressed in yeast, wild-type p53, TAp63, ΔNp63 and TAp73 induced growth inhibition associated with S-phase cell cycle arrest. This growth inhibition was accompanied by reactive oxygen species production and autophagic cell death. Furthermore, they stimulated rapamycin-induced autophagy. On the contrary, none of the tested p53 family members induced apoptosis either per se or after apoptotic stimuli. As previously reported for p53, also TAp63, ΔNp63 and TAp73 increased actin expression levels and its depolarization, suggesting that ACT1 is also a p63 and p73 putative yeast target gene. Additionally, MDM2 and MDMX inhibited the activity of all tested p53 family members in yeast, although the effect was weaker on TAp63. Moreover, Nutlin-3a and SJ-172550 were identified as potential inhibitors of the p73 interaction with MDM2 and MDMX, respectively. Altogether, the yeast-based assays herein developed can be envisaged as a simplified cell system to study the involvement of p53 family members in autophagy, the modulation of their activities by specific interactors (MDM2 and MDMX), and the potential of new small molecules to modulate these interactions.
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