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Li W, Yang C, Cheng Z, Wu Y, Zhou S, Qi X, Zhang Y, Hu J, Xie M, Chen C. Gallium complex K6 inhibits colorectal cancer by increasing ROS levels to induce DNA damage and enhance phosphatase and tensin homolog activity. MedComm (Beijing) 2024; 5:e665. [PMID: 39049965 PMCID: PMC11266899 DOI: 10.1002/mco2.665] [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: 05/31/2023] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide. In the clinical realm, platinum-based drugs hold an important role in the chemotherapy of CRC. Nonetheless, a multitude of patients, due to tumor protein 53 (TP53) gene mutations, experience the emergence of drug resistance. This phenomenon gravely impairs the effectiveness of therapy and long-term prognosis. Gallium, a metallic element akin to iron, has been reported that has the potential to be used to develop new metal anticancer drugs. In this study, we screened and established the gallium complex K6 as a potent antitumor agent in both in vitro and in vivo. K6 exhibited superior efficacy in impeding the growth, proliferation, and viability of CRC cells carrying TP53 mutations compared to oxaliplatin. Mechanistically, K6 escalated reactive oxygen species levels and led deoxyribonucleic acid (DNA) damage. Furthermore, K6 effectively suppressed the phosphoinositide 3-kinase (PI3K)/protein kinase B (PKB)/glycogen synthase kinase 3 beta (GSK3β) pathway, leading to the degradation of its downstream effectors myelocytomatosis (c-Myc) and Krueppel-like factor 5 (KLF5). Conversely, K6 diminished the protein expression of WW domain-containing protein 1 (WWP1) while activating phosphatase and tensin homolog (PTEN) through c-Myc degradation. This dual action further demonstrated the potential of K6 as a promising therapeutic compound for TP53-mutated CRC.
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Affiliation(s)
- Wei Li
- Yunnan Key Laboratory of Animal Models and Human Disease MechanismsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Kunming College of Life SciencesUniversity of Chinese Academy SciencesKunmingChina
| | - Chuanyu Yang
- Yunnan Key Laboratory of Animal Models and Human Disease MechanismsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Zhuo Cheng
- Yunnan Key Laboratory of Animal Models and Human Disease MechanismsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Kunming College of Life SciencesUniversity of Chinese Academy SciencesKunmingChina
| | - Yuanyuan Wu
- School of Chemical Science and TechnologyYunnan UniversityKunmingChina
| | - Sihan Zhou
- School of Chemical Science and TechnologyYunnan UniversityKunmingChina
| | - Xiaowei Qi
- Department of Breast and Thyroid SurgerySouthwest HospitalThe First Affiliated Hospital of the Army Military Medical UniversityChongqingChina
| | - Yi Zhang
- Department of Breast and Thyroid SurgerySouthwest HospitalThe First Affiliated Hospital of the Army Military Medical UniversityChongqingChina
| | - Jinhui Hu
- The First Hospital of Hunan University of Chinese MedicineChangshaChina
| | - Mingjin Xie
- School of Chemical Science and TechnologyYunnan UniversityKunmingChina
| | - Ceshi Chen
- Yunnan Key Laboratory of Animal Models and Human Disease MechanismsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Academy of Biomedical EngineeringKunming Medical UniversityKunmingChina
- The Third Affiliated HospitalKunming Medical UniversityKunmingChina
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2
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Kin K, Bhogale S, Zhu L, Thomas D, Bertol J, Zheng WJ, Sinha S, Fakhouri WD. Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases. Hum Mol Genet 2024:ddae109. [PMID: 39017605 DOI: 10.1093/hmg/ddae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/08/2024] [Accepted: 07/11/2024] [Indexed: 07/18/2024] Open
Abstract
Disease risk prediction based on genomic sequence and transcriptional profile can improve disease screening and prevention. Despite identifying many disease-associated DNA variants, distinguishing deleterious non-coding DNA variations remains poor for most common diseases. In this study, we designed in vitro experiments to uncover the significance of occupancy and competitive binding between P53 and cMYC on common target genes. Analyzing publicly available ChIP-seq data for P53 and cMYC in embryonic stem cells showed that ~344-366 regions are co-occupied, and on average, two cis-overlapping motifs (CisOMs) per region were identified, suggesting that co-occupancy is evolutionarily conserved. Using U2OS and Raji cells untreated and treated with doxorubicin to increase P53 protein level while potentially reducing cMYC level, ChIP-seq analysis illustrated that around 16 to 922 genomic regions were co-occupied by P53 and cMYC, and substitutions of cMYC signals by P53 were detected post doxorubicin treatment. Around 187 expressed genes near co-occupied regions were altered at mRNA level according to RNA-seq data analysis. We utilized a computational motif-matching approach to illustrate that changes in predicted P53 binding affinity in CisOMs of co-occupied elements significantly correlate with alterations in reporter gene expression. We performed a similar analysis using SNPs mapped in CisOMs for P53 and cMYC from ChIP-seq data, and expression of target genes from GTEx portal. We found significant correlation between change in cMYC-motif binding affinity in CisOMs and altered expression. Our study brings us closer to developing a generally applicable approach to filter etiological non-coding variations associated with common diseases.
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Affiliation(s)
- Katherine Kin
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, School of Dentistry, University of Texas Health Science Center at Houston, 7500 Cambridge St, Houston, TX 77054, United States
| | - Shounak Bhogale
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, United States
| | - Lisha Zhu
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St #600, Houston, TX 77030, United States
| | - Derrick Thomas
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, School of Dentistry, University of Texas Health Science Center at Houston, 7500 Cambridge St, Houston, TX 77054, United States
| | - Jessica Bertol
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, School of Dentistry, University of Texas Health Science Center at Houston, 7500 Cambridge St, Houston, TX 77054, United States
| | - W Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St #600, Houston, TX 77030, United States
| | - Saurabh Sinha
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, United States
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, Georgia Institute of Technology, North Avenue Atlanta, GA 30332, United States
| | - Walid D Fakhouri
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, School of Dentistry, University of Texas Health Science Center at Houston, 7500 Cambridge St, Houston, TX 77054, United States
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, TX 77030, United States
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3
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Scholda J, Nguyen TTA, Kopp F. Long noncoding RNAs as versatile molecular regulators of cellular stress response and homeostasis. Hum Genet 2024; 143:813-829. [PMID: 37782337 PMCID: PMC11294412 DOI: 10.1007/s00439-023-02604-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023]
Abstract
Normal cell and body functions need to be maintained and protected against endogenous and exogenous stress conditions. Different cellular stress response pathways have evolved that are utilized by mammalian cells to recognize, process and overcome numerous stress stimuli in order to maintain homeostasis and to prevent pathophysiological processes. Although these stress response pathways appear to be quite different on a molecular level, they all have in common that they integrate various stress inputs, translate them into an appropriate stress response and eventually resolve the stress by either restoring homeostasis or inducing cell death. It has become increasingly appreciated that non-protein-coding RNA species, such as long noncoding RNAs (lncRNAs), can play critical roles in the mammalian stress response. However, the precise molecular functions and underlying modes of action for many of the stress-related lncRNAs remain poorly understood. In this review, we aim to provide a framework for the categorization of mammalian lncRNAs in stress response and homeostasis based on their experimentally validated modes of action. We describe the molecular functions and physiological roles of selected lncRNAs and develop a concept of how lncRNAs can contribute as versatile players in mammalian stress response and homeostasis. These concepts may be used as a starting point for the identification of novel lncRNAs and lncRNA functions not only in the context of stress, but also in normal physiology and disease.
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Affiliation(s)
- Julia Scholda
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Thi Thuy Anh Nguyen
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Florian Kopp
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria.
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4
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Chen Z, Wang X, Gao X, Arslanovic N, Chen K, Tyler J. Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.20.567799. [PMID: 38045243 PMCID: PMC10690177 DOI: 10.1101/2023.11.20.567799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
In response to DNA double strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR / Cas9 screen. Many of the top hits in our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G1 or G2 phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.
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Affiliation(s)
- Zulong Chen
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nina Arslanovic
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
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5
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Liu Y, Su Z, Tavana O, Gu W. Understanding the complexity of p53 in a new era of tumor suppression. Cancer Cell 2024; 42:946-967. [PMID: 38729160 PMCID: PMC11190820 DOI: 10.1016/j.ccell.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
p53 was discovered 45 years ago as an SV40 large T antigen binding protein, coded by the most frequently mutated TP53 gene in human cancers. As a transcription factor, p53 is tightly regulated by a rich network of post-translational modifications to execute its diverse functions in tumor suppression. Although early studies established p53-mediated cell-cycle arrest, apoptosis, and senescence as the classic barriers in cancer development, a growing number of new functions of p53 have been discovered and the scope of p53-mediated anti-tumor activity is largely expanded. Here, we review the complexity of different layers of p53 regulation, and the recent advance of the p53 pathway in metabolism, ferroptosis, immunity, and others that contribute to tumor suppression. We also discuss the challenge regarding how to activate p53 function specifically effective in inhibiting tumor growth without harming normal homeostasis for cancer therapy.
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Affiliation(s)
- Yanqing Liu
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhenyi Su
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Omid Tavana
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Wei Gu
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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6
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Gaballa A, Gebhardt-Wolf A, Krenz B, Mattavelli G, John M, Cossa G, Andreani S, Schülein-Völk C, Montesinos F, Vidal R, Kastner C, Ade CP, Kneitz B, Gasteiger G, Gallant P, Rosenfeldt M, Riedel A, Eilers M. PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma. Nat Commun 2024; 15:1446. [PMID: 38365788 PMCID: PMC10873513 DOI: 10.1038/s41467-024-45760-8] [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: 09/23/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
In pancreatic ductal adenocarcinoma (PDAC), endogenous MYC is required for S-phase progression and escape from immune surveillance. Here we show that MYC in PDAC cells is needed for the recruitment of the PAF1c transcription elongation complex to RNA polymerase and that depletion of CTR9, a PAF1c subunit, enables long-term survival of PDAC-bearing mice. PAF1c is largely dispensable for normal proliferation and regulation of MYC target genes. Instead, PAF1c limits DNA damage associated with S-phase progression by being essential for the expression of long genes involved in replication and DNA repair. Surprisingly, the survival benefit conferred by CTR9 depletion is not due to DNA damage, but to T-cell activation and restoration of immune surveillance. This is because CTR9 depletion releases RNA polymerase and elongation factors from the body of long genes and promotes the transcription of short genes, including MHC class I genes. The data argue that functionally distinct gene sets compete for elongation factors and directly link MYC-driven S-phase progression to tumor immune evasion.
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Affiliation(s)
- Abdallah Gaballa
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Anneli Gebhardt-Wolf
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Bastian Krenz
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Greta Mattavelli
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Mara John
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Giacomo Cossa
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Silvia Andreani
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Christina Schülein-Völk
- Core Unit High-Content Microscopy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Francisco Montesinos
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Raphael Vidal
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Carolin Kastner
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Burkhard Kneitz
- Department of Urology and Pediatric Urology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Georg Gasteiger
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius Maximilian University Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Mathias Rosenfeldt
- Institute of Pathology, Julius Maximilian University Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Angela Riedel
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany.
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany.
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Nishida Y, Ishizawa J, Ayoub E, Montoya RH, Ostermann LB, Muftuoglu M, Ruvolo VR, Patsilevas T, Scruggs DA, Khazaei S, Mak PY, Tao W, Carter BZ, Boettcher S, Ebert BL, Daver NG, Konopleva M, Seki T, Kojima K, Andreeff M. Enhanced TP53 reactivation disrupts MYC transcriptional program and overcomes venetoclax resistance in acute myeloid leukemias. SCIENCE ADVANCES 2023; 9:eadh1436. [PMID: 38019903 PMCID: PMC10686564 DOI: 10.1126/sciadv.adh1436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023]
Abstract
The tumor suppressor TP53 is frequently inactivated in a mutation-independent manner in cancers and is reactivated by inhibiting its negative regulators. We here cotarget MDM2 and the nuclear exporter XPO1 to maximize transcriptional activity of p53. MDM2/XPO1 inhibition accumulated nuclear p53 and elicited a 25- to 60-fold increase of its transcriptional targets. TP53 regulates MYC, and MDM2/XPO1 inhibition disrupted the c-MYC-regulated transcriptome, resulting in the synergistic induction of apoptosis in acute myeloid leukemia (AML). Unexpectedly, venetoclax-resistant AMLs express high levels of c-MYC and are vulnerable to MDM2/XPO1 inhibition in vivo. However, AML cells persisting after MDM2/XPO1 inhibition exhibit a quiescence- and stress response-associated phenotype. Venetoclax overcomes that resistance, as shown by single-cell mass cytometry. The triple inhibition of MDM2, XPO1, and BCL2 was highly effective against venetoclax-resistant AML in vivo. Our results propose a novel, highly translatable therapeutic approach leveraging p53 reactivation to overcome nongenetic, stress-adapted venetoclax resistance.
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Affiliation(s)
- Yuki Nishida
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edward Ayoub
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rafael Heinz Montoya
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren B. Ostermann
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muharrem Muftuoglu
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vivian R Ruvolo
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tallie Patsilevas
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Darah A. Scruggs
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shayaun Khazaei
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Po Yee Mak
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wenjing Tao
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bing Z. Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Steffen Boettcher
- Department of Medical Oncology and Haematology, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
- Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, The Broad Institute, Boston, MA 02115, USA
| | - Benjamin L. Ebert
- Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, The Broad Institute, Boston, MA 02115, USA
| | - Naval G. Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marina Konopleva
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Section of Leukemia Biology Research, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Kensuke Kojima
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Hematology, Kochi University, Nankoku, Kochi 783-8505, Japan
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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8
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Jha RK, Kouzine F, Levens D. MYC function and regulation in physiological perspective. Front Cell Dev Biol 2023; 11:1268275. [PMID: 37941901 PMCID: PMC10627926 DOI: 10.3389/fcell.2023.1268275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
MYC, a key member of the Myc-proto-oncogene family, is a universal transcription amplifier that regulates almost every physiological process in a cell including cell cycle, proliferation, metabolism, differentiation, and apoptosis. MYC interacts with several cofactors, chromatin modifiers, and regulators to direct gene expression. MYC levels are tightly regulated, and deregulation of MYC has been associated with numerous diseases including cancer. Understanding the comprehensive biology of MYC under physiological conditions is an utmost necessity to demark biological functions of MYC from its pathological functions. Here we review the recent advances in biological mechanisms, functions, and regulation of MYC. We also emphasize the role of MYC as a global transcription amplifier.
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Affiliation(s)
| | | | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, United States
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9
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Kin K, Bhogale S, Zhu L, Thomas D, Bertol J, Zheng WJ, Sinha S, Fakhouri WD. Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases. RESEARCH SQUARE 2023:rs.3.rs-3037310. [PMID: 37503250 PMCID: PMC10371153 DOI: 10.21203/rs.3.rs-3037310/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background and methods Disease risk prediction based on DNA sequence and transcriptional profile can improve disease screening, prevention, and potential therapeutic approaches by revealing contributing genetic factors and altered regulatory networks. Despite identifying many disease-associated DNA variants through genome-wide association studies, distinguishing deleterious non-coding DNA variations remains poor for most common diseases. We previously reported that non-coding variations disrupting cis-overlapping motifs (CisOMs) of opposing transcription factors significantly affect enhancer activity. We designed in vitro experiments to uncover the significance of the co-occupancy and competitive binding and inhibition between P53 and cMYC on common target gene expression. Results Analyzing publicly available ChIP-seq data for P53 and cMYC in human embryonic stem cells and mouse embryonic cells showed that ~ 344-366 genomic regions are co-occupied by P53 and cMYC. We identified, on average, two CisOMs per region, suggesting that co-occupancy is evolutionarily conserved in vertebrates. Our data showed that treating U2OS cells with doxorubicin increased P53 protein level while reducing cMYC level. In contrast, no change in protein levels was observed in Raji cells. ChIP-seq analysis illustrated that 16-922 genomic regions were co-occupied by P53 and cMYC before and after treatment, and substitutions of cMYC signals by P53 were detected after doxorubicin treatment in U2OS. Around 187 expressed genes near co-occupied regions were altered at mRNA level according to RNA-seq data. We utilized a computational motif-matching approach to determine that changes in predicted P53 binding affinity by DNA variations in CisOMs of co-occupied elements significantly correlate with alterations in reporter gene expression. We performed a similar analysis using SNPs mapped in CisOMs for P53 and cMYC from ChIP-seq data in U2OS and Raji, and expression of target genes from the GTEx portal. Conclusions We found a significant correlation between change in motif-predicted cMYC binding affinity by SNPs in CisOMs and altered gene expression. Our study brings us closer to developing a generally applicable approach to filter etiological non-coding variations associated with P53 and cMYC-dependent diseases.
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Affiliation(s)
- Katherine Kin
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, School of Dentistry, University of Texas Health Science Center at Houston
| | | | - Lisha Zhu
- School of Biomedical Informatics, University of Texas Health Science Center at Houston
| | - Derrick Thomas
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, School of Dentistry, University of Texas Health Science Center at Houston
| | - Jessica Bertol
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, School of Dentistry, University of Texas Health Science Center at Houston
| | - W Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston
| | - Saurabh Sinha
- The Wallace H. Coulter Department of Biomedical Engineering
| | - Walid D Fakhouri
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, School of Dentistry, University of Texas Health Science Center at Houston
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10
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Venkatachalapathy H, Brzakala C, Batchelor E, Azarin SM, Sarkar CA. Inertial effect of cell state velocity on the quiescence-proliferation fate decision in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541793. [PMID: 37292599 PMCID: PMC10245870 DOI: 10.1101/2023.05.22.541793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Energy landscapes can provide intuitive depictions of population heterogeneity and dynamics. However, it is unclear whether individual cell behavior, hypothesized to be determined by initial position and noise, is faithfully recapitulated. Using the p21-/Cdk2-dependent quiescence-proliferation decision in breast cancer dormancy as a testbed, we examined single-cell dynamics on the landscape when perturbed by hypoxia, a dormancy-inducing stress. Combining trajectory-based energy landscape generation with single-cell time-lapse microscopy, we found that initial position on a p21/Cdk2 landscape did not fully explain the observed cell-fate heterogeneity under hypoxia. Instead, cells with higher cell state velocities prior to hypoxia, influenced by epigenetic parameters, tended to remain proliferative under hypoxia. Thus, the fate decision on this landscape is significantly influenced by "inertia", a velocity-dependent ability to resist directional changes despite reshaping of the underlying landscape, superseding positional effects. Such inertial effects may markedly influence cell-fate trajectories in tumors and other dynamically changing microenvironments.
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Affiliation(s)
- Harish Venkatachalapathy
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cole Brzakala
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric Batchelor
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samira M. Azarin
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Casim A. Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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11
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Purhonen J, Banerjee R, Wanne V, Sipari N, Mörgelin M, Fellman V, Kallijärvi J. Mitochondrial complex III deficiency drives c-MYC overexpression and illicit cell cycle entry leading to senescence and segmental progeria. Nat Commun 2023; 14:2356. [PMID: 37095097 PMCID: PMC10126100 DOI: 10.1038/s41467-023-38027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Accumulating evidence suggests mitochondria as key modulators of normal and premature aging, yet whether primary oxidative phosphorylation (OXPHOS) deficiency can cause progeroid disease remains unclear. Here, we show that mice with severe isolated respiratory complex III (CIII) deficiency display nuclear DNA damage, cell cycle arrest, aberrant mitoses, and cellular senescence in the affected organs such as liver and kidney, and a systemic phenotype resembling juvenile-onset progeroid syndromes. Mechanistically, CIII deficiency triggers presymptomatic cancer-like c-MYC upregulation followed by excessive anabolic metabolism and illicit cell proliferation against lack of energy and biosynthetic precursors. Transgenic alternative oxidase dampens mitochondrial integrated stress response and the c-MYC induction, suppresses the illicit proliferation, and prevents juvenile lethality despite that canonical OXPHOS-linked functions remain uncorrected. Inhibition of c-MYC with the dominant-negative Omomyc protein relieves the DNA damage in CIII-deficient hepatocytes in vivo. Our results connect primary OXPHOS deficiency to genomic instability and progeroid pathogenesis and suggest that targeting c-MYC and aberrant cell proliferation may be therapeutic in mitochondrial diseases.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Rishi Banerjee
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Vilma Wanne
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Nina Sipari
- Viikki Metabolomics Unit, University of Helsinki, P.O.Box 65, Helsinki, Finland
| | - Matthias Mörgelin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, P.O.Box 117, 221 00, Lund, Sweden
- Colzyx AB, Scheelevägen 2, 22381, Lund, Sweden
| | - Vineta Fellman
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
- Department of Clinical Sciences, Lund, Pediatrics, Lund University, P.O.Box 117, 221 00, Lund, Sweden
- Children's Hospital, Clinicum, University of Helsinki, P.O. Box 22, 00014, Helsinki, Finland
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland.
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland.
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12
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Sampadi B, Vermeulen S, Mišovic B, Boei JJ, Batth TS, Chang JG, Paulsen MT, Magnuson B, Schimmel J, Kool H, Olie CS, Everts B, Vertegaal ACO, Olsen JV, Ljungman M, Jeggo PA, Mullenders LHF, Vrieling H. Divergent Molecular and Cellular Responses to Low and High-Dose Ionizing Radiation. Cells 2022; 11:cells11233794. [PMID: 36497055 PMCID: PMC9739411 DOI: 10.3390/cells11233794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer risk after ionizing radiation (IR) is assumed to be linear with the dose; however, for low doses, definite evidence is lacking. Here, using temporal multi-omic systems analyses after a low (LD; 0.1 Gy) or a high (HD; 1 Gy) dose of X-rays, we show that, although the DNA damage response (DDR) displayed dose proportionality, many other molecular and cellular responses did not. Phosphoproteomics uncovered a novel mode of phospho-signaling via S12-PPP1R7, and large-scale dephosphorylation events that regulate mitotic exit control in undamaged cells and the G2/M checkpoint upon IR in a dose-dependent manner. The phosphoproteomics of irradiated DNA double-strand breaks (DSBs) repair-deficient cells unveiled extended phospho-signaling duration in either a dose-dependent (DDR signaling) or independent (mTOR-ERK-MAPK signaling) manner without affecting signal magnitude. Nascent transcriptomics revealed the transcriptional activation of genes involved in NRF2-regulated antioxidant defense, redox-sensitive ERK-MAPK signaling, glycolysis and mitochondrial function after LD, suggesting a prominent role for reactive oxygen species (ROS) in molecular and cellular responses to LD exposure, whereas DDR genes were prominently activated after HD. However, how and to what extent the observed dose-dependent differences in molecular and cellular responses may impact cancer development remain unclear, as the induction of chromosomal damage was found to be dose-proportional (10-200 mGy).
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Affiliation(s)
- Bharath Sampadi
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
- Correspondence: (B.S.); (H.V.)
| | - Sylvia Vermeulen
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Branislav Mišovic
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Jan J. Boei
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Tanveer S. Batth
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Science, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jer-Gung Chang
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Michelle T. Paulsen
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Magnuson
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Cyriel S. Olie
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Bart Everts
- Department of Parasitology, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Jesper V. Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Science, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mats Ljungman
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Penny A. Jeggo
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Leon H. F. Mullenders
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya 464-8601, Japan
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
- Correspondence: (B.S.); (H.V.)
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13
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Fernandez KC, Feeney L, Smolkin RM, Yen WF, Matthews AJ, Alread W, Petrini JHJ, Chaudhuri J. The structure-selective endonucleases GEN1 and MUS81 mediate complementary functions in safeguarding the genome of proliferating B lymphocytes. eLife 2022; 11:e77073. [PMID: 36190107 PMCID: PMC9581529 DOI: 10.7554/elife.77073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/30/2022] [Indexed: 12/04/2022] Open
Abstract
During the development of humoral immunity, activated B lymphocytes undergo vigorous proliferative, transcriptional, metabolic, and DNA remodeling activities; hence, their genomes are constantly exposed to an onslaught of genotoxic agents and processes. Branched DNA intermediates generated during replication and recombinational repair pose genomic threats if left unresolved and so, they must be eliminated by structure-selective endonucleases to preserve the integrity of these DNA transactions for the faithful duplication and propagation of genetic information. To investigate the role of two such enzymes, GEN1 and MUS81, in B cell biology, we established B-cell conditional knockout mouse models and found that deletion of GEN1 and MUS81 in early B-cell precursors abrogates the development and maturation of B-lineage cells while the loss of these enzymes in mature B cells inhibit the generation of robust germinal centers. Upon activation, these double-null mature B lymphocytes fail to proliferate and survive while exhibiting transcriptional signatures of p53 signaling, apoptosis, and type I interferon response. Metaphase spreads of these endonuclease-deficient cells showed severe and diverse chromosomal abnormalities, including a preponderance of chromosome breaks, consistent with a defect in resolving recombination intermediates. These observations underscore the pivotal roles of GEN1 and MUS81 in safeguarding the genome to ensure the proper development and proliferation of B lymphocytes.
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Affiliation(s)
- Keith Conrad Fernandez
- Immunology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell UniversityNew YorkUnited States
| | - Laura Feeney
- Molecular Biology Program, Memorial Sloan-Kettering Cancer CenterNew YorkUnited States
| | - Ryan M Smolkin
- Immunology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Gerstner Sloan Kettering Graduate School of Biomedical SciencesNew YorkUnited States
| | - Wei-Feng Yen
- Immunology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Biochemistry, Cellular and Molecular Biology Allied Program, Weill Cornell Graduate School of Medical Sciences, Cornell UniversityNew YorkUnited States
| | - Allysia J Matthews
- Immunology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell UniversityNew YorkUnited States
| | - William Alread
- Immunology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - John HJ Petrini
- Molecular Biology Program, Memorial Sloan-Kettering Cancer CenterNew YorkUnited States
- Gerstner Sloan Kettering Graduate School of Biomedical SciencesNew YorkUnited States
- Biochemistry, Cellular and Molecular Biology Allied Program, Weill Cornell Graduate School of Medical Sciences, Cornell UniversityNew YorkUnited States
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell UniversityNew YorkUnited States
- Gerstner Sloan Kettering Graduate School of Biomedical SciencesNew YorkUnited States
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14
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Elsayed GH, Fahim AM, Khodair AI. Synthesis, anti-cancer activity, gene expression and docking stimulation of 2-thioxoimidazolidin-4-one derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Design, synthesis, and biological evaluation of tetrahydroquinolinones and tetrahydroquinolines with anticancer activity. Sci Rep 2022; 12:9985. [PMID: 35705657 PMCID: PMC9200803 DOI: 10.1038/s41598-022-13867-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the most commonly diagnosed cancer in Europe and the United States and the second leading cause of cancer related mortality. A therapeutic strategy used for the treatment of CRC involves targeting the intracellular levels of reactive oxygen species (ROS). In this study, we synthesized a series of novel tetrahydroquinolinones and assessed their ability to inhibit CRC growth and proliferation by evoking cellular stress through ROS. Our results revealed that (2-oxo-4-phenyl-5,6,7,8-tetrahydroquinolin-8-yl) N-(3-fluorophenyl)carbamate (20d) exhibited in vitro antiproliferative activity at micromolar concentrations. The compound also suppressed colony formation and the migration of HCT-116 cells, as well as deregulated the expression of several proteins involved in cell proliferation and metastasis. Furthermore, 20d induced massive oxidative stress by disrupting the balance of cells survival resulting in autophagy via the PI3K/AKT/mTOR signaling pathway. These findings suggest that this tetrahydroquinolinone can be an ideal lead compound for drug discovery based on quinone derivatives.
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16
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Date Y, Taniuchi I, Ito K. Oncogenic Runx1-Myc axis in p53-deficient thymic lymphoma. Gene 2022; 819:146234. [PMID: 35114276 DOI: 10.1016/j.gene.2022.146234] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/23/2021] [Accepted: 01/18/2022] [Indexed: 11/04/2022]
Abstract
p53 deficiency and Myc dysregulation are frequently associated with cancer. However, the molecular mechanisms linking these two major oncogenic events are poorly understood. Using an osteosarcoma model caused by p53 loss, we have recently shown that Runx3 aberrantly upregulates Myc via mR1, a Runx consensus site in the Myc promoter. Here, we focus on thymic lymphoma, a major tumour type caused by germline p53 deletion in mice, and examine whether the oncogenic Runx-Myc axis plays a notable role in the development of p53-deficient lymphoma. Mice lacking p53 specifically in thymocytes (LP mice) mostly succumbed to thymic lymphoma. Runx1 and Myc were upregulated in LP mouse lymphoma compared with the normal thymus. Depletion of Runx1 or Myc prolonged the lifespan of LP mice and suppressed lymphoma development. In lymphoma cells isolated from LP mice, knockdown of Runx1 led to Myc suppression, weakening their tumour forming ability in immunocompromised mice. The mR1 locus was enriched by both Runx1 and H3K27ac, an active chromatin marker. LP mice with mutated mR1 had a longer lifespan and a lower incidence of lymphoma. Treatment with AI-10-104, a Runx inhibitor, improved the survival of LP mice. These results suggest that Myc upregulation by Runx1 is a key event in p53-deficient thymic lymphoma development and provide a clinical rationale for targeting the Runx family in p53-deficient malignancies.
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Affiliation(s)
- Yuki Date
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kosei Ito
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan.
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17
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Kawaharada M, Yamazaki M, Maruyama S, AbÉ T, Chan NN, Kitano T, Kobayashi T, Maeda T, Tanuma JI. Novel cytological model for the identification of early oral cancer diagnostic markers: The carcinoma sequence model. Oncol Lett 2022; 23:76. [PMID: 35111245 PMCID: PMC8771650 DOI: 10.3892/ol.2022.13196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/29/2021] [Indexed: 02/06/2023] Open
Abstract
Most oral squamous cell carcinomas (OSCCs) arise from a premalignant lesion, oral epithelial dysplasia; however, useful markers for the early detection of OSCC are lacking. The present study aimed to establish a novel experimental model to observe changes in the sequential expression patterns of mRNAs and proteins in a rat model of tongue cancer using liquid-based cytology techniques. Cytology specimens were collected at 2, 5, 8, 11, 14, 17 and 21 weeks from rats treated with 4-nitroquinoline 1-oxide to induce tongue cancer. The expression of candidate biomarkers was examined by performing immunocytochemistry and reverse transcription-quantitative PCR. The percentage of positively stained nuclei was calculated as the labeling index (LI). All rats developed OSCC of the tongue at 21 weeks. The mRNA expression levels of bromodomain protein 4 (Brd4), c-Myc and Tp53 were upregulated during the progression from negative for intraepithelial lesion or malignancy to squamous cell carcinoma (SCC). Brd4- and c-Myc-LI increased in low-grade squamous intraepithelial lesion, high-grade squamous intraepithelial lesion and SCC specimens. p53-LI was significantly increased in SCC specimens. This novel experimental model allowed the observation of sequential morphological changes and the expression patterns of mRNAs and proteins during carcinogenesis. Combining immunocytochemistry with cytology-based diagnoses may potentially improve the diagnostic accuracy of OSCC.
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Affiliation(s)
- Masami Kawaharada
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan.,Division of Oral Pathology, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan
| | - Manabu Yamazaki
- Division of Oral Pathology, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan
| | - Satoshi Maruyama
- Oral Pathology Section, Department of Surgical Pathology, Niigata University Hospital, Chuo-ku, Niigata 951-8520, Japan
| | - Tatsuya AbÉ
- Division of Oral Pathology, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan
| | - Nyein Nyein Chan
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan.,Division of Oral Pathology, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan
| | - Taiichi Kitano
- Oral Pathology Section, Department of Surgical Pathology, Niigata University Hospital, Chuo-ku, Niigata 951-8520, Japan
| | - Tadaharu Kobayashi
- Division of Reconstructive Surgery for Oral and Maxillofacial Region, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan
| | - Takeyasu Maeda
- Research Center for Advanced Oral Science, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan
| | - Jun-Ichi Tanuma
- Division of Oral Pathology, Faculty of Dentistry and Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8514, Japan
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18
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Patange S, Ball DA, Wan Y, Karpova TS, Girvan M, Levens D, Larson DR. MYC amplifies gene expression through global changes in transcription factor dynamics. Cell Rep 2022; 38:110292. [PMID: 35081348 DOI: 10.1016/j.celrep.2021.110292] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022] Open
Abstract
The MYC oncogene has been studied for decades, yet there is still intense debate over how this transcription factor controls gene expression. Here, we seek to answer these questions with an in vivo readout of discrete events of gene expression in single cells. We engineered an optogenetic variant of MYC (Pi-MYC) and combined this tool with single-molecule RNA and protein imaging techniques to investigate the role of MYC in modulating transcriptional bursting and transcription factor binding dynamics in human cells. We find that the immediate consequence of MYC overexpression is an increase in the duration rather than in the frequency of bursts, a functional role that is different from the majority of human transcription factors. We further propose that the mechanism by which MYC exerts global effects on the active period of genes is by altering the binding dynamics of transcription factors involved in RNA polymerase II complex assembly and productive elongation.
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Affiliation(s)
- Simona Patange
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yihan Wan
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Michelle Girvan
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - David Levens
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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19
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Gao L, Harbaugh B, Parr K, Patel P, Golem S, Zhang D, Woodroof J, Cui W. MYC Expression Is Associated With p53 Expression and TP53 Aberration and Predicts Poor Overall Survival in Acute Lymphoblastic Leukemia/Lymphoma. Am J Clin Pathol 2022; 157:119-129. [PMID: 34528662 DOI: 10.1093/ajcp/aqab105] [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: 01/30/2021] [Accepted: 05/13/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES We evaluated MYC and p53 expression, TP53 aberration, their relationship, and their impact on overall survival (OS) in acute lymphoblastic leukemia (ALL)/lymphoblastic lymphoma (LBL). METHODS We identified 173 patients with ALL and LBL, including 12 cases of mixed-phenotype acute leukemia, 8 cases of therapy-related B-cell ALL (B-ALL), 119 cases of B-ALL, and 34 cases of T-cell ALL/LBL diagnosed from 2003 to 2019. We retrospectively assessed p53 and MYC expression by immunohistochemistry of bone marrow and correlated MYC expression with p53 expression and TP53 aberration. RESULTS Expression of p53 and MYC was present in 11.5% and 27.7% of ALL/LBL cases (n = 20 and n = 48), respectively. MYC expression was significantly correlated with p53 expression and TP53 aberration (P = .002 and P = .03), and p53 expression and MYC expression had an adverse impact on OS in patients with ALL/LBL (P < .05). MYC and p53 dual expression as well as combined MYC expression and TP53 aberration had a negative impact on OS in patients with ALL/LBL. CONCLUSIONS MYC expression is correlated with p53 overexpression, TP53 aberration, and poor OS in patients with ALL/LBL.
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Affiliation(s)
- Linlin Gao
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Brent Harbaugh
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Kevin Parr
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Payal Patel
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Shivani Golem
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Da Zhang
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Janet Woodroof
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Wei Cui
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO, USA
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20
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Progress and challenges in understanding the regulation and function of p53 dynamics. Biochem Soc Trans 2021; 49:2123-2131. [PMID: 34495325 PMCID: PMC8765192 DOI: 10.1042/bst20210148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023]
Abstract
The dynamics of p53 expression provide a mechanism to increase differentiation between cellular stresses and specificity in appropriate responses. Here, we review recent advances in our understanding of the molecular mechanisms regulating p53 dynamics and the functions of the dynamics in the regulation of p53-dependent cell stress responses. We also compare dynamic encoding in the p53 system with that found in other important cell signaling systems, many of which can interact with the p53 network. Finally, we highlight some of the current challenges in understanding dynamic cell signaling within a larger cellular network context.
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21
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Winkler L, Dimitrova N. A mechanistic view of long noncoding RNAs in cancer. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1699. [PMID: 34668345 PMCID: PMC9016092 DOI: 10.1002/wrna.1699] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important modulators of a wide range of biological processes in normal and disease states. In particular, lncRNAs have garnered significant interest as novel players in the molecular pathology of cancer, spurring efforts to define the functions, and elucidate the mechanisms through which cancer‐associated lncRNAs operate. In this review, we discuss the prevalent mechanisms employed by lncRNAs, with a critical assessment of the methodologies used to determine each molecular function. We survey the abilities of cancer‐associated lncRNAs to enact diverse trans functions throughout the nucleus and in the cytoplasm and examine the local roles of cis‐acting lncRNAs in modulating the expression of neighboring genes. In linking lncRNA functions and mechanisms to their roles in cancer biology, we contend that a detailed molecular understanding of lncRNA functionality is key to elucidating their contributions to tumorigenesis and to unlocking their therapeutic potential. This article is categorized under:Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Lauren Winkler
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
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22
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Ahmadi SE, Rahimi S, Zarandi B, Chegeni R, Safa M. MYC: a multipurpose oncogene with prognostic and therapeutic implications in blood malignancies. J Hematol Oncol 2021; 14:121. [PMID: 34372899 PMCID: PMC8351444 DOI: 10.1186/s13045-021-01111-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/12/2021] [Indexed: 12/17/2022] Open
Abstract
MYC oncogene is a transcription factor with a wide array of functions affecting cellular activities such as cell cycle, apoptosis, DNA damage response, and hematopoiesis. Due to the multi-functionality of MYC, its expression is regulated at multiple levels. Deregulation of this oncogene can give rise to a variety of cancers. In this review, MYC regulation and the mechanisms by which MYC adjusts cellular functions and its implication in hematologic malignancies are summarized. Further, we also discuss potential inhibitors of MYC that could be beneficial for treating hematologic malignancies.
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Affiliation(s)
- Seyed Esmaeil Ahmadi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Rahimi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Zarandi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rouzbeh Chegeni
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, USA.
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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23
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The p53 transcriptional response across tumor types reveals core and senescence-specific signatures modulated by long noncoding RNAs. Proc Natl Acad Sci U S A 2021; 118:2025539118. [PMID: 34326251 PMCID: PMC8346867 DOI: 10.1073/pnas.2025539118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The work by Tesfaye and colleagues defines universal and tumor type–specific features of the p53 tumor suppressor transcriptional network. This study determines a “core” signature of the p53 response across different oncogenic contexts, which defines a universal set of p53 target genes. In addition, this study clarifies the basis for outcome specificity downstream of p53 activation in different oncogenic contexts. We observe that while apoptosis in lymphoma cells is not primarily determined by p53’s transcriptional activity, p53 indirectly promotes senescence in lung adenocarcinoma and sarcoma cells by activating the cis-regulatory long noncoding RNA Pvt1b, which represses Myc levels and its proliferative function. The p53 pathway is a universal tumor suppressor mechanism that limits tumor progression by triggering apoptosis or permanent cell cycle arrest, called senescence. In recent years, efforts to reactivate p53 function in cancer have proven to be a successful therapeutic strategy in murine models and have gained traction with the development of a range of small molecules targeting mutant p53. However, knowledge of the downstream mediators of p53 reactivation in different oncogenic contexts has been limited. Here, we utilized a panel of murine cancer cell lines from three distinct tumor types susceptible to alternative outcomes following p53 restoration to define unique and shared p53 transcriptional signatures. While we found that the majority of p53-bound sites and p53-responsive transcripts are tumor-type specific, analysis of shared targets identified a core signature of genes activated by p53 across all contexts. Furthermore, we identified repression of E2F and Myc target genes as a key feature of senescence. Characterization of p53-induced transcripts revealed core and senescence-specific long noncoding RNAs (lncRNAs) that are predominantly chromatin associated and whose production is coupled to cis-regulatory activities. Functional investigation of the contributions of p53-induced lncRNAs to p53-dependent outcomes highlighted Pvt1b, the p53-dependent isoform of Pvt1, as a mediator of p53-dependent senescence via Myc repression. Inhibition of Pvt1b led to decreased activation of senescence markers and increased levels of markers of proliferation. These findings shed light on the core and outcome-specific p53 restoration signatures across different oncogenic contexts and underscore the key role of the p53-Pvt1b-Myc regulatory axis in mediating proliferative arrest.
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24
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McCann C, Kerr EM. Metabolic Reprogramming: A Friend or Foe to Cancer Therapy? Cancers (Basel) 2021; 13:3351. [PMID: 34283054 PMCID: PMC8267696 DOI: 10.3390/cancers13133351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a major cause of cancer treatment failure, effectively driven by processes that promote escape from therapy-induced cell death. The mechanisms driving evasion of apoptosis have been widely studied across multiple cancer types, and have facilitated new and exciting therapeutic discoveries with the potential to improve cancer patient care. However, an increasing understanding of the crosstalk between cancer hallmarks has highlighted the complexity of the mechanisms of drug resistance, co-opting pathways outside of the canonical "cell death" machinery to facilitate cell survival in the face of cytotoxic stress. Rewiring of cellular metabolism is vital to drive and support increased proliferative demands in cancer cells, and recent discoveries in the field of cancer metabolism have uncovered a novel role for these programs in facilitating drug resistance. As a key organelle in both metabolic and apoptotic homeostasis, the mitochondria are at the forefront of these mechanisms of resistance, coordinating crosstalk in the event of cellular stress, and promoting cellular survival. Importantly, the appreciation of this role metabolism plays in the cytotoxic response to therapy, and the ability to profile metabolic adaptions in response to treatment, has encouraged new avenues of investigation into the potential of exploiting metabolic addictions to improve therapeutic efficacy and overcome drug resistance in cancer. Here, we review the role cancer metabolism can play in mediating drug resistance, and the exciting opportunities presented by imposed metabolic vulnerabilities.
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Affiliation(s)
| | - Emma M. Kerr
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, 97 Lisburn Rd, BT9 7AE Belfast, Ireland;
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25
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Liu Y, Xin B, Yamamoto M, Goto M, Ooshio T, Kamikokura Y, Tanaka H, Meng L, Okada Y, Mizukami Y, Nishikawa Y. Generation of combined hepatocellular-cholangiocarcinoma through transdifferentiation and dedifferentiation in p53-knockout mice. Cancer Sci 2021; 112:3111-3124. [PMID: 34051011 PMCID: PMC8353893 DOI: 10.1111/cas.14996] [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] [Received: 01/09/2021] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 12/29/2022] Open
Abstract
The two principal histological types of primary liver cancers, hepatocellular carcinoma (HCC) and cholangiocarcinoma, can coexist within a tumor, comprising combined hepatocellular‐cholangiocarcinoma (cHCC‐CCA). Although the possible involvement of liver stem/progenitor cells has been proposed for the pathogenesis of cHCC‐CCA, the cells might originate from transformed hepatocytes that undergo ductular transdifferentiation or dedifferentiation. We previously demonstrated that concomitant introduction of mutant HRASV12 (HRAS) and Myc into mouse hepatocytes induced dedifferentiated tumors that expressed fetal/neonatal liver genes and proteins. Here, we examine whether the phenotype of HRAS‐ or HRAS/Myc‐induced tumors might be affected by the disruption of the Trp53 gene, which has been shown to induce biliary differentiation in mouse liver tumors. Hepatocyte‐derived liver tumors were induced in heterozygous and homozygous p53‐knockout (KO) mice by hydrodynamic tail vein injection of HRAS‐ or Myc‐containing transposon cassette plasmids, which were modified by deleting loxP sites, with a transposase‐expressing plasmid. The HRAS‐induced and HRAS/Myc‐induced tumors in the wild‐type mice demonstrated histological features of HCC, whereas the phenotype of the tumors generated in the p53‐KO mice was consistent with cHCC‐CCA. The expression of fetal/neonatal liver proteins, including delta‐like 1, was detected in the HRAS/Myc‐induced but not in the HRAS‐induced cHCC‐CCA tissues. The dedifferentiation in the HRAS/Myc‐induced tumors was more marked in the homozygous p53‐KO mice than in the heterozygous p53‐KO mice and was associated with activation of Myc and YAP and suppression of ERK phosphorylation. Our results suggest that the loss of p53 promotes ductular differentiation of hepatocyte‐derived tumor cells through either transdifferentiation or Myc‐mediated dedifferentiation.
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Affiliation(s)
- Yang Liu
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan.,Department of Pathology, the First Affiliated Hospital and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Bing Xin
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Masahiro Yamamoto
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Masanori Goto
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Takako Ooshio
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Yuki Kamikokura
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Hiroki Tanaka
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Lingtong Meng
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Yoko Okada
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Yusuke Mizukami
- Department of Medicine, Cancer Genomics and Precision Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yuji Nishikawa
- Department of Pathology, Division of Tumor Pathology, Asahikawa Medical University, Asahikawa, Japan
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26
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Chyr J, Zhang Z, Chen X, Zhou X. PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines. Comput Struct Biotechnol J 2021; 19:2870-2880. [PMID: 34093998 PMCID: PMC8142020 DOI: 10.1016/j.csbj.2021.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 10/26/2022] Open
Abstract
Topologically associating domains, or TADs, play important roles in genome organization and gene regulation; however, they are often altered in diseases. High-throughput chromatin conformation capturing assays, such as Hi-C, can capture domains of increased interactions, and TADs and boundaries can be identified using well-established analytical tools. However, generating Hi-C data is expensive. In our study, we addressed the relationship between multi-omics data and higher-order chromatin structures using a newly developed machine-learning model called PredTAD. Our tool uses already-available and cost-effective datatypes such as transcription factor and histone modification ChIPseq data. Specifically, PredTAD utilizes both epigenetic and genetic features as well as neighboring information to classify the entire human genome as boundary or non-boundary regions. Our tool can predict boundary changes between normal and breast cancer genomes. Among the most important features for predicting boundary alterations were CTCF, subunits of cohesin (RAD21 and SMC3), and chromosome number, suggesting their roles in conserved and dynamic boundaries formation. Upon further analysis, we observed that genes near altered TAD boundaries were found to be involved in several important breast cancer signaling pathways such as Ras, Jak-STAT, and estrogen signaling pathways. We also discovered a TAD boundary alteration that contributes to RET oncogene overexpression. PredTAD can also successfully predict TAD boundary changes in other conditions and diseases. In conclusion, our newly developed machine learning tool allowed for a more complete understanding of the dynamic 3D chromatin structures involved in signaling pathway activation, altered gene expression, and disease state in breast cancer cells.
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Affiliation(s)
- Jacqueline Chyr
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
| | - Zhigang Zhang
- School of Information Management and Statistics, Hubei University of Economics, Wuhan, Hubei 430205 China
| | - Xi Chen
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
| | - Xiaobo Zhou
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA
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27
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Pellanda P, Dalsass M, Filipuzzi M, Loffreda A, Verrecchia A, Castillo Cano V, Thabussot H, Doni M, Morelli MJ, Soucek L, Kress T, Mazza D, Mapelli M, Beaulieu ME, Amati B, Sabò A. Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription. EMBO J 2021; 40:e105464. [PMID: 33792944 DOI: 10.15252/embj.2020105464] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity. How these binding modes are integrated to determine select transcriptional outputs remains unresolved. We addressed this question by site-directed mutagenesis of the Myc transcription factor. Impairment of non-specific DNA backbone contacts caused pervasive loss of genome interactions and gene regulation, associated with increased intra-nuclear mobility of the Myc protein in murine cells. In contrast, a mutant lacking base-specific contacts retained DNA-binding and mobility profiles comparable to those of the wild-type protein, but failed to recognize its consensus binding motif (E-box) and could not activate Myc-target genes. Incidentally, this mutant gained weak affinity for an alternative motif, driving aberrant activation of different genes. Altogether, our data show that non-specific DNA binding is required to engage onto genomic regulatory regions; sequence recognition in turn contributes to transcriptional activation, acting at distinct levels: stabilization and positioning of Myc onto DNA, and-unexpectedly-promotion of its transcriptional activity. Hence, seemingly pervasive genome interaction profiles, as detected by ChIP-seq, actually encompass diverse DNA-binding modalities, driving defined, sequence-dependent transcriptional responses.
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Affiliation(s)
- Paola Pellanda
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy.,Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Mattia Dalsass
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Alessia Loffreda
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Virginia Castillo Cano
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain
| | | | - Mirko Doni
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Laura Soucek
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Theresia Kress
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marina Mapelli
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Bruno Amati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Arianna Sabò
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
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28
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Integrative analysis of DNA methylation and gene expression profiles identified potential breast cancer-specific diagnostic markers. Biosci Rep 2021; 40:224161. [PMID: 32412047 PMCID: PMC7263199 DOI: 10.1042/bsr20201053] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is a common malignant tumor among women whose prognosis is largely determined by the period and accuracy of diagnosis. We here propose to identify a robust DNA methylation-based breast cancer-specific diagnostic signature. Genome-wide DNA methylation and gene expression profiles of breast cancer patients along with their adjacent normal tissues from the Cancer Genome Atlas (TCGA) were obtained as the training set. CpGs that with significantly elevated methylation level in breast cancer than not only their adjacent normal tissues and the other ten common cancers from TCGA but also the healthy breast tissues from the Gene Expression Omnibus (GEO) were finally remained for logistic regression analysis. Another independent breast cancer DNA methylation dataset from GEO was used as the testing set. Lots of CpGs were hyper-methylated in breast cancer samples compared with adjacent normal tissues, which tend to be negatively correlated with gene expressions. Eight CpGs located at RIIAD1, ENPP2, ESPN, and ETS1, were finally retained. The diagnostic model was reliable in separating BRCA from normal samples. Besides, chromatin accessibility status of RIIAD1, ENPP2, ESPN and ETS1 showed great differences between MCF-7 and MDA-MB-231 cell lines. In conclusion, the present study should be helpful for breast cancer early and accurate diagnosis.
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29
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Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [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] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
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30
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Lago S, Nadai M, Ruggiero E, Tassinari M, Marušič M, Tosoni B, Frasson I, Cernilogar FM, Pirota V, Doria F, Plavec J, Schotta G, Richter SN. The MDM2 inducible promoter folds into four-tetrad antiparallel G-quadruplexes targetable to fight malignant liposarcoma. Nucleic Acids Res 2021; 49:847-863. [PMID: 33410915 PMCID: PMC7826256 DOI: 10.1093/nar/gkaa1273] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Well-differentiated liposarcoma (WDLPS) is a malignant neoplasia hard to diagnose and treat. Its main molecular signature is amplification of the MDM2-containing genomic region. The MDM2 oncogene is the master regulator of p53: its overexpression enhances p53 degradation and inhibits apoptosis, leading to the tumoral phenotype. Here, we show that the MDM2 inducible promoter G-rich region folds into stable G-quadruplexes both in vitro and in vivo and it is specifically recognized by cellular helicases. Cell treatment with G-quadruplex-ligands reduces MDM2 expression and p53 degradation, thus stimulating cancer cell cycle arrest and apoptosis. Structural characterization of the MDM2 G-quadruplex revealed an extraordinarily stable, unique four-tetrad antiparallel dynamic conformation, amenable to selective targeting. These data indicate the feasibility of an out-of-the-box G-quadruplex-targeting approach to defeat WDLPS and all tumours where restoration of wild-type p53 is sought. They also point to G-quadruplex-dependent genomic instability as possible cause of MDM2 expansion and WDLPS tumorigenesis.
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Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Emanuela Ruggiero
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Martina Tassinari
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Maja Marušič
- Slovenian NMR center, National Institute of Chemistry, Hajdrihova, 19, Ljubljana SI-1000, Slovenia
| | - Beatrice Tosoni
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Germany
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, V. le Taramelli 10, 27100, Pavia, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, V. le Taramelli 10, 27100, Pavia, Italy
| | - Janez Plavec
- Slovenian NMR center, National Institute of Chemistry, Hajdrihova, 19, Ljubljana SI-1000, Slovenia
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Germany
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
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31
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Hume S, Dianov GL, Ramadan K. A unified model for the G1/S cell cycle transition. Nucleic Acids Res 2020; 48:12483-12501. [PMID: 33166394 PMCID: PMC7736809 DOI: 10.1093/nar/gkaa1002] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023] Open
Abstract
Efficient S phase entry is essential for development, tissue repair, and immune defences. However, hyperactive or expedited S phase entry causes replication stress, DNA damage and oncogenesis, highlighting the need for strict regulation. Recent paradigm shifts and conflicting reports demonstrate the requirement for a discussion of the G1/S transition literature. Here, we review the recent studies, and propose a unified model for the S phase entry decision. In this model, competition between mitogen and DNA damage signalling over the course of the mother cell cycle constitutes the predominant control mechanism for S phase entry of daughter cells. Mitogens and DNA damage have distinct sensing periods, giving rise to three Commitment Points for S phase entry (CP1-3). S phase entry is mitogen-independent in the daughter G1 phase, but remains sensitive to DNA damage, such as single strand breaks, the most frequently-occurring lesions that uniquely threaten DNA replication. To control CP1-3, dedicated hubs integrate the antagonistic mitogenic and DNA damage signals, regulating the stoichiometric cyclin: CDK inhibitor ratio for ultrasensitive control of CDK4/6 and CDK2. This unified model for the G1/S cell cycle transition combines the findings of decades of study, and provides an updated foundation for cell cycle research.
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Affiliation(s)
- Samuel Hume
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Grigory L Dianov
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 10, 630090 Novosibirsk, Russian Federation
- Novosibirsk State University, 630090 Novosibirsk, Russian Federation
| | - Kristijan Ramadan
- Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
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32
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Olivero CE, Dimitrova N. Identification and characterization of functional long noncoding RNAs in cancer. FASEB J 2020; 34:15630-15646. [PMID: 33058262 PMCID: PMC7756267 DOI: 10.1096/fj.202001951r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as key regulators in a variety of cellular processes that influence disease states. In particular, many lncRNAs are genetically or epigenetically deregulated in cancer. However, whether lncRNA alterations are passengers acquired during cancer progression or can act as tumorigenic drivers is a topic of ongoing investigation. In this review, we examine the current methodologies underlying the identification of cancer-associated lncRNAs and highlight important considerations for evaluating their biological significance as cancer drivers.
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Affiliation(s)
- Christiane E. Olivero
- Department of Molecular, Cellular and Developmental BiologyYale UniversityNew HavenCTUSA
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental BiologyYale UniversityNew HavenCTUSA
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33
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Ghandhi SA, Sima C, Weber WM, Melo DR, Rudqvist N, Morton SR, Turner HC, Amundson SA. Dose and Dose-Rate Effects in a Mouse Model of Internal Exposure to 137Cs. Part 1: Global Transcriptomic Responses in Blood. Radiat Res 2020; 196:478-490. [PMID: 32931585 PMCID: PMC8864709 DOI: 10.1667/rade-20-00041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/18/2020] [Indexed: 11/03/2022]
Abstract
Internal contamination by radionuclides may constitute a major source of exposure and biological damage after radiation accidents and potentially in a dirty bomb or improvised nuclear device scenario. We injected male C57BL/6 mice with radiolabeled cesium chloride solution (137CsCl) to evaluate the biological effects of varying cumulative doses and dose rates in a two-week study. Injection activities of 137CsCl were 5.71, 6.78, 7.67 and 9.29 MBq, calculated to achieve a target dose of 4 Gy at days 14, 7, 5 and 3, respectively. We collected whole blood samples at days 2, 3, 5, 7 and 14 so that we can publish the issue in Decemberfrom all injection groups and measured gene expression using Agilent Mouse Whole Genome microarrays. We identified both dose-rate-independent and dose-rate-dependent gene expression responses in the time series. Gene Ontology analysis indicated a rapid and persistent immune response to the chronic low-dose-rate irradiation, consistent with depletion of radiosensitive B cells. Pathways impacting platelet aggregation and TP53 signaling appeared activated, but not consistently at all times in the study. Clustering of genes by pattern and identification of dose-rate-independent and -dependent genes provided insight into possible drivers of the dynamic transcriptome response in vivo, and also indicated that TP53 signaling may be upstream of very different transcript response patterns. This characterization of the biological response of blood cells to internal radiation at varying doses and dose rates is an important step in understanding the effects of internal contamination after a nuclear event.
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Affiliation(s)
| | - Chao Sima
- Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, Texas 77845
| | - Waylon M. Weber
- The Lovelace Biomedical Research Institute, Albuquerque, New Mexico 87108
| | - Dunstana R. Melo
- The Lovelace Biomedical Research Institute, Albuquerque, New Mexico 87108
| | - Nils Rudqvist
- Columbia University Irving Medical Center, New York, New York 10032
| | - Shad R. Morton
- Columbia University Irving Medical Center, New York, New York 10032
| | - Helen C. Turner
- Columbia University Irving Medical Center, New York, New York 10032
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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Brambilla F, Garcia-Manteiga JM, Monteleone E, Hoelzen L, Zocchi A, Agresti A, Bianchi ME. Nucleosomes effectively shield DNA from radiation damage in living cells. Nucleic Acids Res 2020; 48:8993-9006. [PMID: 32710624 PMCID: PMC7498322 DOI: 10.1093/nar/gkaa613] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/22/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic DNA is organized in nucleosomes, which package DNA and regulate its accessibility to transcription, replication, recombination and repair. Here, we show that in living cells nucleosomes protect DNA from high-energy radiation and reactive oxygen species. We combined sequence-based methods (ATAC-seq and BLISS) to determine the position of both nucleosomes and double strand breaks (DSBs) in the genome of nucleosome-rich malignant mesothelioma cells, and of the same cells partially depleted of nucleosomes. The results were replicated in the human MCF-7 breast carcinoma cell line. We found that, for each genomic sequence, the probability of DSB formation is directly proportional to the fraction of time it is nucleosome-free; DSBs accumulate distal from the nucleosome dyad axis. Nucleosome free regions and promoters of actively transcribed genes are more sensitive to DSB formation, and consequently to mutation. We argue that this may be true for a variety of chemical and physical DNA damaging agents.
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Affiliation(s)
| | - Jose Manuel Garcia-Manteiga
- IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Lena Hoelzen
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
- Faculty of Biology, Albert-Ludwigs-University Freiburg, D79104 Freiburg, Germany
| | - Angelica Zocchi
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
| | - Alessandra Agresti
- IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Marco E Bianchi
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
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36
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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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Age-related dysfunction of p53-regulated phagocytic activity in macrophages. Biochem Biophys Res Commun 2020; 529:462-466. [PMID: 32703452 DOI: 10.1016/j.bbrc.2020.05.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/15/2020] [Indexed: 11/22/2022]
Abstract
Aging promotes polarization of M2-like macrophages to M1-like macrophages and reduces their phagocytic ability. However, the molecular mechanisms underlying these aging-related changes remain poorly understood. Here, we demonstrate that p53 regulates phagocytic activity in macrophages from young mice but not in those from old ones. Macrophages from both old and young mice expressed functional p53 to induce target genes including p21 and Mdm2. In macrophages from young mice, chemically induced p53 decreased phagocytic activity and c-Myc levels, with the latter change reducing M2-related genes. However, in macrophages from old mice, phagocytic activity and c-Myc expression were independent of p53 activity. Furthermore, c-Myc suppression did not affect M2-related genes in old-mouse macrophages. These results demonstrate that dysregulation of p53 function is a molecular mechanism underlying reduced phagocytic activity in aged-mouse macrophages.
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38
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Nie Z, Guo C, Das SK, Chow CC, Batchelor E, Simons SS, Levens D. Dissecting transcriptional amplification by MYC. eLife 2020; 9:52483. [PMID: 32715994 PMCID: PMC7384857 DOI: 10.7554/elife.52483] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 07/08/2020] [Indexed: 12/13/2022] Open
Abstract
Supraphysiological MYC levels are oncogenic. Originally considered a typical transcription factor recruited to E-boxes (CACGTG), another theory posits MYC a global amplifier increasing output at all active promoters. Both models rest on large-scale genome-wide "-omics'. Because the assumptions, statistical parameter and model choice dictates the '-omic' results, whether MYC is a general or specific transcription factor remains controversial. Therefore, an orthogonal series of experiments interrogated MYC's effect on the expression of synthetic reporters. Dose-dependently, MYC increased output at minimal promoters with or without an E-box. Driving minimal promoters with exogenous (glucocorticoid receptor) or synthetic transcription factors made expression more MYC-responsive, effectively increasing MYC-amplifier gain. Mutations of conserved MYC-Box regions I and II impaired amplification, whereas MYC-box III mutations delivered higher reporter output indicating that MBIII limits over-amplification. Kinetic theory and experiments indicate that MYC activates at least two steps in the transcription-cycle to explain the non-linear amplification of transcription that is essential for global, supraphysiological transcription in cancer.
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Affiliation(s)
- Zuqin Nie
- Laboratory of Pathology, CCR, NCI, NIH, Bethesda, United States
| | - Chunhua Guo
- Steroid Hormones Section, NIDDK/LERB, NIH, Bethesda, United States
| | - Subhendu K Das
- Laboratory of Pathology, CCR, NCI, NIH, Bethesda, United States
| | - Carson C Chow
- Mathematical Biology Section, NIDDK/LBM, NIH, Bethesda, United States
| | - Eric Batchelor
- Laboratory of Pathology, CCR, NCI, NIH, Bethesda, United States.,Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, United States.,Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, United States
| | - S Stoney Simons
- Steroid Hormones Section, NIDDK/LERB, NIH, Bethesda, United States
| | - David Levens
- Laboratory of Pathology, CCR, NCI, NIH, Bethesda, United States
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From cancer to rejuvenation: incomplete regeneration as the missing link (part II: rejuvenation circle). Future Sci OA 2020; 6:FSO610. [PMID: 32983567 PMCID: PMC7491027 DOI: 10.2144/fsoa-2020-0085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the first part of our study, we substantiated that the embryonic reontogenesis and malignant growth (disintegrating growth) pathways are the same, but occur at different stages of ontogenesis, this mechanism is carried out in opposite directions. Cancer has been shown to be epigenetic-blocked redifferentiation and unfinished somatic embryogenesis. We formulated that only this approach of aging elimination has real prospects for a future that is fraught with cancer, as we will be able to convert this risk into a rejuvenation process through the continuous cycling of cell dedifferentiation-differentiation processes (permanent remorphogenesis). Here, we continue to develop the idea of looped ontogenesis and formulate the concept of the rejuvenation circle.
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Date Y, Ito K. Oncogenic RUNX3: A Link between p53 Deficiency and MYC Dysregulation. Mol Cells 2020; 43:176-181. [PMID: 31991537 PMCID: PMC7057839 DOI: 10.14348/molcells.2019.0285] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 12/12/2019] [Indexed: 12/26/2022] Open
Abstract
The RUNX transcription factors serve as master regulators of development and are frequently dysregulated in human cancers. Among the three family members, RUNX3 is the least studied, and has long been considered to be a tumor-suppressor gene in human cancers. This idea is mainly based on the observation that RUNX3 is inactivated by genetic/epigenetic alterations or protein mislocalization during the initiation of tumorigenesis. Recently, this paradigm has been challenged, as several lines of evidence have shown that RUNX3 is upregulated over the course of tumor development. Resolving this paradox and understanding how a single gene can exhibit both oncogenic and tumor-suppressive properties is essential for successful drug targeting of RUNX. We propose a simple explanation for the duality of RUNX3: p53 status. In this model, p53 deficiency causes RUNX3 to become an oncogene, resulting in aberrant upregulation of MYC.
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Affiliation(s)
- Yuki Date
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan
- Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Kosei Ito
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan
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41
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Lim KRQ, Nguyen Q, Yokota T. DUX4 Signalling in the Pathogenesis of Facioscapulohumeral Muscular Dystrophy. Int J Mol Sci 2020; 21:E729. [PMID: 31979100 PMCID: PMC7037115 DOI: 10.3390/ijms21030729] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/17/2020] [Accepted: 01/18/2020] [Indexed: 12/17/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a disabling inherited muscular disorder characterized by asymmetric, progressive muscle weakness and degeneration. Patients display widely variable disease onset and severity, and sometimes present with extra-muscular symptoms. There is a consensus that FSHD is caused by the aberrant production of the double homeobox protein 4 (DUX4) transcription factor in skeletal muscle. DUX4 is normally expressed during early embryonic development, and is then effectively silenced in all tissues except the testis and thymus. Its reactivation in skeletal muscle disrupts numerous signalling pathways that mostly converge on cell death. Here, we review studies on DUX4-affected pathways in skeletal muscle and provide insights into how understanding these could help explain the unique pathogenesis of FSHD.
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Affiliation(s)
- Kenji Rowel Q. Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada; (K.R.Q.L.); (Q.N.)
| | - Quynh Nguyen
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada; (K.R.Q.L.); (Q.N.)
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada; (K.R.Q.L.); (Q.N.)
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada, HM Toupin Neurological Science Research Chair, Edmonton, AB T6G2H7, Canada
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p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis. Mol Cell 2020; 77:761-774.e8. [PMID: 31973890 DOI: 10.1016/j.molcel.2019.12.014] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/20/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
The tumor suppressor p53 transcriptionally activates target genes to suppress cellular proliferation during stress. p53 has also been implicated in the repression of the proto-oncogene Myc, but the mechanism has remained unclear. Here, we identify Pvt1b, a p53-dependent isoform of the long noncoding RNA (lncRNA) Pvt1, expressed 50 kb downstream of Myc, which becomes induced by DNA damage or oncogenic signaling and accumulates near its site of transcription. We show that production of the Pvt1b RNA is necessary and sufficient to suppress Myc transcription in cis without altering the chromatin organization of the locus. Inhibition of Pvt1b increases Myc levels and transcriptional activity and promotes cellular proliferation. Furthermore, Pvt1b loss accelerates tumor growth, but not tumor progression, in an autochthonous mouse model of lung cancer. These findings demonstrate that Pvt1b acts at the intersection of the p53 and Myc transcriptional networks to reinforce the anti-proliferative activities of p53.
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43
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Bisso A, Sabò A, Amati B. MYC in Germinal Center-derived lymphomas: Mechanisms and therapeutic opportunities. Immunol Rev 2019; 288:178-197. [PMID: 30874346 DOI: 10.1111/imr.12734] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/11/2018] [Indexed: 12/13/2022]
Abstract
The rearrangement of immunoglobulin loci during the germinal center reaction is associated with an increased risk of chromosomal translocations that activate oncogenes such as MYC, BCL2 or BCL6, thus contributing to the development of B-cell lymphomas. MYC and BCL2 activation are initiating events in Burkitt's (BL) and Follicular Lymphoma (FL), respectively, but can occur at later stages in other subtypes such as Diffuse Large-B Cell Lymphoma (DLBCL). MYC can also be activated during the progression of FL to the transformed stage. Thus, either DLBCL or FL can give rise to aggressive double-hit lymphomas (DHL) with concurrent activation of MYC and BCL2. Research over the last three decades has improved our understanding of the functions of these oncogenes and the basis for their cooperative action in lymphomagenesis. MYC, in particular, is a transcription factor that contributes to cell activation, growth and proliferation, while concomitantly sensitizing cells to apoptosis, the latter being blocked by BCL2. Here, we review our current knowledge about the role of MYC in germinal center B-cells and lymphomas, discuss MYC-induced dependencies that can sensitize cancer cells to select pharmacological inhibitors, and illustrate their therapeutic potential in aggressive lymphomas-and in particular in DHL, in combination with BCL2 inhibitors.
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Affiliation(s)
- Andrea Bisso
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Arianna Sabò
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Bruno Amati
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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Tesi A, de Pretis S, Furlan M, Filipuzzi M, Morelli MJ, Andronache A, Doni M, Verrecchia A, Pelizzola M, Amati B, Sabò A. An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation. EMBO Rep 2019; 20:e47987. [PMID: 31334602 PMCID: PMC6726900 DOI: 10.15252/embr.201947987] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 06/18/2019] [Accepted: 06/27/2019] [Indexed: 12/18/2022] Open
Abstract
Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size, accompanied by activation of energy-producing and anabolic pathways, widespread chromatin decompaction, and elevated transcriptional activity. These changes depend upon prior induction of the Myc transcription factor, but how Myc controls them remains unclear. We addressed this issue by profiling the response to LPS stimulation in wild-type and c-myc-deleted primary mouse B-cells. Myc is rapidly induced, becomes detectable on virtually all active promoters and enhancers, but has no direct impact on global transcriptional activity. Instead, Myc contributes to the swift up- and down-regulation of several hundred genes, including many known regulators of the aforementioned cellular processes. Myc-activated promoters are enriched for E-box consensus motifs, bind Myc at the highest levels, and show enhanced RNA Polymerase II recruitment, the opposite being true at down-regulated loci. Remarkably, the Myc-dependent signature identified in activated B-cells is also enriched in Myc-driven B-cell lymphomas: hence, besides modulation of new cancer-specific programs, the oncogenic action of Myc may largely rely on sustained deregulation of its normal physiological targets.
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Affiliation(s)
- Alessandra Tesi
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
| | - Stefano de Pretis
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
| | - Marco Filipuzzi
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
- Present address:
Center for Translational Genomics and BioinformaticsIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Adrian Andronache
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
- Present address:
Experimental Therapeutics Program of IFOM ‐ The FIRC Institute of Molecular OncologyMilanItaly
| | - Mirko Doni
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
| | - Alessandro Verrecchia
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
| | - Bruno Amati
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
| | - Arianna Sabò
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
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45
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Ferreira D, Martins B, Soares M, Correia J, Adega F, Ferreira F, Chaves R. Gene expression association study in feline mammary carcinomas. PLoS One 2019; 14:e0221776. [PMID: 31461477 PMCID: PMC6713336 DOI: 10.1371/journal.pone.0221776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/14/2019] [Indexed: 12/15/2022] Open
Abstract
Works on cancer-related genes expression using feline mammary carcinomas (FMCs) are scarce but crucial, not only to validate these tumours as models for human breast cancer studies but also to improve small animal practice. Here, the expression of the cancer-related genes TP53, CCND1, FUS, YBX1, PTBP1, c-MYC and PKM2 was evaluated by real-time RT-qPCR, in a population of FMCs clinically characterized and compared with the disease-free tissue of the same individual. In most of the FMCs analysed, RNA quantification revealed normal expression levels for TP53, c-MYC, YBX1 and FUS, but overexpression in the genes CCND1, PTBP1 and PKM2. The expression levels of these cancer-related genes are strongly correlated with each other, with exception of c-MYC and PKM2 genes. The integration of clinicopathological data with the transcriptional levels revealed several associations. The oral contraceptive administration showed to be positively related with the TP53, YBX1, CCND1, FUS and PTBP1 RNA levels. Positive associations were found between tumour size and YBX1 RNA, and lymph node metastasis with c-MYC RNA levels. This work allowed to verify that many of these cancer-related genes are associated but may also, indirectly, influence other genes, creating a complex molecular cancer network that in the future can provide new cancer biomarkers.
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Affiliation(s)
- Daniela Ferreira
- CAG - Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Bárbara Martins
- CAG - Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Maria Soares
- CBiOS - Research Center for Biosciences & Health Technologies, Faculdade de Medicina Veterinária, Universidade Lusófona de Humanidades e Tecnologias, Lisbon, Portugal
| | - Jorge Correia
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Filomena Adega
- CAG - Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Fernando Ferreira
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Raquel Chaves
- CAG - Laboratory of Cytogenomics and Animal Genomics, Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Silva E, Ideker T. Transcriptional responses to DNA damage. DNA Repair (Amst) 2019; 79:40-49. [PMID: 31102970 PMCID: PMC6570417 DOI: 10.1016/j.dnarep.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/20/2019] [Accepted: 05/04/2019] [Indexed: 12/31/2022]
Abstract
In response to the threat of DNA damage, cells exhibit a dramatic and multi-factorial response spanning from transcriptional changes to protein modifications, collectively known as the DNA damage response (DDR). Here, we review the literature surrounding the transcriptional response to DNA damage. We review differences in observed transcriptional responses as a function of cell cycle stage and emphasize the importance of experimental design in these transcriptional response studies. We additionally consider topics including structural challenges in the transcriptional response to DNA damage as well as the connection between transcription and protein abundance.
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Affiliation(s)
- Erica Silva
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA.
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA; Program in Bioinformatics, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.
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Agarwal S, Milazzo G, Rajapakshe K, Bernardi R, Chen Z, Barbieri E, Koster J, Perini G, Coarfa C, Shohet JM. MYCN acts as a direct co-regulator of p53 in MYCN amplified neuroblastoma. Oncotarget 2018; 9:20323-20338. [PMID: 29755654 PMCID: PMC5945521 DOI: 10.18632/oncotarget.24859] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/06/2018] [Indexed: 12/30/2022] Open
Abstract
The MYC oncogenes and p53 have opposing yet interrelated roles in normal development and tumorigenesis. How MYCN expression alters the biology and clinical responsiveness of pediatric neuroblastoma remains poorly defined. Neuroblastoma is p53 wild type at diagnosis and repression of p53 signaling is required for tumorigenesis. Here, we tested the hypothesis that MYCN amplification alters p53 transcriptional activity in neuroblastoma. Interestingly, we found that MYCN directly binds to the tetrameric form of p53 at its C-terminal domain, and this interaction is independent of MYCN/MAX heterodimer formation. Chromatin analysis of MYCN and p53 targets reveals dramatic changes in binding, as well as co-localization of the MYCN-p53 complex at p53-REs and E-boxes of genes critical to DNA damage responses and cell cycle progression. RNA sequencing studies show that MYCN-p53 co-localization significantly modulated the expression of p53 target genes. Furthermore, MYCN-p53 interaction leads to regulation of alternative p53 targets not regulated in the presence of low MYCN levels. These novel targets include a number of genes involved in lipid metabolism, DNA repair, and apoptosis. Taken together, our findings demonstrate a novel oncogenic role of MYCN as a transcriptional co-regulator of p53 in high-risk MYCN amplified neuroblastoma. Targeting this novel oncogenic function of MYCN may enhance p53-mediated responses and sensitize MYCN amplified tumors to chemotherapy.
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Affiliation(s)
- Saurabh Agarwal
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Kimal Rajapakshe
- Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ronald Bernardi
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Zaowen Chen
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Eveline Barbieri
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Cristian Coarfa
- Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Jason M Shohet
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Bravatà V, Cava C, Minafra L, Cammarata FP, Russo G, Gilardi MC, Castiglioni I, Forte GI. Radiation-Induced Gene Expression Changes in High and Low Grade Breast Cancer Cell Types. Int J Mol Sci 2018; 19:E1084. [PMID: 29617354 PMCID: PMC5979377 DOI: 10.3390/ijms19041084] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND There is extensive scientific evidence that radiation therapy (RT) is a crucial treatment, either alone or in combination with other treatment modalities, for many types of cancer, including breast cancer (BC). BC is a heterogeneous disease at both clinical and molecular levels, presenting distinct subtypes linked to the hormone receptor (HR) status and associated with different clinical outcomes. The aim of this study was to assess the molecular changes induced by high doses of ionizing radiation (IR) on immortalized and primary BC cell lines grouped according to Human epidermal growth factor receptor (HER2), estrogen, and progesterone receptors, to study how HR status influences the radiation response. Our genomic approach using in vitro and ex-vivo models (e.g., primary cells) is a necessary first step for a translational study to describe the common driven radio-resistance features associated with HR status. This information will eventually allow clinicians to prescribe more personalized total doses or associated targeted therapies for specific tumor subtypes, thus enhancing cancer radio-sensitivity. METHODS Nontumorigenic (MCF10A) and BC (MCF7 and MDA-MB-231) immortalized cell lines, as well as healthy (HMEC) and BC (BCpc7 and BCpcEMT) primary cultures, were divided into low grade, high grade, and healthy groups according to their HR status. At 24 h post-treatment, the gene expression profiles induced by two doses of IR treatment with 9 and 23 Gy were analyzed by cDNA microarray technology to select and compare the differential gene and pathway expressions among the experimental groups. RESULTS We present a descriptive report of the substantial alterations in gene expression levels and pathways after IR treatment in both immortalized and primary cell cultures. Overall, the IR-induced gene expression profiles and pathways appear to be cell-line dependent. The data suggest that some specific gene and pathway signatures seem to be linked to HR status. CONCLUSIONS Genomic biomarkers and gene-signatures of specific tumor subtypes, selected according to their HR status and molecular features, could facilitate personalized biological-driven RT treatment planning alone and in combination with targeted therapies.
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Affiliation(s)
- Valentina Bravatà
- Institute of Molecular Bioimaging and Physiology, National Research Council, 90015 Cefalù (Pa), Italy.
| | - Claudia Cava
- Institute of Molecular Bioimaging and Physiology, National Research Council, 20090 Segrate (Mi), Italy .
| | - Luigi Minafra
- Institute of Molecular Bioimaging and Physiology, National Research Council, 90015 Cefalù (Pa), Italy.
| | - Francesco Paolo Cammarata
- Institute of Molecular Bioimaging and Physiology, National Research Council, 90015 Cefalù (Pa), Italy.
| | - Giorgio Russo
- Institute of Molecular Bioimaging and Physiology, National Research Council, 90015 Cefalù (Pa), Italy.
| | - Maria Carla Gilardi
- Institute of Molecular Bioimaging and Physiology, National Research Council, 90015 Cefalù (Pa), Italy.
- Institute of Molecular Bioimaging and Physiology, National Research Council, 20090 Segrate (Mi), Italy .
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology, National Research Council, 20090 Segrate (Mi), Italy .
| | - Giusi Irma Forte
- Institute of Molecular Bioimaging and Physiology, National Research Council, 90015 Cefalù (Pa), Italy.
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