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Baniulyte G, Hicks SM, Sammons MA. p53motifDB: integration of genomic information and tumor suppressor p53 binding motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614594. [PMID: 39386591 PMCID: PMC11463528 DOI: 10.1101/2024.09.24.614594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
The tumor suppressor gene TP53 encodes the DNA binding transcription factor p53 and is one of the most commonly mutated genes in human cancer. Tumor suppressor activity requires binding of p53 to its DNA response elements and subsequent transcriptional activation of a diverse set of target genes. Despite decades of close study, the logic underlying p53 interactions with its numerous potential genomic binding sites and target genes is not yet fully understood. Here, we present a database of DNA and chromatin-based information focused on putative p53 binding sites in the human genome to allow users to generate and test new hypotheses related to p53 activity in the genome. Users can query genomic locations based on experimentally observed p53 binding, regulatory element activity, genetic variation, evolutionary conservation, chromatin modification state, and chromatin structure. We present multiple use cases demonstrating the utility of this database for generating novel biological hypotheses, such as chromatin-based determinants of p53 binding and potential cell type-specific p53 activity. All database information is also available as a precompiled sqlite database for use in local analysis or as a Shiny web application.
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Boutelle AM, Mabene AR, Yao D, Xu H, Wang M, Tang YJ, Lopez SS, Sinha S, Demeter J, Cheng R, Benard BA, Valente LJ, Drainas AP, Fischer M, Majeti R, Petrov DA, Jackson PK, Yang F, Winslow MM, Bassik MC, Attardi LD. Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.612743. [PMID: 39345444 PMCID: PMC11429870 DOI: 10.1101/2024.09.17.612743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
TP53 , the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seq Ultra somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3 - Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.
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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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Ravari A, Ghoreishi SF, Imani M. Optimal Inference of Hidden Markov Models Through Expert-Acquired Data. IEEE TRANSACTIONS ON ARTIFICIAL INTELLIGENCE 2024; 5:3985-4000. [PMID: 39144916 PMCID: PMC11324238 DOI: 10.1109/tai.2024.3358261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
This paper focuses on inferring a general class of hidden Markov models (HMMs) using data acquired from experts. Expert-acquired data contain decisions/actions made by humans/users for various objectives, such as navigation data reflecting drivers' behavior, cybersecurity data carrying defender decisions, and biological data containing the biologist's actions (e.g., interventions and experiments). Conventional inference methods rely on temporal changes in data without accounting for expert knowledge. This paper incorporates expert knowledge into the inference of HMMs by modeling expert behavior as an imperfect reinforcement learning agent. The proposed method optimally quantifies experts' perceptions about the system model, which, alongside the temporal changes in data, contributes to the inference process. The proposed inference method is derived through a combination of dynamic programming and optimal recursive Bayesian estimation. The applicability of this method is demonstrated to a wide range of inference criteria, such as maximum likelihood and maximum a posteriori. The performance of the proposed method is investigated through a comprehensive numerical experiment using a benchmark problem and biological networks.
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Affiliation(s)
- Amirhossein Ravari
- Department of Electrical and Computer Engineering at Northeastern University
| | - Seyede Fatemeh Ghoreishi
- Department of Civil and Environmental Engineering and Khoury College of Computer Sciences at Northeastern University
| | - Mahdi Imani
- Department of Electrical and Computer Engineering at Northeastern University
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Fischer M, Sammons MA. Determinants of p53 DNA binding, gene regulation, and cell fate decisions. Cell Death Differ 2024; 31:836-843. [PMID: 38951700 PMCID: PMC11239874 DOI: 10.1038/s41418-024-01326-1] [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: 03/09/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024] Open
Abstract
The extent to which transcription factors read and respond to specific information content within short DNA sequences remains an important question that the tumor suppressor p53 is helping us answer. We discuss recent insights into how local information content at p53 binding sites might control modes of p53 target gene activation and cell fate decisions. Significant prior work has yielded data supporting two potential models of how p53 determines cell fate through its target genes: a selective target gene binding and activation model and a p53 level threshold model. Both of these models largely revolve around an analogy of whether p53 is acting in a "smart" or "dumb" manner. Here, we synthesize recent and past studies on p53 decoding of DNA sequence, chromatin context, and cellular signaling cascades to elicit variable cell fates critical in human development, homeostasis, and disease.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
| | - Morgan A Sammons
- Department of Biological Sciences and The RNA Institute, The State University of New York at Albany, 1400 Washington Avenue, Albany, NY, 12222, USA.
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Fischer M. Gene regulation by the tumor suppressor p53 - The omics era. Biochim Biophys Acta Rev Cancer 2024; 1879:189111. [PMID: 38740351 DOI: 10.1016/j.bbcan.2024.189111] [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: 11/27/2023] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
The transcription factor p53 is activated in response to a variety of cellular stresses and serves as a prominent and potent tumor suppressor. Since its discovery, we have sought to understand how p53 functions as both a transcription factor and a tumor suppressor. Two decades ago, the field of gene regulation entered the omics era and began to study the regulation of entire genomes. The omics perspective has greatly expanded our understanding of p53 functions and has begun to reveal its gene regulatory network. In this mini-review, I discuss recent insights into the p53 transcriptional program from high-throughput analyses.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany.
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Castaño BA, Schorer S, Guo Y, Calzetta NL, Gottifredi V, Wiesmüller L, Biber S. The levels of p53 govern the hierarchy of DNA damage tolerance pathway usage. Nucleic Acids Res 2024; 52:3740-3760. [PMID: 38321962 PMCID: PMC11039994 DOI: 10.1093/nar/gkae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 02/08/2024] Open
Abstract
It is well-established that, through canonical functions in transcription and DNA repair, the tumor suppressor p53 plays a central role in safeguarding cells from the consequences of DNA damage. Recent data retrieved in tumor and stem cells demonstrated that p53 also carries out non-canonical functions when interacting with the translesion synthesis (TLS) polymerase iota (POLι) at DNA replication forks. This protein complex triggers a DNA damage tolerance (DDT) mechanism controlling the DNA replication rate. Given that the levels of p53 trigger non-binary rheostat-like functions in response to stress or during differentiation, we explore the relevance of the p53 levels for its DDT functions at the fork. We show that subtle changes in p53 levels modulate the contribution of some DDT factors including POLι, POLη, POLζ, REV1, PCNA, PRIMPOL, HLTF and ZRANB3 to the DNA replication rate. Our results suggest that the levels of p53 are central to coordinate the balance between DDT pathways including (i) fork-deceleration by the ZRANB3-mediated fork reversal factor, (ii) POLι-p53-mediated fork-slowing, (iii) POLι- and POLη-mediated TLS and (iv) PRIMPOL-mediated fork-acceleration. Collectively, our study reveals the relevance of p53 protein levels for the DDT pathway choice in replicating cells.
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Affiliation(s)
- Bryan A Castaño
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Sabrina Schorer
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Yitian Guo
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | | | | | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Stephanie Biber
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
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Mouillet-Richard S, Gougelet A, Passet B, Brochard C, Le Corre D, Pitasi CL, Joubel C, Sroussi M, Gallois C, Lavergne J, Castille J, Vilotte M, Daniel-Carlier N, Pilati C, de Reyniès A, Djouadi F, Colnot S, André T, Taieb J, Vilotte JL, Romagnolo B, Laurent-Puig P. Wnt, glucocorticoid and cellular prion protein cooperate to drive a mesenchymal phenotype with poor prognosis in colon cancer. J Transl Med 2024; 22:337. [PMID: 38589873 PMCID: PMC11003154 DOI: 10.1186/s12967-024-05164-0] [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: 02/12/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND The mesenchymal subtype of colorectal cancer (CRC), associated with poor prognosis, is characterized by abundant expression of the cellular prion protein PrPC, which represents a candidate therapeutic target. How PrPC is induced in CRC remains elusive. This study aims to elucidate the signaling pathways governing PrPC expression and to shed light on the gene regulatory networks linked to PrPC. METHODS We performed in silico analyses on diverse datasets of in vitro, ex vivo and in vivo models of mouse CRC and patient cohorts. We mined ChIPseq studies and performed promoter analysis. CRC cell lines were manipulated through genetic and pharmacological approaches. We created mice combining conditional inactivation of Apc in intestinal epithelial cells and overexpression of the human prion protein gene PRNP. Bio-informatic analyses were carried out in two randomized control trials totalizing over 3000 CRC patients. RESULTS In silico analyses combined with cell-based assays identified the Wnt-β-catenin and glucocorticoid pathways as upstream regulators of PRNP expression, with subtle differences between mouse and human. We uncover multiple feedback loops between PrPC and these two pathways, which translate into an aggravation of CRC pathogenesis in mouse. In stage III CRC patients, the signature defined by PRNP-CTNNB1-NR3C1, encoding PrPC, β-catenin and the glucocorticoid receptor respectively, is overrepresented in the poor-prognosis, mesenchymal subtype and associates with reduced time to recurrence. CONCLUSIONS An unleashed PrPC-dependent vicious circle is pathognomonic of poor prognosis, mesenchymal CRC. Patients from this aggressive subtype of CRC may benefit from therapies targeting the PRNP-CTNNB1-NR3C1 axis.
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Affiliation(s)
- Sophie Mouillet-Richard
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France.
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France.
| | - Angélique Gougelet
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
| | - Bruno Passet
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Camille Brochard
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Department of Pathology, APHP.Centre-Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Delphine Le Corre
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Caterina Luana Pitasi
- Université Paris Cité, Institut Cochin, Inserm, CNRS, F-75014, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Camille Joubel
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Marine Sroussi
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Claire Gallois
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Hepatogastroenterology and GI Oncology Department, APHP.Centre-Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Julien Lavergne
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Histology, Imaging and Cytometry Center (CHIC), Paris, France
| | - Johan Castille
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Marthe Vilotte
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Nathalie Daniel-Carlier
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Camilla Pilati
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Aurélien de Reyniès
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Fatima Djouadi
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Sabine Colnot
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Thierry André
- Saint-Antoine Hospital, INSERM, Unité Mixte de Recherche Scientifique 938, Sorbonne Université, Paris, France
| | - Julien Taieb
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Hepatogastroenterology and GI Oncology Department, APHP.Centre-Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Jean-Luc Vilotte
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Béatrice Romagnolo
- Université Paris Cité, Institut Cochin, Inserm, CNRS, F-75014, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France.
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France.
- Institut du Cancer Paris CARPEM, APHP, Department of Biology, APHP.Centre-Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France.
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Yue Z, Lin J, Lu X, Gao Q, Pan M, Zhang Y, Shen S, Zhu WG, Paus R. Keratin 17 Impacts Global Gene Expression and Controls G2/M Cell Cycle Transition in Ionizing Radiation-Induced Skin Damage. J Invest Dermatol 2023; 143:2436-2446.e13. [PMID: 37414246 DOI: 10.1016/j.jid.2023.02.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 01/30/2023] [Accepted: 02/08/2023] [Indexed: 07/08/2023]
Abstract
Keratin 17 (K17) is a cytoskeletal protein that is part of the intermediate filaments in epidermal keratinocytes. In K17-/- mice, ionizing radiation induced more severe hair follicle damage, whereas the epidermal inflammatory response was attenuated compared with that in wild-type mice. Both p53 and K17 have a major impact on global gene expression because over 70% of the differentially expressed genes in the skin of wild-type mice showed no expression change in p53-/- or K17-/- skin after ionizing radiation. K17 does not interfere with the dynamics of p53 activation; rather, global p53 binding in the genome is altered in K17-/- mice. The absence of K17 leads to aberrant cell cycle progression and mitotic catastrophe in epidermal keratinocytes, which is due to nuclear retention, thus reducing the degradation of B-Myb, a key regulator of the G2/M cell cycle transition. These results expand our understanding of the role of K17 in regulating global gene expression and ionizing radiation-induced skin damage.
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Affiliation(s)
- ZhiCao Yue
- Department of Cell Biology & Medical Genetics, Shenzhen University Medical School, Shenzhen, China; International Cancer Center, Shenzhen University Medical School, Shenzhen, China; Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, China.
| | - JianQiong Lin
- Department of Cell Biology & Medical Genetics, Shenzhen University Medical School, Shenzhen, China; International Cancer Center, Shenzhen University Medical School, Shenzhen, China; Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, China
| | - XiaoPeng Lu
- International Cancer Center, Shenzhen University Medical School, Shenzhen, China; Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, China; Department of Biochemistry & Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - QingXiang Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, China
| | - MeiPing Pan
- Institute of Life Sciences, Fuzhou University, Fuzhou, China
| | - YaFei Zhang
- Department of Cell Biology & Medical Genetics, Shenzhen University Medical School, Shenzhen, China; International Cancer Center, Shenzhen University Medical School, Shenzhen, China; Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, China
| | - SiTing Shen
- Department of Cell Biology & Medical Genetics, Shenzhen University Medical School, Shenzhen, China; International Cancer Center, Shenzhen University Medical School, Shenzhen, China; Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, China
| | - Wei-Guo Zhu
- International Cancer Center, Shenzhen University Medical School, Shenzhen, China; Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, China; Department of Biochemistry & Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Ralf Paus
- Dr. Philip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA; Center for Dermatology Research, School of Biological Sciences, The University of Manchester and NIHR Biomedical Research Center, Manchester, United Kingdom
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Rakotopare J, Lejour V, Duval C, Eldawra E, Escoffier H, Toledo F. A systematic approach identifies p53-DREAM pathway target genes associated with blood or brain abnormalities. Dis Model Mech 2023; 16:dmm050376. [PMID: 37661832 PMCID: PMC10581385 DOI: 10.1242/dmm.050376] [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: 06/30/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
p53 (encoded by Trp53) is a tumor suppressor, but mouse models have revealed that increased p53 activity may cause bone marrow failure, likely through dimerization partner, RB-like, E2F4/E2F5 and MuvB (DREAM) complex-mediated gene repression. Here, we designed a systematic approach to identify p53-DREAM pathway targets, the repression of which might contribute to abnormal hematopoiesis. We used Gene Ontology analysis to study transcriptomic changes associated with bone marrow cell differentiation, then chromatin immunoprecipitation-sequencing (ChIP-seq) data to identify DREAM-bound promoters. We next created positional frequency matrices to identify evolutionary conserved sequence elements potentially bound by DREAM. The same approach was developed to find p53-DREAM targets associated with brain abnormalities, also observed in mice with increased p53 activity. Putative DREAM-binding sites were found for 151 candidate target genes, of which 106 are mutated in a blood or brain genetic disorder. Twenty-one DREAM-binding sites were tested and found to impact gene expression in luciferase assays, to notably regulate genes mutated in dyskeratosis congenita (Rtel1), Fanconi anemia (Fanca), Diamond-Blackfan anemia (Tsr2), primary microcephaly [Casc5 (or Knl1), Ncaph and Wdr62] and pontocerebellar hypoplasia (Toe1). These results provide clues on the role of the p53-DREAM pathway in regulating hematopoiesis and brain development, with implications for tumorigenesis.
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Affiliation(s)
- Jeanne Rakotopare
- Genetics of Tumor Suppression, Institut Curie, Paris 75248 Cedex 05, France
- CNRS UMR3244, Paris 75005, France
- Sorbonne University, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Vincent Lejour
- Genetics of Tumor Suppression, Institut Curie, Paris 75248 Cedex 05, France
- CNRS UMR3244, Paris 75005, France
- Sorbonne University, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Carla Duval
- Genetics of Tumor Suppression, Institut Curie, Paris 75248 Cedex 05, France
- CNRS UMR3244, Paris 75005, France
- Sorbonne University, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Eliana Eldawra
- Genetics of Tumor Suppression, Institut Curie, Paris 75248 Cedex 05, France
- CNRS UMR3244, Paris 75005, France
- Sorbonne University, Paris 75005, France
- PSL Research University, Paris 75005, France
| | | | - Franck Toledo
- Genetics of Tumor Suppression, Institut Curie, Paris 75248 Cedex 05, France
- CNRS UMR3244, Paris 75005, France
- Sorbonne University, Paris 75005, France
- PSL Research University, Paris 75005, France
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11
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Baniulyte G, Durham SA, Merchant LE, Sammons MA. Shared Gene Targets of the ATF4 and p53 Transcriptional Networks. Mol Cell Biol 2023; 43:426-449. [PMID: 37533313 PMCID: PMC10448979 DOI: 10.1080/10985549.2023.2229225] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 08/04/2023] Open
Abstract
The master tumor suppressor p53 regulates multiple cell fate decisions, such as cell cycle arrest and apoptosis, via transcriptional control of a broad gene network. Dysfunction in the p53 network is common in cancer, often through mutations that inactivate p53 or other members of the pathway. Induction of tumor-specific cell death by restoration of p53 activity without off-target effects has gained significant interest in the field. In this study, we explore the gene regulatory mechanisms underlying a putative anticancer strategy involving stimulation of the p53-independent integrated stress response (ISR). Our data demonstrate the p53 and ISR pathways converge to independently regulate common metabolic and proapoptotic genes. We investigated the architecture of multiple gene regulatory elements bound by p53 and the ISR effector ATF4 controlling this shared regulation. We identified additional key transcription factors that control basal and stress-induced regulation of these shared p53 and ATF4 target genes. Thus, our results provide significant new molecular and genetic insight into gene regulatory networks and transcription factors that are the target of numerous antitumor therapies.
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Affiliation(s)
- Gabriele Baniulyte
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Serene A. Durham
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Lauren E. Merchant
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Morgan A. Sammons
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
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12
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Lin KH, Lee SC, Dacheux MA, Norman DD, Balogh A, Bavaria M, Lee H, Tigyi G. E2F7 drives autotaxin/Enpp2 transcription via chromosome looping: Repression by p53 in murine but not in human carcinomas. FASEB J 2023; 37:e23058. [PMID: 37358838 PMCID: PMC10364077 DOI: 10.1096/fj.202300838r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/31/2023] [Accepted: 06/13/2023] [Indexed: 06/27/2023]
Abstract
Dysregulation of the autotaxin (ATX, Enpp2)-lysophosphatidic acid (LPA) signaling in cancerous cells contributes to tumorigenesis and therapy resistance. We previously found that ATX activity was elevated in p53-KO mice compared to wild-type (WT) mice. Here, we report that ATX expression was upregulated in mouse embryonic fibroblasts from p53-KO and p53R172H mutant mice. ATX promoter analysis combined with yeast one-hybrid testing revealed that WT p53 directly inhibits ATX expression via E2F7. Knockdown of E2F7 reduced ATX expression and chromosome immunoprecipitation showed that E2F7 promotes Enpp2 transcription through cooperative binding to two E2F7 sites (promoter region -1393 bp and second intron 996 bp). Using chromosome conformation capture, we found that chromosome looping brings together the two E2F7 binding sites. We discovered a p53 binding site in the first intron of murine Enpp2, but not in human ENPP2. Binding of p53 disrupted the E2F7-mediated chromosomal looping and repressed Enpp2 transcription in murine cells. In contrast, we found no disruption of E2F7-mediated ENPP2 transcription via direct p53 binding in human carcinoma cells. In summary, E2F7 is a common transcription factor that upregulates ATX in human and mouse cells but is subject to steric interference by direct intronic p53 binding only in mice.
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Affiliation(s)
- Kuan-Hung Lin
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Sue Chin Lee
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Mélanie A Dacheux
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Derek D Norman
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Andrea Balogh
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Mitul Bavaria
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Hsinyu Lee
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Gabor Tigyi
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
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13
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Fischer M, Riege K, Hoffmann S. The landscape of human p53-regulated long non-coding RNAs reveals critical host gene co-regulation. Mol Oncol 2023. [PMID: 36852646 DOI: 10.1002/1878-0261.13405] [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: 11/23/2022] [Revised: 01/20/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023] Open
Abstract
The role of long non-coding RNAs (lncRNAs) in p53-mediated tumor suppression has become increasingly appreciated in the past decade. Thus, the identification of p53-regulated lncRNAs can be a promising starting point to select and prioritize lncRNAs for functional analyses. By integrating transcriptome and transcription factor-binding data, we identified 379 lncRNAs that are recurrently differentially regulated by p53. Dissecting the mechanisms by which p53 regulates many of them, we identified sets of lncRNAs regulated either directly by p53 or indirectly through the p53-RFX7 and p53-p21-DREAM/RB:E2F pathways. Importantly, we identified multiple p53-responsive lncRNAs that are co-regulated with their protein-coding host genes, revealing an important mechanism by which p53 may regulate lncRNAs. Further analysis of transcriptome data and clinical data from cancer patients showed that recurrently p53-regulated lncRNAs are associated with patient survival. Together, the integrative analysis of the landscape of p53-regulated lncRNAs provides a powerful resource facilitating the identification of lncRNA function and displays the mechanisms of p53-dependent regulation that could be exploited for developing anticancer approaches.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
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14
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Ravari A, Ghoreishi SF, Imani M. Optimal Recursive Expert-Enabled Inference in Regulatory Networks. IEEE CONTROL SYSTEMS LETTERS 2022; 7:1027-1032. [PMID: 36644010 PMCID: PMC9835687 DOI: 10.1109/lcsys.2022.3229054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Accurate inference of biological systems, such as gene regulatory networks and microbial communities, is a key to a deep understanding of their underlying mechanisms. Despite several advances in the inference of regulatory networks in recent years, the existing techniques cannot incorporate expert knowledge into the inference process. Expert knowledge contains valuable biological information and is often reflected in available biological data, such as interventions made by biologists for treating diseases. Given the complexity of regulatory networks and the limitation of biological data, ignoring expert knowledge can lead to inaccuracy in the inference process. This paper models the regulatory networks using Boolean network with perturbation. We develop an expert-enabled inference method for inferring the unknown parameters of the network model using expert-acquired data. Given the availability of information about data-acquiring objectives and expert confidence, the proposed method optimally quantifies the expert knowledge along with the temporal changes in the data for the inference process. The numerical experiments investigate the performance of the proposed method using the well-known p53-MDM2 gene regulatory network.
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Affiliation(s)
- Amirhossein Ravari
- Department of Electrical and Computer Engineering, Northeastern University
| | - Seyede Fatemeh Ghoreishi
- Department of Civil and Environmental Engineering and Khoury College of Computer Sciences at Northeastern University
| | - Mahdi Imani
- Department of Electrical and Computer Engineering, Northeastern University
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15
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Synthesizing genome regulation data with vote-counting. Trends Genet 2022; 38:1208-1216. [PMID: 35817619 DOI: 10.1016/j.tig.2022.06.012] [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: 03/28/2022] [Revised: 05/31/2022] [Accepted: 06/16/2022] [Indexed: 01/24/2023]
Abstract
The increasing availability of high-throughput datasets allows amalgamating research information across a large body of genome regulation studies. Given the recent success of meta-analyses on transcriptional regulators, epigenetic marks, and enhancer:gene associations, we expect that such surveys will continue to provide novel and reproducible insights. However, meta-analyses are severely hampered by the diversity of available data, concurring protocols, an eclectic amount of bioinformatics tools, and myriads of conceivable parameter combinations. Such factors can easily bar life scientists from synthesizing omics data and substantially curb their interpretability. Despite statistical challenges of the method, we would like to emphasize the advantages of joining data from different sources through vote-counting and showcase examples that achieve a simple but highly intuitive data integration.
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16
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Fischer M, Schade AE, Branigan TB, Müller GA, DeCaprio JA. Coordinating gene expression during the cell cycle. Trends Biochem Sci 2022; 47:1009-1022. [PMID: 35835684 DOI: 10.1016/j.tibs.2022.06.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 02/08/2023]
Abstract
Cell cycle-dependent gene transcription is tightly controlled by the retinoblastoma (RB):E2F and DREAM complexes, which repress all cell cycle genes during quiescence. Cyclin-dependent kinase (CDK) phosphorylation of RB and DREAM allows for the expression of two gene sets. The first set of genes, with peak expression in G1/S, is activated by E2F transcription factors (TFs) and is required for DNA synthesis. The second set, with maximum expression during G2/M, is required for mitosis and is coordinated by the MuvB complex, together with B-MYB and Forkhead box M1 (FOXM1). In this review, we summarize the key findings that established the distinct control mechanisms regulating G1/S and G2/M gene expression in mammals and discuss recent advances in the understanding of the temporal control of these genes.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
| | - Amy E Schade
- Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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17
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Mohibi S, Chen X, Zhang J. ZFP14 Regulates Cancer Cell Growth and Migration by Modulating p53 Protein Stability as Part of the MDM2 E3 Ubiquitin Ligase Complex. Cancers (Basel) 2022; 14:cancers14215226. [PMID: 36358645 PMCID: PMC9655198 DOI: 10.3390/cancers14215226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/16/2022] Open
Abstract
Multi-zinc finger proteins that contain a KRAB domain are part of the biggest family of transcription factors in mammals. However, the physiological or pathological functions for the majority of them are unknown. Here, we showed that ZFP14 (also known as ZNF531) is a p53 target gene that can be induced upon genotoxic stress in a p53-dependent manner. To determine the function of ZFP14 in mouse and human cancer cell lines, we generated multiple cell lines where ZFP14 was knocked out. We showed that ZFP14-KO inhibits cancer cell growth and migration. We also showed that, as a target of p53, ZFP14, in turn, represses p53 expression and that the knockdown of p53 restores the potential of ZFP14-KO cells to proliferate and migrate. Mechanistically, we found that ZFP14 modulates p53 protein stability by increasing its ubiquitination via associating with and possibly enhancing MDM2/p53 complex integrity through its zinc finger domains. Our findings suggest that the reciprocal regulation of p53 and ZFP14 represents a novel p53-ZFP14 regulatory loop and that ZFP14 plays a role in p53-dependent tumor suppression.
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18
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Wang CY, Wang CH, Mai RT, Chen TW, Li CW, Chao CH. Mutant p53-microRNA-200c-ZEB2-Axis-Induced CPT1C Elevation Contributes to Metabolic Reprogramming and Tumor Progression in Basal-Like Breast Cancers. Front Oncol 2022; 12:940402. [PMID: 35936710 PMCID: PMC9351713 DOI: 10.3389/fonc.2022.940402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
TP53 is mutated in more than 80% of basal-like breast cancers (BLBCs). BLBCs with TP53 mutation are usually high-grade and have worse responses to chemotherapy, leading to poor clinical outcomes. Wild-type p53 (WTp53) is well-accepted to promote fatty acid oxidation (FAO); however, in this study, we demonstrate that mutant p53 (Mutp53) enhances FAO activity through constitutively upregulating CPT1C via dysregulating the miR-200c-ZEB2 axis. Sustained CPT1C expression contributes to the metabolic preference of FAO, epithelial-mesenchymal transition (EMT) phenotypes, migration, invasion, and cancer stemness in BLBC, which is mediated by modulating the redox status. Furthermore, interference of CPT1C expression impairs tumor growth and pulmonary colonization of BLBC cells in vivo, and even postpones the occurrence of spontaneous metastasis, resulting in a prolonged disease-specific survival (DSS). Consistently, clinical validation reveals that high CPT1C is observed in breast cancer patients with metastasis and is correlated with poor overall, disease-free, progression-free, and disease-specific survival in BLBC patients. Together, unlike WTp53 which transiently transactivates CPT1C, Mutp53 provides long-term benefits through sustaining CPT1C expression by disturbing the miR-200c-ZEB2 axis, which potentiates FAO and facilitates tumor progression in BLBC, suggesting that targeting Mutp53-CPT1C-driven metabolic reprogramming is promising to serve as novel therapeutic strategies for BLBC in the future.
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Affiliation(s)
- Chen-Yun Wang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Cing-Hong Wang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ru-Tsun Mai
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ting-Wen Chen
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Chia-Wei Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chi-Hong Chao
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- *Correspondence: Chi-Hong Chao,
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19
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Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency. Int J Mol Sci 2022; 23:ijms23147960. [PMID: 35887312 PMCID: PMC9316806 DOI: 10.3390/ijms23147960] [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: 06/28/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 02/01/2023] Open
Abstract
The formation of a tetrameric assembly is essential for the ability of the tumor suppressor protein p53 to act as a transcription factor. Such a quaternary conformation is driven by a specific tetramerization domain, separated from the central DNA-binding domain by a flexible linker. Despite the distance, functional crosstalk between the two domains has been reported. This phenomenon can explain the pathogenicity of some inherited or somatically acquired mutations in the tetramerization domain, including the widespread R337H missense mutation present in the population in south Brazil. In this work, we combined computational predictions through extended all-atom molecular dynamics simulations with functional assays in a genetically defined yeast-based model system to reveal structural features of p53 tetramerization domains and their transactivation capacity and specificity. In addition to the germline and cancer-associated R337H and R337C, other rationally designed missense mutations targeting a significant salt-bridge interaction that stabilizes the p53 tetramerization domain were studied (i.e., R337D, D352R, and the double-mutation R337D plus D352R). The simulations revealed a destabilizing effect of the pathogenic mutations within the p53 tetramerization domain and highlighted the importance of electrostatic interactions between residues 337 and 352. The transactivation assay, performed in yeast by tuning the expression of wild-type and mutant p53 proteins, revealed that p53 tetramerization mutations could decrease the transactivation potential and alter transactivation specificity, in particular by better tolerating negative features in weak DNA-binding sites. These results establish the effect of naturally occurring variations at positions 337 and 352 on p53’s conformational stability and function.
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20
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Padariya M, Jooste ML, Hupp T, Fåhraeus R, Vojtesek B, Vollrath F, Kalathiya U, Karakostis K. The Elephant evolved p53 isoforms that escape mdm2-mediated repression and cancer. Mol Biol Evol 2022; 39:6632613. [PMID: 35792674 PMCID: PMC9279639 DOI: 10.1093/molbev/msac149] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The p53 tumor suppressor is a transcription factor with roles in cell development, apoptosis, oncogenesis, aging, and homeostasis in response to stresses and infections. p53 is tightly regulated by the MDM2 E3 ubiquitin ligase. The p53–MDM2 pathway has coevolved, with MDM2 remaining largely conserved, whereas the TP53 gene morphed into various isoforms. Studies on prevertebrate ancestral homologs revealed the transition from an environmentally induced mechanism activating p53 to a tightly regulated system involving cell signaling. The evolution of this mechanism depends on structural changes in the interacting protein motifs. Elephants such as Loxodonta africana constitute ideal models to investigate this coevolution as they are large and long-living as well as having 20 copies of TP53 isoformic sequences expressing a variety of BOX-I MDM2-binding motifs. Collectively, these isoforms would enhance sensitivity to cellular stresses, such as DNA damage, presumably accounting for strong cancer defenses and other adaptations favoring healthy aging. Here we investigate the molecular evolution of the p53–MDM2 system by combining in silico modeling and in vitro assays to explore structural and functional aspects of p53 isoforms retaining the MDM2 interaction, whereas forming distinct pools of cell signaling. The methodology used demonstrates, for the first time that in silico docking simulations can be used to explore functional aspects of elephant p53 isoforms. Our observations elucidate structural and mechanistic aspects of p53 regulation, facilitate understanding of complex cell signaling, and suggest testable hypotheses of p53 evolution referencing Peto’s Paradox.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
| | - Mia-Lyn Jooste
- Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XR, UK
| | - Ted Hupp
- Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XR, UK
| | - Robin Fåhraeus
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire , Université Paris 7, Hôpital St. Louis, F-75010 Paris , France
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute , 65653 Brno , Czech Republic
- Department of Medical Biosciences, Umeå University , 90185 Umeå , Sweden
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute , 65653 Brno , Czech Republic
| | - Fritz Vollrath
- Department of Zoology, Zoology Research and Administration Building, University of Oxford , Oxford, UK
- Save the Elephants Marula Manor , Marula Lane, Karen P.O. Box 54667. Nairobi 00200. Kenya Office: +254 720 441 178
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
| | - Konstantinos Karakostis
- Inserm UMRS1131, Institut de Génétique Moléculaire , Université Paris 7, Hôpital St. Louis, F-75010 Paris , France
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona) , Spain
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21
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Wang CY, Chao CH. p53-Mediated Indirect Regulation on Cellular Metabolism: From the Mechanism of Pathogenesis to the Development of Cancer Therapeutics. Front Oncol 2022; 12:895112. [PMID: 35707366 PMCID: PMC9190692 DOI: 10.3389/fonc.2022.895112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
The transcription factor p53 is the most well-characterized tumor suppressor involved in multiple cellular processes, which has expanded to the regulation of metabolism in recent decades. Accumulating evidence reinforces the link between the disturbance of p53-relevant metabolic activities and tumor development. However, a full-fledged understanding of the metabolic roles of p53 and the underlying detailed molecular mechanisms in human normal and cancer cells remain elusive, and persistent endeavor is required to foster the entry of drugs targeting p53 into clinical use. This mini-review summarizes the indirect regulation of cellular metabolism by wild-type p53 as well as mutant p53, in which mechanisms are categorized into three major groups: through modulating downstream transcriptional targets, protein-protein interaction with other transcription factors, and affecting signaling pathways. Indirect mechanisms expand the p53 regulatory networks of cellular metabolism, making p53 a master regulator of metabolism and a key metabolic sensor. Moreover, we provide a brief overview of recent achievements and potential developments in the therapeutic strategies targeting mutant p53, emphasizing synthetic lethal methods targeting mutant p53 with metabolism. Then, we delineate synthetic lethality targeting mutant p53 with its indirect regulation on metabolism, which expands the synthetic lethal networks of mutant p53 and broadens the horizon of developing novel therapeutic strategies for p53 mutated cancers, providing more opportunities for cancer patients with mutant p53. Finally, the limitations and current research gaps in studies of metabolic networks controlled by p53 and challenges of research on p53-mediated indirect regulation on metabolism are further discussed.
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Affiliation(s)
- Chen-Yun Wang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Chi-Hong Chao
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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22
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Fischer M, Schwarz R, Riege K, DeCaprio JA, Hoffmann S. TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation. NAR Cancer 2022; 4:zcac009. [PMID: 35350773 PMCID: PMC8946727 DOI: 10.1093/narcan/zcac009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/03/2022] [Accepted: 03/07/2022] [Indexed: 02/03/2023] Open
Abstract
In recent years, our web-atlas at www.TargetGeneReg.org has enabled many researchers to uncover new biological insights and to identify novel regulatory mechanisms that affect p53 and the cell cycle – signaling pathways that are frequently dysregulated in diseases like cancer. Here, we provide a substantial upgrade of the database that comprises an extension to include non-coding genes and the transcription factors ΔNp63 and RFX7. TargetGeneReg 2.0 combines gene expression profiling and transcription factor DNA binding data to determine, for each gene, the response to p53, ΔNp63, and cell cycle signaling. It can be used to dissect common, cell type and treatment-specific effects, identify the most promising candidates, and validate findings. We demonstrate the increased power and more intuitive layout of the resource using realistic examples.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Robert Schwarz
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
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23
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Coronel L, Häckes D, Schwab K, Riege K, Hoffmann S, Fischer M. p53-mediated AKT and mTOR inhibition requires RFX7 and DDIT4 and depends on nutrient abundance. Oncogene 2022; 41:1063-1069. [PMID: 34907345 PMCID: PMC8837532 DOI: 10.1038/s41388-021-02147-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 11/08/2022]
Abstract
In recent years the tumor suppressor p53 has been increasingly recognized as a potent regulator of the cell metabolism and for its ability to inhibit the critical pro-survival kinases AKT and mTOR. The mechanisms through which p53 controls AKT and mTOR, however, are largely unclear. Here, we demonstrate that p53 activates the metabolic regulator DDIT4 indirectly through the regulatory factor X 7 (RFX7). We provide evidence that DDIT4 is required for p53 to inhibit mTOR complex 2 (mTORC2)-dependent AKT activation. Most strikingly, we also find that the DDIT4 regulator RFX7 is required for p53-mediated inhibition of mTORC1 and AKT. Our results suggest that AMPK activation plays no role and p53-mediated AKT inhibition is not critical for p53-mediated mTORC1 inhibition. Moreover, using recently developed physiological cell culture media we uncover that basal p53 and RFX7 activity can play a critical role in restricting mTORC1 activity under physiological nutrient conditions, and we propose a nutrient-dependent model for p53-RFX7-mediated mTORC1 inhibition. These results establish RFX7 and its downstream target DDIT4 as essential effectors in metabolic control elicited by p53.
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Affiliation(s)
- Luis Coronel
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - David Häckes
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Katjana Schwab
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
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24
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Abstract
Cytomegaloviruses (CMVs) are among the largest pathogenic viruses in mammals. To enable replication of their long double-stranded DNA genomes, CMVs induce profound changes in cell cycle regulation. A hallmark of CMV cell cycle control is the establishment of an unusual cell cycle arrest at the G1/S transition, which is characterized by the coexistence of cell cycle stimulatory and inhibitory activities. While CMVs interfere with cellular DNA synthesis and cell division, they activate S-phase-specific gene expression and nucleotide metabolism. This is facilitated by a set of CMV gene products that target master regulators of G1/S progression such as cyclin E and A kinases, Rb-E2F transcription factors, p53-p21 checkpoint proteins, the APC/C ubiquitin ligase, and the nucleotide hydrolase SAMHD1. While the major themes of cell cycle regulation are well conserved between human and murine CMVs (HCMV and MCMV), there are considerable differences at the level of viral cell cycle effectors and their mechanisms of action. Furthermore, both viruses have evolved unique mechanisms to sense the host cell cycle state and modulate the infection program accordingly. This review provides an overview of conserved and divergent features of G1/S control by MCMV and HCMV.
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25
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Coronel L, Riege K, Schwab K, Förste S, Häckes D, Semerau L, Bernhart SH, Siebert R, Hoffmann S, Fischer M. Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress. Nucleic Acids Res 2021; 49:7437-7456. [PMID: 34197623 PMCID: PMC8287911 DOI: 10.1093/nar/gkab575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/25/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Despite its prominence, the mechanisms through which the tumor suppressor p53 regulates most genes remain unclear. Recently, the regulatory factor X 7 (RFX7) emerged as a suppressor of lymphoid neoplasms, but its regulation and target genes mediating tumor suppression remain unknown. Here, we identify a novel p53-RFX7 signaling axis. Integrative analysis of the RFX7 DNA binding landscape and the RFX7-regulated transcriptome in three distinct cell systems reveals that RFX7 directly controls multiple established tumor suppressors, including PDCD4, PIK3IP1, MXD4, and PNRC1, across cell types and is the missing link for their activation in response to p53 and stress. RFX7 target gene expression correlates with cell differentiation and better prognosis in numerous cancer types. Interestingly, we find that RFX7 sensitizes cells to Doxorubicin by promoting apoptosis. Together, our work establishes RFX7’s role as a ubiquitous regulator of cell growth and fate determination and a key node in the p53 transcriptional program.
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Affiliation(s)
- Luis Coronel
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Katjana Schwab
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Silke Förste
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - David Häckes
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Lena Semerau
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Stephan H Bernhart
- Transcriptome Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
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26
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Li D, Xie L, Qiao Z, Mai S, Zhu J, Zhang F, Chen S, Li L, Shen F, Qin Y, Yao H, He S, Ma F. STING-mediated degradation of IFI16 negatively regulates apoptosis by inhibiting p53 phosphorylation at serine 392. J Biol Chem 2021; 297:100930. [PMID: 34216619 PMCID: PMC8326736 DOI: 10.1016/j.jbc.2021.100930] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/17/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
Interferon-γ-inducible factor 16 (IFI16) triggers stimulator of interferon (IFN) genes (STING)-dependent type I IFN production during host antiviral immunity and facilitates p53-dependent apoptosis during suppressing tumorigenesis. We have previously reported that STING-mediated IFI16 degradation negatively regulates type I IFN production. However, it is unknown whether STING also suppresses IFI16/p53-dependent apoptosis via degradation of IFI16. Here, our results from flow cytometry apoptosis detection and immunoblot assays show that IFI16 and nutlin-3, a p53 pathway activator, synergistically induce apoptosis in U2OS and A549 cells. Protein kinase R-triggered phosphorylation of p53 at serine 392 is critical for the IFI16-p53-dependent apoptosis. However, overexpression of STING suppresses p53 serine 392 phosphorylation, p53 transcriptional activity, expression of p53 target genes, and p53-dependent mitochondrial depolarization and apoptosis. In summary, our current study demonstrates that STING-mediated IFI16 degradation negatively regulates IFI16-mediated p53-dependent apoptosis in osteosarcoma and non-small cell lung cancer cells, which suggests a protumorigenic role for STING in certain cancer types because of its potent ability to degrade upstream IFI16.
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Affiliation(s)
- Dapei Li
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China.
| | - Lifen Xie
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Zigang Qiao
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Sanyue Mai
- Department of Laboratory Medicine, 988 Central Hospital of People's Liberation Army, Zhengzhou, China
| | - Jingfei Zhu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Fan Zhang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Shengchuan Chen
- Suzhou Institute of Systems Medicine, Suzhou, China; Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liang Li
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China; Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fangrong Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yanghua Qin
- Department of Laboratory Diagnosis, Changhai Hospital of the Second Military Medical University, Shanghai, China
| | - Haiping Yao
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Sudan He
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China
| | - Feng Ma
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Suzhou Institute of Systems Medicine, Suzhou, China; Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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27
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Amundson SA. Transcriptomics for radiation biodosimetry: progress and challenges. Int J Radiat Biol 2021; 99:925-933. [PMID: 33970766 PMCID: PMC10026363 DOI: 10.1080/09553002.2021.1928784] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/08/2021] [Accepted: 04/19/2021] [Indexed: 01/08/2023]
Abstract
PURPOSE Transcriptomic-based approaches are being developed to meet the needs for large-scale radiation dose and injury assessment and provide population triage following a radiological or nuclear event. This review provides background and definition of the need for new biodosimetry approaches, and summarizes the major advances in this field. It discusses some of the major model systems used in gene signature development, and highlights some of the remaining challenges, including individual variation in gene expression, potential confounding factors, and accounting for the complexity of realistic exposure scenarios. CONCLUSIONS Transcriptomic approaches show great promise for both dose reconstruction and for prediction of individual radiological injury. However, further work will be needed to ensure that gene expression signatures will be robust and appropriate for their intended use in radiological or nuclear emergencies.
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Affiliation(s)
- Sally A Amundson
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, USA
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28
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Scarpa M, Marchiori C, Scarpa M, Castagliuolo I. CD80 expression is upregulated by TP53 activation in human cancer epithelial cells. Oncoimmunology 2021; 10:1907912. [PMID: 33868791 PMCID: PMC8023236 DOI: 10.1080/2162402x.2021.1907912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
CD80 is recognized as one of the most potent costimulatory molecules by which immune cells limit cancer progression; however, the current understanding of the regulation of its expression on human tumor cells is limited. The TP53 tumor suppressor plays a critical role in cancer and its significant role in the control of immune responses is emerging. Here, we evaluated the role of TP53 as a regulator of CD80 expression in human cancer cells. A set of well-known TP53-reactivating compounds were used on TP53-wild-type, TP53-deficient, TP53-mutated and TP53-knockdown cancer cell lines to determine if TP53 can regulate CD80. CD80 expression was analyzed in samples from patients with TP53-active vs TP53-inactive Colon Adenocarcinomas (COAD) from TCGA panCancer Atlas. We report that the pharmacological activation of TP53 can stimulate the expression of CD80 in human tumor cells of epithelial origin. We also provide evidence that CD80 expression exhibits a strong correlation with TP53 activation in a subgroup of colon tumors with better overall survival. These results confirm the link between TP53 and immune surveillance in human cancer and provide the possibility that conventional TP53-activation approaches for tumoricidal effects may be repurposed for immunotherapy strategies.
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Affiliation(s)
- Melania Scarpa
- Laboratory of Advanced Translational Research, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Chiara Marchiori
- Department of Molecular Medicine DMM, University of Padua, Padua, Italy
| | - Marco Scarpa
- Clinica Chirurgica I, Azienda Ospedaliera Di Padova, Padua, Italy
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29
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Valente LJ, Tarangelo A, Li AM, Naciri M, Raj N, Boutelle AM, Li Y, Mello SS, Bieging-Rolett K, DeBerardinis RJ, Ye J, Dixon SJ, Attardi LD. p53 deficiency triggers dysregulation of diverse cellular processes in physiological oxygen. J Cell Biol 2021; 219:152074. [PMID: 32886745 PMCID: PMC7594498 DOI: 10.1083/jcb.201908212] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 06/17/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022] Open
Abstract
The mechanisms by which TP53, the most frequently mutated gene in human cancer, suppresses tumorigenesis remain unclear. p53 modulates various cellular processes, such as apoptosis and proliferation, which has led to distinct cellular mechanisms being proposed for p53-mediated tumor suppression in different contexts. Here, we asked whether during tumor suppression p53 might instead regulate a wide range of cellular processes. Analysis of mouse and human oncogene-expressing wild-type and p53-deficient cells in physiological oxygen conditions revealed that p53 loss concurrently impacts numerous distinct cellular processes, including apoptosis, genome stabilization, DNA repair, metabolism, migration, and invasion. Notably, some phenotypes were uncovered only in physiological oxygen. Transcriptomic analysis in this setting highlighted underappreciated functions modulated by p53, including actin dynamics. Collectively, these results suggest that p53 simultaneously governs diverse cellular processes during transformation suppression, an aspect of p53 function that would provide a clear rationale for its frequent inactivation in human cancer.
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Affiliation(s)
- Liz J Valente
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - Amy Tarangelo
- Department of Biology, Stanford University, Stanford, CA
| | - Albert Mao Li
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - Marwan Naciri
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA.,École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
| | - Nitin Raj
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - Anthony M Boutelle
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - Yang Li
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - Stephano Spano Mello
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA.,Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY
| | - Kathryn Bieging-Rolett
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiangbin Ye
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA
| | - Laura D Attardi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
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30
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Nita A, Muto Y, Katayama Y, Matsumoto A, Nishiyama M, Nakayama KI. The autism-related protein CHD8 contributes to the stemness and differentiation of mouse hematopoietic stem cells. Cell Rep 2021; 34:108688. [PMID: 33535054 DOI: 10.1016/j.celrep.2021.108688] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/26/2020] [Accepted: 12/30/2020] [Indexed: 01/26/2023] Open
Abstract
Chromodomain helicase DNA-binding protein 8 (CHD8) is an ATP-dependent chromatin-remodeling factor that is encoded by the most frequently mutated gene in individuals with autism spectrum disorder. CHD8 is expressed not only in neural tissues but also in many other organs; however, its functions are largely unknown. Here, we show that CHD8 is highly expressed in and maintains the stemness of hematopoietic stem cells (HSCs). Conditional deletion of Chd8 specifically in mouse bone marrow induces cell cycle arrest, apoptosis, and a differentiation block in HSCs in association with upregulation of the expression of p53 target genes. A colony formation assay and bone marrow transplantation reveal that CHD8 deficiency also compromises the stemness of HSCs. Furthermore, additional ablation of p53 rescues the impaired stem cell function and differentiation block of CHD8-deficient HSCs. Our results thus suggest that the CHD8-p53 axis plays a key role in regulation of the stemness and differentiation of HSCs.
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Affiliation(s)
- Akihiro Nita
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yoshiharu Muto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yuta Katayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Masaaki Nishiyama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
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31
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Boutelle AM, Attardi LD. p53 and Tumor Suppression: It Takes a Network. Trends Cell Biol 2021; 31:298-310. [PMID: 33518400 DOI: 10.1016/j.tcb.2020.12.011] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023]
Abstract
The TP53 tumor suppressor is the most frequently mutated gene in human cancer. p53 suppresses tumorigenesis by transcriptionally regulating a network of target genes that play roles in various cellular processes. Though originally characterized as a critical regulator for responses to acute DNA damage (activation of apoptosis and cell cycle arrest), recent studies have highlighted new pathways and transcriptional targets downstream of p53 regulating genomic integrity, metabolism, redox biology, stemness, and non-cell autonomous signaling in tumor suppression. Here, we summarize our current understanding of p53-mediated tumor suppression, situating recent findings from mouse models and unbiased screens in the context of previous studies and arguing for the importance of the pleiotropic effects of the p53 transcriptional network in inhibiting cancer.
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Affiliation(s)
- Anthony M Boutelle
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura D Attardi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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32
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Riege K, Kretzmer H, Sahm A, McDade SS, Hoffmann S, Fischer M. Dissecting the DNA binding landscape and gene regulatory network of p63 and p53. eLife 2020; 9:e63266. [PMID: 33263276 PMCID: PMC7735755 DOI: 10.7554/elife.63266] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
The transcription factor p53 is the best-known tumor suppressor, but its sibling p63 is a master regulator of epidermis development and a key oncogenic driver in squamous cell carcinomas (SCC). Despite multiple gene expression studies becoming available, the limited overlap of reported p63-dependent genes has made it difficult to decipher the p63 gene regulatory network. Particularly, analyses of p63 response elements differed substantially among the studies. To address this intricate data situation, we provide an integrated resource that enables assessing the p63-dependent regulation of any human gene of interest. We use a novel iterative de novo motif search approach in conjunction with extensive ChIP-seq data to achieve a precise global distinction between p53-and p63-binding sites, recognition motifs, and potential co-factors. We integrate these data with enhancer:gene associations to predict p63 target genes and identify those that are commonly de-regulated in SCC representing candidates for prognosis and therapeutic interventions.
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Affiliation(s)
- Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University BelfastBelfastUnited Kingdom
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)JenaGermany
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33
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Feder S, Bruckmann A, McMullen N, Sinal CJ, Buechler C. Chemerin Isoform-Specific Effects on Hepatocyte Migration and Immune Cell Inflammation. Int J Mol Sci 2020; 21:ijms21197205. [PMID: 33003572 PMCID: PMC7582997 DOI: 10.3390/ijms21197205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Murine chemerin is C-terminally processed to the bioactive isoforms, muChem-156 and muChem-155, among which the longer variant protects from hepatocellular carcinoma (HCC). However, the role of muChem-155 is mostly unknown. Here, we aimed to compare the effects of these isoforms on the proliferation, migration and the secretome of the human hepatocyte cell lines HepG2 and Huh7 and the murine Hepa1-6 cell line. Therefore, huChem-157 and -156 were overexpressed in the human cells, and the respective murine variants, muChem-156 and -155, in the murine hepatocytes. Both chemerin isoforms produced by HepG2 and Hepa1-6 cells activated the chemerin receptors chemokine-like receptor 1 (CMKLR1) and G protein-coupled receptor 1 (GPR1). HuChem-157 was the active isoform in the Huh7 cell culture medium. The potencies of muChem-155 and muChem-156 to activate human GPR1 and mouse CMKLR1 were equivalent. Human CMKLR1 was most responsive to muChem-156. Chemerin variants showed no effect on cell viability and proliferation. Activation of the mitogen-activated protein kinases Erk1/2 and p38, and protein levels of the epithelial–mesenchymal transition marker, E-cadherin, were not regulated by the chemerin variants. Migration was reduced in HepG2 and Hepa1-6 cells by the longer isoform. Protective effects of chemerin in HCC include the modulation of cytokines but huChem-156 and huChem-157 overexpression did not change IL-8, CCL20 or osteopontin in the hepatocytes. The conditioned medium of the transfected hepatocytes failed to alter these soluble factors in the cell culture medium of peripheral blood mononuclear cells (PBMCs). Interestingly, the cell culture medium of Huh7 cells producing the inactive variant huChem-155 reduced CCL2 and IL-8 in PBMCs. To sum up, huChem-157 and muChem-156 inhibited hepatocyte migration and may protect from HCC metastasis. HuChem-155 was the only human isoform exerting anti-inflammatory effects on immune cells.
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Affiliation(s)
- Susanne Feder
- Department of Internal Medicine I, Regensburg University Hospital, 93053 Regensburg, Germany;
| | - Astrid Bruckmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93042 Regensburg, Germany;
| | - Nichole McMullen
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (N.M.); (C.J.S.)
| | - Christopher J. Sinal
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (N.M.); (C.J.S.)
| | - Christa Buechler
- Department of Internal Medicine I, Regensburg University Hospital, 93053 Regensburg, Germany;
- Correspondence: ; Tel.: +49-941-944-7009
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34
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Sammons MA, Nguyen TAT, McDade SS, Fischer M. Tumor suppressor p53: from engaging DNA to target gene regulation. Nucleic Acids Res 2020; 48:8848-8869. [PMID: 32797160 PMCID: PMC7498329 DOI: 10.1093/nar/gkaa666] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/24/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
The p53 transcription factor confers its potent tumor suppressor functions primarily through the regulation of a large network of target genes. The recent explosion of next generation sequencing protocols has enabled the study of the p53 gene regulatory network (GRN) and underlying mechanisms at an unprecedented depth and scale, helping us to understand precisely how p53 controls gene regulation. Here, we discuss our current understanding of where and how p53 binds to DNA and chromatin, its pioneer-like role, and how this affects gene regulation. We provide an overview of the p53 GRN and the direct and indirect mechanisms through which p53 affects gene regulation. In particular, we focus on delineating the ubiquitous and cell type-specific network of regulatory elements that p53 engages; reviewing our understanding of how, where, and when p53 binds to DNA and the mechanisms through which these events regulate transcription. Finally, we discuss the evolution of the p53 GRN and how recent work has revealed remarkable differences between vertebrates, which are of particular importance to cancer researchers using mouse models.
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Affiliation(s)
- Morgan A Sammons
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Thuy-Ai T Nguyen
- Genome Integrity & Structural Biology Laboratory and Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
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35
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Fischer M. Mice Are Not Humans: The Case of p53. Trends Cancer 2020; 7:12-14. [PMID: 32950424 DOI: 10.1016/j.trecan.2020.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022]
Abstract
Mouse models represent powerful tools in cancer research that have influenced much of our understanding of tumor development and our current anticancer strategies. Yet, central signaling pathways differ considerably between mouse and human, including gene regulatory networks (GRNs) of the most important tumor suppressor p53 and its oncogenic sibling p63.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.
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p53 drives a transcriptional program that elicits a non-cell-autonomous response and alters cell state in vivo. Proc Natl Acad Sci U S A 2020; 117:23663-23673. [PMID: 32900967 DOI: 10.1073/pnas.2008474117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion of Mdm2, a gene that encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 chromatin immunoprecipitation (ChIP) sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes, which included Mdm2 but not p21 Global p53 activation caused a metaplastic phenotype in the pancreas that was missing in mice with acinar-specific p53 activation, suggesting non-cell-autonomous effects. The p53 cellular response at single-cell resolution in the intestine altered transcriptional cell state, leading to a proximal enterocyte population enriched for genes within oxidative phosphorylation pathways. In addition, a population of active CD8+ T cells was recruited. Combined, this study provides a comprehensive profile of the p53 transcriptional response in vivo, revealing both tissue-specific transcriptomes and a unique signature, which were integrated to induce both cell-autonomous and non-cell-autonomous responses and transcriptional plasticity.
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37
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Kim HJ, Lee SE, Na H, Roe JS, Roh JI, Lee HW. Divergence of the PIERCE1 expression between mice and humans as a p53 target gene. PLoS One 2020; 15:e0236881. [PMID: 32745107 PMCID: PMC7398528 DOI: 10.1371/journal.pone.0236881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/16/2020] [Indexed: 12/23/2022] Open
Abstract
PIERCE1, p53 induced expression 1 in Rb null cells, is a novel p53 target involved in the DNA damage response and cell cycle in mice. These facts prompted us to study the function of PIERCE1 with respect to p53-associated pathophysiology of cancer in humans. Unexpectedly, PIERCE1 did not respond to overexpression and activation of p53 in humans. In this study, we swapped p53 protein expression in human and mouse cells to find the clue of this difference between species. Human p53 expression in mouse cells upregulated PIERCE1 expression, suggesting that p53-responsive elements on the PIERCE1 promoter are crucial, but not the p53 protein itself. Indeed, in silico analyses of PIERCE1 promoters revealed that p53-responsive elements identified in mice are not conserved in humans. Consistently, chromatin immunoprecipitation-sequencing (ChIP-seq) analyses confirmed p53 enrichment against the PIERCE1 promoter region in mice, not in human cells. To complement the p53 study in mice, further promoter analyses suggested that the human PIERCE1 promoter is more similar to guinea pigs, lemurs, and dogs than to rodents. Taken together, our results confirm the differential responsiveness of PIERCE1 expression to p53 due to species differences in PIERCE1 promoters. The results also show partial dissimilarity after p53 induction between mice and humans.
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Affiliation(s)
- Hye Jeong Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Seung Eon Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Heeju Na
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jae-Seok Roe
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jae-il Roh
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- * E-mail: (JIR); (HWL)
| | - Han-Woong Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- * E-mail: (JIR); (HWL)
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38
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Schade AE, Fischer M, DeCaprio JA. RB, p130 and p107 differentially repress G1/S and G2/M genes after p53 activation. Nucleic Acids Res 2020; 47:11197-11208. [PMID: 31667499 PMCID: PMC6868438 DOI: 10.1093/nar/gkz961] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/09/2019] [Accepted: 10/26/2019] [Indexed: 12/19/2022] Open
Abstract
Cell cycle gene expression occurs in two waves. The G1/S genes encode factors required for DNA synthesis and the G2/M genes contribute to mitosis. The Retinoblastoma protein (RB) and DREAM complex (DP, RB-like, E2F4 and MuvB) cooperate to repress all cell cycle genes during G1 and inhibit entry into the cell cycle. DNA damage activates p53 leading to increased levels of p21 and inhibition of cell cycle progression. Whether the G1/S and G2/M genes are differentially repressed by RB and the RB-like proteins p130 and p107 in response to DNA damage is not known. We performed gene expression profiling of primary human fibroblasts upon DNA damage and assessed the effects on G1/S and G2/M genes. Upon p53 activation, p130 and RB cooperated to repress the G1/S genes. In addition, in the absence of RB and p130, p107 contributed to repression of G1/S genes. In contrast, G2/M genes were repressed by p130 and p107 after p53 activation. Furthermore, repression of G2/M genes by p107 and p130 led to reduced entry into mitosis. Our data demonstrates specific roles for RB, p130-DREAM, and p107-DREAM in p53 and p21 mediated repression of cell cycle genes.
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Affiliation(s)
- Amy E Schade
- Program in Virology, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Boston, MA 02115, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Martin Fischer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany
| | - James A DeCaprio
- Program in Virology, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Boston, MA 02115, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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39
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Takasugi M, Firsanov D, Tombline G, Ning H, Ablaeva J, Seluanov A, Gorbunova V. Naked mole-rat very-high-molecular-mass hyaluronan exhibits superior cytoprotective properties. Nat Commun 2020; 11:2376. [PMID: 32398747 PMCID: PMC7217962 DOI: 10.1038/s41467-020-16050-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/10/2020] [Indexed: 12/14/2022] Open
Abstract
Naked mole-rat (NMR), the longest-living rodent, produces very-high-molecular-mass hyaluronan (vHMM-HA), compared to other mammalian species. However, it is unclear if exceptional polymer length of vHMM-HA is important for longevity. Here, we show that vHMM-HA (>6.1 MDa) has superior cytoprotective properties compared to the shorter HMM-HA. It protects not only NMR cells, but also mouse and human cells from stress-induced cell-cycle arrest and cell death in a polymer length-dependent manner. The cytoprotective effect is dependent on the major HA-receptor, CD44. We find that vHMM-HA suppresses CD44 protein-protein interactions, whereas HMM-HA promotes them. As a result, vHMM-HA and HMM-HA induce opposing effects on the expression of CD44-dependent genes, which are associated with the p53 pathway. Concomitantly, vHMM-HA partially attenuates p53 and protects cells from stress in a p53-dependent manner. Our results implicate vHMM-HA in anti-aging mechanisms and suggest the potential applications of vHMM-HA for enhancing cellular stress resistance.
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Affiliation(s)
- Masaki Takasugi
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Denis Firsanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Hanbing Ning
- Department of Digestive Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Zhengzhou, Henan, 450052, People's Republic of China
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
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p53 controls genomic stability and temporal differentiation of human neural stem cells and affects neural organization in human brain organoids. Cell Death Dis 2020; 11:52. [PMID: 31974372 PMCID: PMC6978389 DOI: 10.1038/s41419-019-2208-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 12/25/2022]
Abstract
In this study, we take advantage of human induced pluripotent stem (iPS) cell-derived neural stem cells and brain organoids to study the role of p53 during human brain development. We knocked down (KD) p53 in human neuroepithelial stem (NES) cells derived from iPS cells. Upon p53KD, NES cells rapidly show centrosome amplification and genomic instability. Furthermore, a reduced proliferation rate, downregulation of genes involved in oxidative phosphorylation (OXPHOS), and an upregulation of glycolytic capacity was apparent upon loss of p53. In addition, p53KD neural stem cells display an increased pace of differentiating into neurons and exhibit a phenotype corresponding to more mature neurons compared to control neurons. Using brain organoids, we modeled more specifically cortical neurogenesis. Here we found that p53 loss resulted in brain organoids with disorganized stem cell layer and reduced cortical progenitor cells and neurons. Similar to NES cells, neural progenitors isolated from brain organoids also show a downregulation in several OXPHOS genes. Taken together, this demonstrates an important role for p53 in controlling genomic stability of neural stem cells and regulation of neuronal differentiation, as well as maintaining structural organization and proper metabolic gene profile of neural progenitors in human brain organoids.
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