1
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Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Hong SH, Suresh B, Kim KS, Ramakrishna S. USP19 Negatively Regulates p53 and Promotes Cervical Cancer Progression. Mol Biotechnol 2024; 66:2032-2045. [PMID: 37572221 DOI: 10.1007/s12033-023-00814-y] [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: 11/18/2022] [Accepted: 06/29/2023] [Indexed: 08/14/2023]
Abstract
p53 is a tumor suppressor gene activated in response to cellular stressors that inhibits cell cycle progression and induces pro-apoptotic signaling. The protein level of p53 is well balanced by the action of several E3 ligases and deubiquitinating enzymes (DUBs). Several DUBs have been reported to negatively regulate and promote p53 degradation in tumors. In this study, we identified USP19 as a negative regulator of p53 protein level. We demonstrate a direct interaction between USP19 and p53 by pull down assay. The overexpression of USP19 promoted ubiquitination of p53 and reduced its protein half-life. We also demonstrate that CRISPR/Cas9-mediated knockout of USP19 in cervical cancer cells elevates p53 protein levels, resulting in reduced colony formation, cell migration, and cell invasion. Overall, our results indicate that USP19 negatively regulates p53 protein levels in cervical cancer progression.
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Affiliation(s)
- Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea
| | | | - Jencia Carminha Colaco
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea
| | - Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea
| | - Ainsley Mike Antao
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea
| | - Kamini Kaushal
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea
| | - Saba Haq
- Department of Life Science, College of Natural Sciences, Hanyang University, 04763, Seoul, South Korea
| | | | - Soumyadip Das
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea
| | - Vijai Singh
- Department of Biosciences, School of Science, Rajpur, Indrashil University, 382715, Mehsana, Gujarat, India
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Bharathi Suresh
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea.
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea.
- College of Medicine, Hanyang University, 04763, Seoul, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, 04763, Seoul, South Korea
- College of Medicine, Hanyang University, 04763, Seoul, South Korea
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2
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Wichmann CW, Morgan KA, Cao Z, Osellame LD, Guo N, Gan H, Reilly E, Burvenich IJG, O'Keefe GJ, Donnelly PS, Scott AM. Radiolabeling and Preclinical Evaluation of Therapeutic Efficacy of 225Ac-ch806 in Glioblastoma and Colorectal Cancer Xenograft Models. J Nucl Med 2024:jnumed.123.266894. [PMID: 39054282 DOI: 10.2967/jnumed.123.266894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 06/05/2024] [Indexed: 07/27/2024] Open
Abstract
The epidermal growth factor receptor (EGFR) protein is highly expressed in a range of malignancies. Although therapeutic interventions directed toward EGFR have yielded therapeutic responses in cancer patients, side effects are common because of normal-tissue expression of wild-type EGFR. We developed a novel tumor-specific anti-EGFR chimeric antibody ch806 labeled with 225Ac and evaluated its in vitro properties and therapeutic efficacy in murine models of glioblastoma and colorectal cancer. Methods: 225Ac-ch806 was prepared using different chelators, yielding [225Ac]Ac-macropa-tzPEG3Sq-ch806 and [225Ac]Ac-DOTA-dhPzPEG4-ch806. Radiochemical yield, purity, apparent specific activity, and serum stability of 225Ac-ch806 were quantified. In vitro cell killing effect was examined. The biodistribution and therapeutic efficacy of 225Ac-ch806 were investigated in mice with U87MG.de2-7 and DiFi tumors. Pharmacodynamic analysis of tumors after therapy was performed, including DNA double-strand break immunofluorescence of γH2AX, as well as immunohistochemistry for proliferation, cell cycle arrest, and apoptosis. Results: [225Ac]Ac-macropa-tzPEG3Sq-ch806 surpassed [225Ac]Ac-DOTA-dhPzPEG4-ch806 in radiochemical yield, purity, apparent specific activity, and serum stability. [225Ac]Ac-macropa-tzPEG3Sq-ch806 was therefore used for both in vitro and in vivo studies. It displayed a significant, specific, and dose-dependent in vitro cell-killing effect in U87MG.de2-7 cells. 225Ac-ch806 also displayed high tumor uptake and minimal uptake in normal tissues. 225Ac-ch806 significantly inhibited tumor growth and prolonged survival in both U87MG.de2-7 and DiFi models. Enhanced γH2AX staining was observed in 225Ac-ch806-treated tumors compared with controls. Reduced Ki-67 expression was evident in all 225Ac-ch806-treated tumors. Increased expression of p21 and cleaved caspase 3 was shown in U87MG.de2-7 and DiFi tumors treated with 225Ac-ch806. Conclusion: In glioblastoma and colorectal tumor models, 225Ac-ch806 significantly inhibited tumor growth via induction of double-strand breaks, thereby constraining cancer cell proliferation while inducing cell cycle arrest and apoptosis. These findings underscore the potential clinical applicability of 225Ac-ch806 as a potential therapy for EGFR-expressing solid tumors.
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Affiliation(s)
- Christian W Wichmann
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia;
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine A Morgan
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Zhipeng Cao
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
| | - Laura D Osellame
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Nancy Guo
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Hui Gan
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Edward Reilly
- AbbVie-Oncology Discovery, North Chicago, Illinois; and
| | - Ingrid J G Burvenich
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Graeme J O'Keefe
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
| | - Paul S Donnelly
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew M Scott
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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3
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Higbee PS, Dayhoff GW, Anbanandam A, Varma S, Daughdrill G. Structural Adaptation of Secondary p53 Binding Sites on MDM2 and MDMX. J Mol Biol 2024; 436:168626. [PMID: 38810774 DOI: 10.1016/j.jmb.2024.168626] [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: 03/12/2024] [Revised: 04/24/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
Abstract
The thermodynamics of secondary p53 binding sites on MDM2 and MDMX were evaluated using p53 peptides containing residues 16-29, 17-35, and 1-73. All the peptides had large, negative heat capacity (ΔCp), consistent with the burial of p53 residues F19, W23, and L26 in the primary binding sites of MDM2 and MDMX. MDMX has a higher affinity and more negative ΔCp than MDM2 for p5317-35, which is due to MDMX stabilization and not additional interactions with the secondary binding site. ΔCp measurements show binding to the secondary site is inhibited by the disordered tails of MDM2 for WT p53 but not a more helical mutant where proline 27 is changed to alanine. This result is supported by all-atom molecular dynamics simulations showing that p53 residues 30-35 turn away from the disordered tails of MDM2 in P27A17-35 and make direct contact with this region in p5317-35. Molecular dynamics simulations also suggest that an intramolecular methionine-aromatic motif found in both MDM2 and MDMX structurally adapts to support multiple p53 binding modes with the secondary site. ΔCp measurements also show that tighter binding of the P27A mutant to MDM2 and MDMX is due to increased helicity, which reduces the energetic penalty associated with coupled folding and binding. Our results will facilitate the design of selective p53 inhibitors for MDM2 and MDMX.
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Affiliation(s)
- Pirada Serena Higbee
- The Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Guy W Dayhoff
- The Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Asokan Anbanandam
- The Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Sameer Varma
- The Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA; The Department of Physics, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Gary Daughdrill
- The Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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4
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Ingelshed K, Melssen MM, Kannan P, Chandramohan A, Partridge AW, Jiang L, Wermeling F, Lane DP, Nestor M, Spiegelberg D. MDM2/MDMX inhibition by Sulanemadlin synergizes with anti-Programmed Death 1 immunotherapy in wild-type p53 tumors. iScience 2024; 27:109862. [PMID: 38784022 PMCID: PMC11112618 DOI: 10.1016/j.isci.2024.109862] [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: 10/03/2023] [Revised: 11/29/2023] [Accepted: 04/27/2024] [Indexed: 05/25/2024] Open
Abstract
Immunotherapy has revolutionized cancer treatment but its efficacy depends on a robust immune response in the tumor. Silencing of the tumor suppressor p53 is common in tumors and can affect the recruitment and activation of different immune cells, leading to immune evasion and poor therapy response. We found that the p53 activating stapled peptide MDM2/MDMX inhibitor Sulanemadlin (ALRN-6924) inhibited p53 wild-type cancer cell growth in vitro and in vivo. In mice carrying p53 wild-type CT26.WT tumors, monotherapy with the PD-1 inhibitor DX400 or Sulanemadlin delayed tumor doubling time by 50% and 37%, respectively, while combination therapy decreased tumor doubling time by 93% leading to an increased median survival time. Sulanemadlin treatment led to increased immunogenicity and combination treatment with PD-1 inhibition resulted in an increased tumor infiltration of lymphocytes. This combination treatment strategy could potentially turn partial responders into responders of immunotherapy, expanding the patient target group for PD-1-targeting immunotherapy.
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Affiliation(s)
- Katrine Ingelshed
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Marit M. Melssen
- Department of Immunology, Genetics and Pathology, Uppsala University, 75185 Uppsala, Sweden
| | - Pavitra Kannan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | | | | | - Long Jiang
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet, 17177 Stockholm, Sweden
- Center for Molecular Medicine, 17176 Stockholm, Sweden
| | - Fredrik Wermeling
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet, 17177 Stockholm, Sweden
- Center for Molecular Medicine, 17176 Stockholm, Sweden
| | - David P. Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Marika Nestor
- Department of Immunology, Genetics and Pathology, Uppsala University, 75185 Uppsala, Sweden
| | - Diana Spiegelberg
- Department of Immunology, Genetics and Pathology, Uppsala University, 75185 Uppsala, Sweden
- Department of Surgical Sciences, Uppsala University, 75185 Uppsala, Sweden
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5
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de Souza Gama FH, Dutra LA, Hawgood M, Dos Reis CV, Serafim RAM, Ferreira MA, Teodoro BVM, Takarada JE, Santiago AS, Balourdas DI, Nilsson AS, Urien B, Almeida VM, Gileadi C, Ramos PZ, Salmazo A, Vasconcelos SNS, Cunha MR, Mueller S, Knapp S, Massirer KB, Elkins JM, Gileadi O, Mascarello A, Lemmens BBLG, Guimarães CRW, Azevedo H, Couñago RM. Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε. J Med Chem 2024; 67:8609-8629. [PMID: 38780468 DOI: 10.1021/acs.jmedchem.3c02250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.
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Affiliation(s)
| | - Luiz A Dutra
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Michael Hawgood
- Science for Life Laboratory, Sweden, Tomtebodavägen 23A, 17165 Solna, Sweden
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Caio Vinícius Dos Reis
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Ricardo A M Serafim
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Marcos A Ferreira
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, São Paulo 07034-904, Brazil
| | - Bruno V M Teodoro
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, São Paulo 07034-904, Brazil
| | - Jéssica Emi Takarada
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - André S Santiago
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Ann-Sofie Nilsson
- Science for Life Laboratory, Sweden, Tomtebodavägen 23A, 17165 Solna, Sweden
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Bruno Urien
- Science for Life Laboratory, Sweden, Tomtebodavägen 23A, 17165 Solna, Sweden
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Vitor M Almeida
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Carina Gileadi
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Priscila Z Ramos
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Anita Salmazo
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Stanley N S Vasconcelos
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Micael R Cunha
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Susanne Mueller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Katlin B Massirer
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Jonathan M Elkins
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | - Opher Gileadi
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
| | | | - Bennie B L G Lemmens
- Science for Life Laboratory, Sweden, Tomtebodavägen 23A, 17165 Solna, Sweden
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | | | - Hatylas Azevedo
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, São Paulo 07034-904, Brazil
| | - Rafael M Couñago
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, São Paulo Brazil
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6
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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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7
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Liu M, Li H, Huo Z, Chen H, Kang X, Xu B. Bioinformatics Research and qRT-PCR Verify Hub Genes and a Transcription Factor-MicroRNA Feedback Network in Intervertebral Disc Degeneration. Appl Biochem Biotechnol 2024; 196:3184-3198. [PMID: 37632659 DOI: 10.1007/s12010-023-04699-0] [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] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
The present study explores the potentials of bioinformatics analysis to identify hub genes linked to intervertebral disc degeneration (IDD) and explored the potential molecular mechanism of transcription factor-microRNA regulatory network. Furthermore, the hub genes were identified through quantitative reverse transcriptase PCR (qRT-PCR). GEO database expression profile datasets for candidate genes (GSE124272) were downloaded. Genes that were differentially expressed (DEGs) were detected utilizing limma technique in the R programming language. Search Tool for the Retrieval of Interacting Genes/Proteins and NetworkAnalyst software identified hub genes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis as well as Gene Ontology annotation of the DEGs were performed using Metascape. Using Bioinformatics data from the TRRUST, StarBase, and TransmiR databases, a TF-miRNA-hub genes network was constructed. qRT-PCR was utilized to confirm the result. As compared to healthy persons, 521 DEGs, comprising 203 down-regulated and 318 up-regulated genes, as well as 7 core genes, were found in people with IDD. Analysis revealed that all seven essential genes were under-expressed. qRT-PCR further confirmed the low expression of these seven important genes. Based on the TRRUST database, 16 TFs that could target five junction genes were then predicted. According to the StarBase database, four miRNAs were linked to crucial genes, while the TransmiR database predicted regulatory connections between four miRNAs and five TFs. The expression of the TP53-(hsa-miR-183-5p)-CCNB1 TF-miRNA-mRNA interaction network was discovered to be correlated with IDD. Throughout this investigation, a network of TF-miRNA-mRNA connections was built for investigation of the probable molecular mechanisms responsible for IDD. The identification of hub genes associated with IDD may reveal promising IDD treatment strategies.
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Affiliation(s)
- Mingli Liu
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Hao Li
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Zhenxin Huo
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Houcong Chen
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Xinjian Kang
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, No. 406 Jiefangnan Road, Hexi District, Tianjin, 300211, China.
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8
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Yedla P, Bhamidipati P, Syed R, Amanchy R. Working title: Molecular involvement of p53-MDM2 interactome in gastrointestinal cancers. Cell Biochem Funct 2024; 42:e4075. [PMID: 38924101 DOI: 10.1002/cbf.4075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
The interaction between murine double minute 2 (MDM2) and p53, marked by transcriptional induction and feedback inhibition, orchestrates a functional loop dictating cellular fate. The functional loop comprising p53-MDM2 axis is made up of an interactome consisting of approximately 81 proteins, which are spatio-temporally regulated and involved in DNA repair mechanisms. Biochemical and genetic alterations of the interactome result in dysregulation of the p53-mdm2 axis that leads to gastrointestinal (GI) cancers. A large subset of interactome is well known and it consists of proteins that either stabilize p53 or MDM2 and proteins that target the p53-MDM2 complex for ubiquitin-mediated destruction. Upstream signaling events brought about by growth factors and chemical messengers invoke a wide variety of posttranslational modifications in p53-MDM2 axis. Biochemical changes in the transactivation domain of p53 impact the energy landscape, induce conformational switching, alter interaction potential and could change solubility of p53 to redefine its co-localization, translocation and activity. A diverse set of chemical compounds mimic physiological effectors and simulate biochemical modifications of the p53-MDM2 interactome. p53-MDM2 interactome plays a crucial role in DNA damage and repair process. Genetic aberrations in the interactome, have resulted in cancers of GI tract (pancreas, liver, colorectal, gastric, biliary, and esophageal). We present in this article a review of the overall changes in the p53-MDM2 interactors and the effectors that form an epicenter for the development of next-generation molecules for understanding and targeting GI cancers.
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Affiliation(s)
- Poornachandra Yedla
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
- Department of Pharmacogenomics, Institute of Translational Research, Asian Healthcare Foundation, Hyderabad, Telangana, India
| | - Pranav Bhamidipati
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
- Department of Life Sciences, Imperial College London, London, UK
| | - Riyaz Syed
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
| | - Ramars Amanchy
- Division of Applied Biology, CSIR-IICT (Indian Institute of Chemical Technology), Ministry of Science and Technology (GOI), Hyderabad, Telangana, India
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9
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Khan R, Pari B, Puszynski K. Comprehensive Bioinformatic Investigation of TP53 Dysregulation in Diverse Cancer Landscapes. Genes (Basel) 2024; 15:577. [PMID: 38790205 PMCID: PMC11121236 DOI: 10.3390/genes15050577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
P53 overexpression plays a critical role in cancer pathogenesis by disrupting the intricate regulation of cellular proliferation. Despite its firmly established function as a tumor suppressor, elevated p53 levels can paradoxically contribute to tumorigenesis, influenced by factors such as exposure to carcinogens, genetic mutations, and viral infections. This phenomenon is observed across a spectrum of cancer types, including bladder (BLCA), ovarian (OV), cervical (CESC), cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), diffuse large B-cell lymphoma (DLBC), esophageal carcinoma (ESCA), head and neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), kidney renal clear cell carcinoma (KIRC), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), and uterine corpus endometrial carcinoma (UCEC). This broad spectrum of cancers is often associated with increased aggressiveness and recurrence risk. Effective therapeutic strategies targeting tumors with p53 overexpression require a comprehensive approach, integrating targeted interventions aimed at the p53 gene with conventional modalities such as chemotherapy, radiation therapy, and targeted drugs. In this extensive study, we present a detailed analysis shedding light on the multifaceted role of TP53 across various cancers, with a specific emphasis on its impact on disease-free survival (DFS). Leveraging data from the TCGA database and the GTEx dataset, along with GEPIA, UALCAN, and STRING, we identify TP53 overexpression as a significant prognostic indicator, notably pronounced in prostate adenocarcinoma (PRAD). Supported by compelling statistical significance (p < 0.05), our analysis reveals the distinct influence of TP53 overexpression on DFS outcomes in PRAD. Additionally, graphical representations of overall survival (OS) underscore the notable disparity in OS duration between tumors exhibiting elevated TP53 expression (depicted by the red line) and those with lower TP53 levels (indicated by the blue line). The hazard ratio (HR) further emphasizes the profound impact of TP53 on overall survival. Moreover, our investigation delves into the intricate TP53 protein network, unveiling genes exhibiting robust positive correlations with TP53 expression across 13 out of 27 cancers. Remarkably, negative correlations emerge with pivotal tumor suppressor genes. This network analysis elucidates critical proteins, including SIRT1, CBP, p300, ATM, DAXX, HSP 90-alpha, Mdm2, RPA70, 14-3-3 protein sigma, p53, and ASPP2, pivotal in regulating cell cycle dynamics, DNA damage response, and transcriptional regulation. Our study underscores the paramount importance of deciphering TP53 dynamics in cancer, providing invaluable insights into tumor behavior, disease-free survival, and potential therapeutic avenues.
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Affiliation(s)
- Ruby Khan
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
| | - Bakht Pari
- Principal, Nursing School, Lady Reading Hospital Peshawar, Peshawar 25000, Pakistan;
| | - Krzysztof Puszynski
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
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10
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Chauhan S, Jaiswal S, Jakhmola V, Singh B, Bhattacharya S, Garg M, Sengupta S. Potential role of p53 deregulation in modulating immune responses in human malignancies: A paradigm to develop immunotherapy. Cancer Lett 2024; 588:216766. [PMID: 38408603 PMCID: PMC7615729 DOI: 10.1016/j.canlet.2024.216766] [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: 01/19/2024] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
The crucial role played by the oncogenic expression of TP53, stemming from mutation or amyloid formation, in various human malignancies has been extensively studied over the past two decades. Interestingly, the potential role of TP53 as a crucial player in modulating immune responses has provided new insight into the field of cancer biology. The loss of p53's transcriptional functions and/or the acquisition of tumorigenic properties can efficiently modulate the recruitment and functions of myeloid and lymphoid cells, ultimately leading to the evasion of immune responses in human tumors. Consequently, the oncogenic nature of the tumor suppressor p53 can dynamically alter the function of immune cells, providing support for tumor progression and metastasis. This review comprehensively explores the dual role of p53 as both the guardian of the genome and an oncogenic driver, especially in the context of regulation of autophagy, apoptosis, the tumor microenvironment, immune cells, innate immunity, and adaptive immune responses. Additionally, the focus of this review centers on how p53 status in the immune response can be harnessed for the development of tailored therapeutic strategies and their potential application in immunotherapy against human malignancies.
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Affiliation(s)
- Shivi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Shivani Jaiswal
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Vibhuti Jakhmola
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Bhavana Singh
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Sujata Bhattacharya
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India.
| | - Shinjinee Sengupta
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India.
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11
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Sabile JMG, Swords R, Tyner JW. Evaluating targeted therapies in older patients with TP53-mutated AML. Leuk Lymphoma 2024:1-18. [PMID: 38646877 DOI: 10.1080/10428194.2024.2344057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
Mutation of thetumor suppressor gene, TP53 (tumor protein 53), occurs in up to 15% of all patients with acute myeloid leukemia (AML) and is enriched within specific clinical subsets, most notably in older adults, and including secondary AML cases arising from preceding myeloproliferative neoplasm (MPN), myelodysplastic syndrome (MDS), patients exposed to prior DNA-damaging, cytotoxic therapies. In all cases, these tumors have remained difficult to effectively treat with conventional therapeutic regimens. Newer approaches fortreatmentofTP53-mutated AML have shifted to interventions that maymodulateTP53 function, target downstream molecular vulnerabilities, target non-p53 dependent molecular pathways, and/or elicit immunogenic responses. This review will describe the basic biology of TP53, the clinical and biological patterns of TP53 within myeloid neoplasms with a focus on elderly AML patients and will summarize newer therapeutic strategies and current clinical trials.
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Affiliation(s)
- Jean M G Sabile
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Ronan Swords
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR, USA
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12
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Lin CP, Levy PL, Alflen A, Apriamashvili G, Ligtenberg MA, Vredevoogd DW, Bleijerveld OB, Alkan F, Malka Y, Hoekman L, Markovits E, George A, Traets JJH, Krijgsman O, van Vliet A, Poźniak J, Pulido-Vicuña CA, de Bruijn B, van Hal-van Veen SE, Boshuizen J, van der Helm PW, Díaz-Gómez J, Warda H, Behrens LM, Mardesic P, Dehni B, Visser NL, Marine JC, Markel G, Faller WJ, Altelaar M, Agami R, Besser MJ, Peeper DS. Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness. Cancer Cell 2024; 42:623-645.e10. [PMID: 38490212 PMCID: PMC11003465 DOI: 10.1016/j.ccell.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/03/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Genes limiting T cell antitumor activity may serve as therapeutic targets. It has not been systematically studied whether there are regulators that uniquely or broadly contribute to T cell fitness. We perform genome-scale CRISPR-Cas9 knockout screens in primary CD8 T cells to uncover genes negatively impacting fitness upon three modes of stimulation: (1) intense, triggering activation-induced cell death (AICD); (2) acute, triggering expansion; (3) chronic, causing dysfunction. Besides established regulators, we uncover genes controlling T cell fitness either specifically or commonly upon differential stimulation. Dap5 ablation, ranking highly in all three screens, increases translation while enhancing tumor killing. Loss of Icam1-mediated homotypic T cell clustering amplifies cell expansion and effector functions after both acute and intense stimulation. Lastly, Ctbp1 inactivation induces functional T cell persistence exclusively upon chronic stimulation. Our results functionally annotate fitness regulators based on their unique or shared contribution to traits limiting T cell antitumor activity.
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Affiliation(s)
- Chun-Pu Lin
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre L Levy
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Tumor Immunology and Immunotherapy Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Astrid Alflen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Hematology and Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ferhat Alkan
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Yuval Malka
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ettai Markovits
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Austin George
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Carlos Ariel Pulido-Vicuña
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Susan E van Hal-van Veen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pim W van der Helm
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Judit Díaz-Gómez
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hamdy Warda
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Leonie M Behrens
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Paula Mardesic
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bilal Dehni
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Gal Markel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel
| | - William J Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel; Felsenstein Medical Research Center, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands.
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13
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Rutherford KA, McManus KJ. PROTACs: Current and Future Potential as a Precision Medicine Strategy to Combat Cancer. Mol Cancer Ther 2024; 23:454-463. [PMID: 38205881 PMCID: PMC10985480 DOI: 10.1158/1535-7163.mct-23-0747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Proteolysis targeting chimeras (PROTAC) are an emerging precision medicine strategy, which targets key proteins for proteolytic degradation to ultimately induce cancer cell killing. These hetero-bifunctional molecules hijack the ubiquitin proteasome system to selectively add polyubiquitin chains onto a specific protein target to induce proteolytic degradation. Importantly, PROTACs have the capacity to target virtually any intracellular and transmembrane protein for degradation, including oncoproteins previously considered undruggable, which strategically positions PROTACs at the crossroads of multiple cancer research areas. In this review, we present normal functions of the ubiquitin regulation proteins and describe the application of PROTACs to improve the efficacy of current broad-spectrum therapeutics. We subsequently present the potential for PROTACs to exploit specific cancer vulnerabilities through synthetic genetic approaches, which may expedite the development, translation, and utility of novel synthetic genetic therapies in cancer. Finally, we describe the challenges associated with PROTACs and the ongoing efforts to overcome these issues to streamline clinical translation. Ultimately, these efforts may lead to their routine clinical use, which is expected to revolutionize cancer treatment strategies, delay familial cancer onset, and ultimately improve the lives and outcomes of those living with cancer.
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Affiliation(s)
- Kailee A. Rutherford
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciencs, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J. McManus
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciencs, University of Manitoba, Winnipeg, Manitoba, Canada
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14
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Okuno K, Ikemura K, Okamoto R, Oki K, Watanabe A, Kuroda Y, Kidachi M, Fujino S, Nie Y, Higuchi T, Chuman M, Washio M, Sakuraya M, Niihara M, Kumagai K, Sangai T, Kumamoto Y, Naitoh T, Hiki N, Yamashita K. CAF-associated genes putatively representing distinct prognosis by in silico landscape of stromal components of colon cancer. PLoS One 2024; 19:e0299827. [PMID: 38557819 PMCID: PMC10984474 DOI: 10.1371/journal.pone.0299827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
Comprehensive understanding prognostic relevance of distinct tumor microenvironment (TME) remained elusive in colon cancer. In this study, we performed in silico analysis of the stromal components of primary colon cancer, with a focus on the markers of cancer-associated fibroblasts (CAF) and tumor-associated endothelia (TAE), as well as immunological infiltrates like tumor-associated myeloid cells (TAMC) and cytotoxic T lymphocytes (CTL). The relevant CAF-associated genes (CAFG)(representing R index = 0.9 or beyond with SPARC) were selected based on stroma specificity (cancer stroma/epithelia, cS/E = 10 or beyond) and expression amounts, which were largely exhibited negative prognostic impacts. CAFG were partially shared with TAE-associated genes (TAEG)(PLAT, ANXA1, and PTRF) and TAMC-associated genes (TAMCG)(NNMT), but not with CTL-associated genes (CTLG). Intriguingly, CAFG were prognostically subclassified in order of fibrosis (representing COL5A2, COL5A1, and COL12A1) followed by exclusive TAEG and TAMCG. Prognosis was independently stratified by CD8A, a CTL marker, in the context of low expression of the strongest negative prognostic CAFG, COL8A1. CTLG were comprehensively identified as IFNG, B2M, and TLR4, in the group of low S/E, representing good prognosis. Our current in silico analysis of the micro-dissected stromal gene signatures with prognostic relevance clarified comprehensive understanding of clinical features of the TME and provides deep insights of the landscape.
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Affiliation(s)
- Kota Okuno
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kyonosuke Ikemura
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Riku Okamoto
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Keiko Oki
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Akiko Watanabe
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yu Kuroda
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Mikiko Kidachi
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Shiori Fujino
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yusuke Nie
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
| | - Tadashi Higuchi
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Motohiro Chuman
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Marie Washio
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Mikiko Sakuraya
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Masahiro Niihara
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Koshi Kumagai
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Takafumi Sangai
- Department of Breast and Thyroid Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yusuke Kumamoto
- Department of General-Pediatric-Hepatobiliary Pancreatic Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Takeshi Naitoh
- Department of Lower Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Naoki Hiki
- Department of Upper Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Keishi Yamashita
- Division of Advanced Surgical Oncology, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Japan
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15
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Lin C, Kuffour EO, Li T, Gertzen CGW, Kaiser J, Luedde T, König R, Gohlke H, Münk C. The ISG15-Protease USP18 Is a Pleiotropic Enhancer of HIV-1 Replication. Viruses 2024; 16:485. [PMID: 38675828 PMCID: PMC11053637 DOI: 10.3390/v16040485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The innate immune response to viruses is formed in part by interferon (IFN)-induced restriction factors, including ISG15, p21, and SAMHD1. IFN production can be blocked by the ISG15-specific protease USP18. HIV-1 has evolved to circumvent host immune surveillance. This mechanism might involve USP18. In our recent studies, we demonstrate that HIV-1 infection induces USP18, which dramatically enhances HIV-1 replication by abrogating the antiviral function of p21. USP18 downregulates p21 by accumulating misfolded dominant negative p53, which inactivates wild-type p53 transactivation, leading to the upregulation of key enzymes involved in de novo dNTP biosynthesis pathways and inactivated SAMHD1. Despite the USP18-mediated increase in HIV-1 DNA in infected cells, it is intriguing to note that the cGAS-STING-mediated sensing of the viral DNA is abrogated. Indeed, the expression of USP18 or knockout of ISG15 inhibits the sensing of HIV-1. We demonstrate that STING is ISGylated at residues K224, K236, K289, K347, K338, and K370. The inhibition of STING K289-linked ISGylation suppresses its oligomerization and IFN induction. We propose that human USP18 is a novel factor that potentially contributes in multiple ways to HIV-1 replication.
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Affiliation(s)
- Chaohui Lin
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Edmund Osei Kuffour
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Taolan Li
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Christoph G. W. Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
| | - Tom Luedde
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany;
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.G.W.G.); (J.K.); (H.G.)
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Carsten Münk
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (C.L.); (E.O.K.); (T.L.); (T.L.)
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16
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Erdemir Sayan S, Sreekumar R, Bhome R, Mirnezami A, Yagci T, Sayan AE. ERCC1 abundance is an indicator of DNA repair-apoptosis decision upon DNA damage. Cell Death Discov 2024; 10:47. [PMID: 38272916 PMCID: PMC10810800 DOI: 10.1038/s41420-024-01817-7] [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: 08/12/2023] [Revised: 01/06/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
DNA repair is essential for successful propagation of genetic material and fidelity of transcription. Nucleotide excision repair (NER) is one of the earliest DNA repair mechanisms, functionally conserved from bacteria to human. The fact that number of NER genes vary significantly between prokaryotes and metazoans gives the insight that NER proteins have evolved to acquire additional functions to combat challenges associated with a diploid genome, including being involved in the decision between DNA repair and apoptosis. However, no direct association between apoptosis and NER proteins has been shown to date. In this study, we induced apoptosis with a variety of agents, including oxaliplatin, doxorubicin and TRAIL, and observed changes in the abundance and molecular weight of NER complex proteins. Our results showed that XPA, XPC and ERCC1 protein levels change during DNA damage-induced apoptosis. Among these, ERCC1 decrease was observed as a pre-mitochondria depolarisation event which marks the "point of no return" in apoptosis signalling. ERCC1 decrease was due to proteasomal degradation upon lethal doses of oxaliplatin exposure. When ERCC1 protein was stabilised using proteasome inhibitors, the pro-apoptotic activity of oxaliplatin was attenuated. These results explain why clinical trials using proteasome inhibitors and platinum derivatives showed limited efficacy in carcinoma treatment and also the importance of how deep understanding of DNA repair mechanisms can improve cancer therapy.
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Affiliation(s)
- Sule Erdemir Sayan
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, 41400, Turkey
| | - Rahul Sreekumar
- Cancer Sciences Unit, University of Southampton, Southampton General Hospital, Somers Cancer Research Building, Southampton, SO16 6YD, UK
| | - Rahul Bhome
- Cancer Sciences Unit, University of Southampton, Southampton General Hospital, Somers Cancer Research Building, Southampton, SO16 6YD, UK
| | - Alex Mirnezami
- Cancer Sciences Unit, University of Southampton, Southampton General Hospital, Somers Cancer Research Building, Southampton, SO16 6YD, UK
| | - Tamer Yagci
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, 41400, Turkey
| | - A Emre Sayan
- Cancer Sciences Unit, University of Southampton, Southampton General Hospital, Somers Cancer Research Building, Southampton, SO16 6YD, UK.
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17
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Chakraborty B, Agarwal S, Kori S, Das R, Kashaw V, Iyer AK, Kashaw SK. Multiple Protein Biomarkers and Different Treatment Strategies for Colorectal Carcinoma: A Comprehensive Prospective. Curr Med Chem 2024; 31:3286-3326. [PMID: 37151060 DOI: 10.2174/0929867330666230505165031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 05/09/2023]
Abstract
In this review, we emphasized important biomarkers, pathogenesis, and newly developed therapeutic approaches in the treatment of colorectal cancer (CRC). This includes a complete description of small-molecule inhibitors, phytopharmaceuticals with antiproliferative potential, monoclonal antibodies for targeted therapy, vaccinations as immunotherapeutic agents, and many innovative strategies to intervene in the interaction of oncogenic proteins. Many factors combine to determine the clinical behavior of colorectal cancer and it is still difficult to comprehend the molecular causes of a person's vulnerability to CRC. It is also challenging to identify the causes of the tumor's onset, progression, and responsiveness or resistance to antitumor treatment. Current recommendations for targeted medications are being updated by guidelines throughout the world in light of the growing number of high-quality clinical studies. So, being concerned about the aforementioned aspects, we have tried to present a summarized pathogenic view, including a brief description of biomarkers and an update of compounds with their underlying mechanisms that are currently under various stages of clinical testing. This will help to identify gaps or shortfalls that can be addressed in upcoming colorectal cancer research.
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Affiliation(s)
- Biswadip Chakraborty
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Shivangi Agarwal
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Shivam Kori
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Ratnesh Das
- Department of Chemistry, ISF College of Pharmacy, Moga-Punjab, India
| | - Varsha Kashaw
- Sagar Institute of Pharmaceutical Sciences, Sagar (M.P.), India
| | - Arun K Iyer
- Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
- Molecular Imaging Program, Karmanos Cancer Institute, Detroit, Michigan, USA
| | - Sushil Kumar Kashaw
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
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18
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Yaseen MM, Abuharfeil NM, Darmani H. The Role of p53 in HIV Infection. Curr HIV/AIDS Rep 2023; 20:419-427. [PMID: 38010468 DOI: 10.1007/s11904-023-00684-8] [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] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE OF REVIEW This review aims to elucidate the multifaceted role of the tumor suppressor protein p53 in the context of HIV infection. We explore how p53, a pivotal regulator of cellular processes, interacts with various facets of the HIV life cycle. Understanding these interactions could provide valuable insights into potential therapeutic interventions and the broader implications of p53 in viral infections. RECENT FINDINGS Recent research has unveiled a complex interplay between p53 and HIV. Several reports have highlighted the involvement of p53 in restricting the replication of HIV within both immune and nonimmune cells. Various mechanisms have been suggested to unveil how p53 enforces this restriction on HIV replication. However, HIV has developed strategies to manipulate p53, benefiting its replication and evading host defenses. In summary, p53 plays a multifaceted role in HIV infection, impacting viral replication and disease progression. Recent findings underscore the importance of understanding the intricate interactions between p53 and HIV for the development of innovative therapeutic approaches. Manipulating p53 pathways may offer potential avenues to suppress viral replication and ameliorate immune dysfunction, ultimately contributing to the management of HIV/AIDS. Further research is warranted to fully exploit the therapeutic potential of p53 in the context of HIV infection.
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Affiliation(s)
- Mahmoud Mohammad Yaseen
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan.
| | - Nizar Mohammad Abuharfeil
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
| | - Homa Darmani
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
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19
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Venugopal S, Loghavi S. Current State and Future Prospects of Diagnosis and Management of TP53-Mutated Myeloid Neoplasms. Pathobiology 2023; 91:45-54. [PMID: 37839402 DOI: 10.1159/000534566] [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: 03/06/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023] Open
Abstract
TP53-mutated myeloid neoplasms including acute myeloid leukemia (AML) and myelodysplastic neoplasms (MDS) are notoriously treatment resistant with uniformly poor outcomes. TP53 status is an important prognostic indicator and early knowledge of the TP53 mutation/allelic state may assist in appropriate management including clinical trial enrollment for eligible patients. Thus far, no therapy has shown to demonstrate durable response or incremental survival benefit in TP53-mutated AML or MDS. Therefore, there is an urgent need for innovative therapies to improve the outcomes in this notoriously recalcitrant genomic subset. In this review, we dissect the biology, classification, prognosis, current treatment landscape, and the early phase evaluation of investigational agents in TP53-mutated AML and MDS.
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Affiliation(s)
- Sangeetha Venugopal
- Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Sanam Loghavi
- Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas, USA
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20
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Song Z, Zhang J, Sun Y, Jiang Z, Liu X. Establishment and validation of an immune infiltration predictive model for ovarian cancer. BMC Med Genomics 2023; 16:227. [PMID: 37759229 PMCID: PMC10538244 DOI: 10.1186/s12920-023-01657-x] [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: 11/08/2022] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The most prevalent mutation in ovarian cancer is the TP53 mutation, which impacts the development and prognosis of the disease. We looked at how the TP53 mutation associates the immunophenotype of ovarian cancer and the prognosis of the disease. METHODS We investigated the state of TP53 mutations and expression profiles in culturally diverse groups and datasets and developed an immune infiltration predictive model relying on immune-associated genes differently expressed between TP53 WT and TP53 MUT ovarian cancer cases. We aimed to construct an immune infiltration predictive model (IPM) to enhance the prognosis of ovarian cancer and investigate the impact of the IPM on the immunological microenvironment. RESULTS TP53 mutagenesis affected the expression of seventy-seven immune response-associated genes. An IPM was implemented and evaluated on ovarian cancer patients to distinguish individuals with low- and high-IPM subgroups of poor survival. For diagnostic and therapeutic use, a nomogram is thus created. According to pathway enrichment analysis, the pathways of the human immune response and immune function abnormalities were the most associated functions and pathways with the IPM genes. Furthermore, patients in the high-risk group showed low proportions of macrophages M1, activated NK cells, CD8+ T cells, and higher CTLA-4, PD-1, PD-L1, and TIM-3 than patients in the low-risk group. CONCLUSIONS The IPM model may identify high-risk patients and integrate other clinical parameters to predict their overall survival, suggesting it is a potential methodology for optimizing ovarian cancer prognosis.
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Affiliation(s)
- Zhenxia Song
- Department of Obstetrics, Qingdao women and childeren's hospital, #6 Tongfu Road, Shibei District, Qingdao, Shandong, 266000, P. R. China
| | - Jingwen Zhang
- Department of Obstetrics, Qingdao women and childeren's hospital, #6 Tongfu Road, Shibei District, Qingdao, Shandong, 266000, P. R. China
| | - Yue Sun
- Department of Obstetrics, Qingdao women and childeren's hospital, #6 Tongfu Road, Shibei District, Qingdao, Shandong, 266000, P. R. China
| | - Zhongmin Jiang
- Department of Pathology, Tian Jin Fifth's Central Hospital, #41 Zhejiang Road, Binhai District, Tianjin, 300450, P. R. China
| | - Xiaoning Liu
- Department of Obstetrics, Qingdao women and childeren's hospital, #6 Tongfu Road, Shibei District, Qingdao, Shandong, 266000, P. R. China.
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21
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Marchesin S, Menotti L, Giachelle F, Silvello G, Alonso O. Building a large gene expression-cancer knowledge base with limited human annotations. Database (Oxford) 2023; 2023:baad061. [PMID: 37768281 PMCID: PMC10533344 DOI: 10.1093/database/baad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Cancer prevention is one of the most pressing challenges that public health needs to face. In this regard, data-driven research is central to assist medical solutions targeting cancer. To fully harness the power of data-driven research, it is imperative to have well-organized machine-readable facts into a knowledge base (KB). Motivated by this urgent need, we introduce the Collaborative Oriented Relation Extraction (CORE) system for building KBs with limited manual annotations. CORE is based on the combination of distant supervision and active learning paradigms and offers a seamless, transparent, modular architecture equipped for large-scale processing. We focus on precision medicine and build the largest KB on 'fine-grained' gene expression-cancer associations-a key to complement and validate experimental data for cancer research. We show the robustness of CORE and discuss the usefulness of the provided KB. Database URL https://zenodo.org/record/7577127.
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Affiliation(s)
- Stefano Marchesin
- Department of Information Engineering, University of Padova, Via G. Gradenigo 6b, Padova 35131, Italy
| | - Laura Menotti
- Department of Information Engineering, University of Padova, Via G. Gradenigo 6b, Padova 35131, Italy
| | - Fabio Giachelle
- Department of Information Engineering, University of Padova, Via G. Gradenigo 6b, Padova 35131, Italy
| | - Gianmaria Silvello
- Department of Information Engineering, University of Padova, Via G. Gradenigo 6b, Padova 35131, Italy
| | - Omar Alonso
- Applied Science, Amazon, 3075 Olcott St., Santa Clara, California 95054, USA
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22
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Nakanishi S, Li J, Berglund AE, Kim Y, Zhang Y, Zhang L, Yang C, Song J, Mirmira RG, Cleveland JL. The Polyamine-Hypusine Circuit Controls an Oncogenic Translational Program Essential for Malignant Conversion in MYC-Driven Lymphoma. Blood Cancer Discov 2023; 4:294-317. [PMID: 37070973 PMCID: PMC10320645 DOI: 10.1158/2643-3230.bcd-22-0162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/01/2023] [Accepted: 04/13/2023] [Indexed: 04/19/2023] Open
Abstract
The MYC oncoprotein is activated in a broad spectrum of human malignancies and transcriptionally reprograms the genome to drive cancer cell growth. Given this, it is unclear if targeting a single effector of MYC will have therapeutic benefit. MYC activates the polyamine-hypusine circuit, which posttranslationally modifies the eukaryotic translation factor eIF5A. The roles of this circuit in cancer are unclear. Here we report essential intrinsic roles for hypusinated eIF5A in the development and maintenance of MYC-driven lymphoma, where the loss of eIF5A hypusination abolishes malignant transformation of MYC-overexpressing B cells. Mechanistically, integrating RNA sequencing, ribosome sequencing, and proteomic analyses revealed that efficient translation of select targets is dependent upon eIF5A hypusination, including regulators of G1-S phase cell-cycle progression and DNA replication. This circuit thus controls MYC's proliferative response, and it is also activated across multiple malignancies. These findings suggest the hypusine circuit as a therapeutic target for several human tumor types. SIGNIFICANCE Elevated EIF5A and the polyamine-hypusine circuit are manifest in many malignancies, including MYC-driven tumors, and eIF5A hypusination is necessary for MYC proliferative signaling. Not-ably, this circuit controls an oncogenic translational program essential for the development and maintenance of MYC-driven lymphoma, supporting this axis as a target for cancer prevention and treatment. See related commentary by Wilson and Klein, p. 248. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Shima Nakanishi
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jiannong Li
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Anders E. Berglund
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Youngchul Kim
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Yonghong Zhang
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ling Zhang
- Department of Pathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Chunying Yang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jinming Song
- Department of Pathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | - John L. Cleveland
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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23
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Haraoka Y, Miyake M, Ishitani T. Zebrafish imaging reveals hidden oncogenic-normal cell communication during primary tumorigenesis. Cell Struct Funct 2023; 48:113-121. [PMID: 37164759 PMCID: PMC10721949 DOI: 10.1247/csf.23026] [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: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 05/12/2023] Open
Abstract
Oncogenic mutations drive tumorigenesis, and single cells with oncogenic mutations act as the tumor seeds that gradually evolve into fully transformed tumors. However, oncogenic cell behavior and communication with neighboring cells during primary tumorigenesis remain poorly understood. We used the zebrafish, a small vertebrate model suitable for in vivo cell biology, to address these issues. We describe the cooperative and competitive communication between oncogenic cells and neighboring cells, as revealed by our recent zebrafish imaging studies. Newly generated oncogenic cells are actively eliminated by neighboring cells in healthy epithelia, whereas oncogenic cells cooperate with their neighbors to prime tumorigenesis in unhealthy epithelia via additional mutations or inflammation. In addition, we discuss the potential of zebrafish in vivo imaging to determine the initial steps of human tumorigenesis.Key words: zebrafish, imaging, cell-cell communication, cell competition, EDAC, senescence, primary tumorigenesis.
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Affiliation(s)
- Yukinari Haraoka
- Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mai Miyake
- Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tohru Ishitani
- Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
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24
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Nakajima S, Kaneta A, Okayama H, Saito K, Kikuchi T, Endo E, Matsumoto T, Fukai S, Sakuma M, Sato T, Mimura K, Saito M, Saze Z, Sakamoto W, Onozawa H, Momma T, Kono K. The Impact of Tumor Cell-Intrinsic Expression of Cyclic GMP-AMP Synthase (cGAS)-Stimulator of Interferon Genes (STING) on the Infiltration of CD8 + T Cells and Clinical Outcomes in Mismatch Repair Proficient/Microsatellite Stable Colorectal Cancer. Cancers (Basel) 2023; 15:2826. [PMID: 37345163 DOI: 10.3390/cancers15102826] [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: 03/09/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway plays a crucial role in activating immune cells in the tumor microenvironment, thereby contributing to a more favorable response to immune checkpoint inhibitors (ICI) in colorectal cancer (CRC). However, the impact of the expression of cGAS-STING in tumor cells on the infiltration of CD8+ T cells and clinical outcomes in mismatch repair proficient/microsatellite stable (pMMR/MSS) CRC remains largely unknown. Our findings reveal that 56.8% of all pMMR CRC cases were cGAS-negative/STING-negative expressions (cGAS-/STING-) in tumor cells, whereas only 9.9% of all pMMR CRC showed cGAS-positive/STING-positive expression (cGAS+/STING+) in tumor cells. The frequency of cGAS+/STING+ cases was reduced in the advanced stages of pMMR/MSS CRC, and histone methylation might be involved in the down-regulation of STING expression in tumor cells. Since the expression level of cGAS-STING in tumor cells has been associated with the infiltration of CD8+ and/or CD4+ T cells and the frequency of recurrence in pMMR/MSS CRC, decreased expression of cGAS-STING in tumor cells might lead to poor immune cell infiltration and worse prognosis in most pMMR/MSS CRC patients. Our current findings provide a novel insight for the treatment of patients with pMMR/MSS CRC.
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Affiliation(s)
- Shotaro Nakajima
- Department of Multidisciplinary Treatment of Cancer and Regional Medical Support, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Akinao Kaneta
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Hirokazu Okayama
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Katsuharu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Tomohiro Kikuchi
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Eisei Endo
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Takuro Matsumoto
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Satoshi Fukai
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Mei Sakuma
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Takahiro Sato
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kosaku Mimura
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Zenichiro Saze
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Wataru Sakamoto
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Hisashi Onozawa
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Tomoyuki Momma
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Koji Kono
- Department of Multidisciplinary Treatment of Cancer and Regional Medical Support, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
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25
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Xie J, Lin Y, Li Y, Fang A, Li X, Wang S, Li W. lncRNA TRHDE-AS1 Correlated with Genomic Landscape and Clinical Outcome in Glioma. Genes (Basel) 2023; 14:genes14051052. [PMID: 37239411 DOI: 10.3390/genes14051052] [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: 03/27/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The role of lncRNA in cancer development has received more and more attention in research. A variety of lncRNAs are associated with the occurrence and development of glioma. However, the role of TRHDE-AS1 in glioma is still unknown. In this study, we explored the role of TRHDE-AS1 in glioma through bioinformatic methods. We first identified an association between TRHDE-AS1 and tumor prognosis in pan-cancer analysis. Subsequently, the expression levels of TRHDE-AS1 in various clinical types of glioma were compared, and significant differences were found in pathological classification, WHO classification, molecular classification, IDH mutation, and age stratification. We analyzed the genes co-expressed with TRHDE-AS1 in glioma. In the functional analysis of TRHDE-AS1, we found that TRHDE-AS1 may be involved in the regulation of synapse-related functions. In glioma cancer driver gene correlation analysis, it was also found that TRHDE-AS1 was significantly correlated with the expression levels of multiple driver genes such as TP53, BRAF, and IDH1. By comparing the mutant profiles of the high and low TRHDE-AS1 groups, we also found that there may be differences in TP53 and CIC gene mutations in low-grade gliomas. Subsequent correlation analysis between TRHDE-AS1 and glioma immune microenvironment showed that the expression level of TRHDE-AS1 was correlated with a variety of immune cells. Therefore, we believe that TRHDE-AS1 is involved in the occurrence and development of glioma and has the ability to predict the prognosis of glioma as a biomarker of glioma.
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Affiliation(s)
- Jinxuan Xie
- School of Public Health, Capital Medical University, Beijing 100069, China
- National Institute for Data Science in Health and Medicine, Capital Medical University, Beijing 100069, China
| | - Yi Lin
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yajie Li
- National Institute for Data Science in Health and Medicine, Capital Medical University, Beijing 100069, China
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Aizhong Fang
- National Institute for Data Science in Health and Medicine, Capital Medical University, Beijing 100069, China
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Xin Li
- School of Public Health, Capital Medical University, Beijing 100069, China
- National Institute for Data Science in Health and Medicine, Capital Medical University, Beijing 100069, China
| | - Songlin Wang
- Salivary Gland Disease Center and Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Beijing Laboratory of Oral Health, Capital Medical University, Beijing 100050, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Wenbin Li
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
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26
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Zhang Y, Wang Y, Zhang B, Li P, Zhao Y. Methods and biomarkers for early detection, prediction, and diagnosis of colorectal cancer. Biomed Pharmacother 2023; 163:114786. [PMID: 37119736 DOI: 10.1016/j.biopha.2023.114786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common digestive diseases worldwide. It has steadily ascended to the top three cancers in terms of incidence and mortality. The primary cause is the inability to diagnose it at an early stage. Therefore, early detection and diagnosis are essential for colorectal cancer prevention. Although there are now various methods for CRC early detection, in addition to recent developments in surgical and multimodal therapy, the poor prognosis and late detection of CRC still remain significant. Thus, it is important to investigate novel technologies and biomarkers to improve the sensitization and specification of CRC diagnosis. Here, we present some common methods and biomarkers for early detection and diagnosis of CRC, we hope this review will encourage the adoption of screening programs and the clinical use of these potential molecules as biomarkers for CRC early detection and prognosis.
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Affiliation(s)
- Yue Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China; Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Maternal and Child Health Care Hospital of Shandong Province affiliated to Qingdao University, Shandong Province, China
| | - Bingqiang Zhang
- Key Laboratory of Cancer and Immune Cells of Qingdao, Qingdao 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
| | - Yi Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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27
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Ito K, Otani S, Date Y. p53 Deficiency-Dependent Oncogenicity of Runx3. Cells 2023; 12:cells12081122. [PMID: 37190031 DOI: 10.3390/cells12081122] [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: 02/03/2023] [Revised: 04/01/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
The RUNX transcription factors are frequently dysregulated in human cancers, suggesting their potential as attractive targets for drug treatment. However, all three transcription factors have been described as both tumor suppressors and oncogenes, indicating the need to determine their molecular mechanisms of action. Although RUNX3 has long been considered a tumor suppressor in human cancers, several recent studies have shown that RUNX3 is upregulated during the development or progression of various malignant tumors, suggesting it may act as a "conditional" oncogene. 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. This review describes the evidence for the activities of RUNX3 in human cancer and proposes an explanation for the duality of RUNX3 involving the status of p53. In this model, p53 deficiency causes RUNX3 to become oncogenic, leading to aberrant upregulation of MYC.
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Affiliation(s)
- Kosei Ito
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Shohei Otani
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Yuki Date
- Department of Molecular Bone Biology, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
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28
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Marx O, Mankarious M, Yochum G. Molecular genetics of early-onset colorectal cancer. World J Biol Chem 2023; 14:13-27. [PMID: 37034132 PMCID: PMC10080548 DOI: 10.4331/wjbc.v14.i2.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 02/13/2023] [Indexed: 03/24/2023] Open
Abstract
Early-onset colorectal cancer (EOCRC) has been rising in global prevalence and incidence over the past several decades. Environmental influences, including generational lifestyle changes and rising obesity, contribute to these increased rates. While the rise in EOCRC is best documented in western countries, it is seen throughout the world, although EOCRC may have distinct genetic mutations in patients of different ethnic backgrounds. Pathological and molecular characterizations show that EOCRC has a distinct presentation compared with later-onset colorectal cancer (LOCRC). Recent studies have identified DNA, RNA, and protein-level alterations unique to EOCRC, revealing much-needed biomarkers and potential novel therapeutic targets. Many molecular EOCRC studies have been performed with Caucasian and Asian EOCRC cohorts, however, studies of other ethnic backgrounds are limited. In addition, certain molecular characterizations that have been conducted for LOCRC have not yet been repeated in EOCRC, including high-throughput analyses of histone modifications, mRNA splicing, and proteomics on large cohorts. We propose that the complex relationship between cancer and aging should be considered when studying the molecular underpinnings of EOCRC. In this review, we summarize current EOCRC literature, focusing on sporadic molecular alterations in tumors, and their clinical implications. We conclude by discussing current challenges and future directions of EOCRC research efforts.
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Affiliation(s)
- Olivia Marx
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Marc Mankarious
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA 17033, United States
| | - Gregory Yochum
- Department of Biochemistry & Molecular Biology & Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
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29
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Wang H, Guo M, Wei H, Chen Y. Targeting p53 pathways: mechanisms, structures, and advances in therapy. Signal Transduct Target Ther 2023; 8:92. [PMID: 36859359 PMCID: PMC9977964 DOI: 10.1038/s41392-023-01347-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/19/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
The TP53 tumor suppressor is the most frequently altered gene in human cancers, and has been a major focus of oncology research. The p53 protein is a transcription factor that can activate the expression of multiple target genes and plays critical roles in regulating cell cycle, apoptosis, and genomic stability, and is widely regarded as the "guardian of the genome". Accumulating evidence has shown that p53 also regulates cell metabolism, ferroptosis, tumor microenvironment, autophagy and so on, all of which contribute to tumor suppression. Mutations in TP53 not only impair its tumor suppressor function, but also confer oncogenic properties to p53 mutants. Since p53 is mutated and inactivated in most malignant tumors, it has been a very attractive target for developing new anti-cancer drugs. However, until recently, p53 was considered an "undruggable" target and little progress has been made with p53-targeted therapies. Here, we provide a systematic review of the diverse molecular mechanisms of the p53 signaling pathway and how TP53 mutations impact tumor progression. We also discuss key structural features of the p53 protein and its inactivation by oncogenic mutations. In addition, we review the efforts that have been made in p53-targeted therapies, and discuss the challenges that have been encountered in clinical development.
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Affiliation(s)
- Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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30
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Hou Y, Zhang X, Yao H, Hou L, Zhang Q, Tao E, Zhu X, Jiang S, Ren Y, Hong X, Lu S, Leng X, Xie Y, Gao Y, Liang Y, Zhong T, Long B, Fang JY, Meng X. METTL14 modulates glycolysis to inhibit colorectal tumorigenesis in p53-wild-type cells. EMBO Rep 2023; 24:e56325. [PMID: 36794620 PMCID: PMC10074077 DOI: 10.15252/embr.202256325] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/17/2023] Open
Abstract
The frequency of p53 mutations in colorectal cancer (CRC) is approximately 40-50%. A variety of therapies are being developed to target tumors expressing mutant p53. However, potential therapeutic targets for CRC expressing wild-type p53 are rare. In this study, we show that METTL14 is transcriptionally activated by wild-type p53 and suppresses tumor growth only in p53-wild-type (p53-WT) CRC cells. METTL14 deletion promotes both AOM/DSS and AOM-induced CRC growth in mouse models with the intestinal epithelial cell-specific knockout of METTL14. Additionally, METTL14 restrains aerobic glycolysis in p53-WT CRC, by repressing SLC2A3 and PGAM1 expression via selectively promoting m6 A-YTHDF2-dependent pri-miR-6769b/pri-miR-499a processing. Biosynthetic mature miR-6769b-3p and miR-499a-3p decrease SLC2A3 and PGAM1 levels, respectively, and suppress malignant phenotypes. Clinically, METTL14 only acts as a beneficial prognosis factor for the overall survival of p53-WT CRC patients. These results uncover a new mechanism for METTL14 inactivation in tumors and, most importantly, reveal that the activation of METTL14 is a critical mechanism for p53-dependent cancer growth inhibition, which could be targeted for therapy in p53-WT CRC.
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Affiliation(s)
- Yichao Hou
- Shanghai Key Laboratory of Gut Microecology and Associated Major Diseases Research, Digestive Disease Research and Clinical Translation Center, Department of Gastroenterology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xintian Zhang
- Shanghai Key Laboratory of Gut Microecology and Associated Major Diseases Research, Digestive Disease Research and Clinical Translation Center, Department of Gastroenterology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Han Yao
- Shanghai Key Laboratory of Gut Microecology and Associated Major Diseases Research, Digestive Disease Research and Clinical Translation Center, Department of Gastroenterology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lidan Hou
- Shanghai Key Laboratory of Gut Microecology and Associated Major Diseases Research, Digestive Disease Research and Clinical Translation Center, Department of Gastroenterology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qingwei Zhang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Enwei Tao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqiang Zhu
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shanshan Jiang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yimeng Ren
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xialu Hong
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shiyuan Lu
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxu Leng
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yile Xie
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yaqi Gao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Liang
- Shanghai Key Laboratory of Gut Microecology and Associated Major Diseases Research, Digestive Disease Research and Clinical Translation Center, Department of Gastroenterology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Zhong
- Shanghai Key Laboratory of Gut Microecology and Associated Major Diseases Research, Digestive Disease Research and Clinical Translation Center, Department of Gastroenterology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bohan Long
- Shanghai Key Laboratory of Gut Microecology and Associated Major Diseases Research, Digestive Disease Research and Clinical Translation Center, Department of Gastroenterology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangjun Meng
- Shanghai Key Laboratory of Gut Microecology and Associated Major Diseases Research, Digestive Disease Research and Clinical Translation Center, Department of Gastroenterology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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31
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Zhang P, Liu ZY, Yu D, Xu CX, Hu Y, Liang YP, Jin J, Li M. Microplitis bicoloratus parasitism promotes cyclophilin D-p53 interaction to induce apoptosis of hemocytes in Spodoptera litura. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 112:e21970. [PMID: 36200410 DOI: 10.1002/arch.21970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Microplitis bicoloratus parasitism can induce apoptosis of hemocytes in the M. bicolortus host, Spodoptera litura. However, it is unclear how M. bicolortus parasitism regulates host signaling pathways to induce apoptosis. Expression of cyclophilin D (CypD) and p53 was significantly upregulated in S. litura hemocytes at 6 days postparasitization. In the parasitized hemocytes, there was mitochondrial membrane potential (△Ψm ) loss, cytochrome c (Cyt C) release from mitochondria, and caspase-3 activation. These occurred while hemocytes were undergoing upregulation of CypD and p53. Parasitism also promoted the interaction between CypD and p53. CypD silencing could rescue the apoptotic phenotypes induced by parasitism, but had no effect on apoptosis in unparasitized S. litura. These findings suggest that the CypD-p53 pathway may be an important component of the parasitism-induced immunosuppressive response and establish a basis for further studies of parasitoid/host interactions.
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Affiliation(s)
- Pan Zhang
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulation, School of Life Sciences, Yunnan University, Kunming, China
| | - Zi-Yan Liu
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulation, School of Life Sciences, Yunnan University, Kunming, China
- Center of Molecular Biology of Tropical Crops, Yunnan Institute of Tropical Crops, Jinghong, China
| | - Dan Yu
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulation, School of Life Sciences, Yunnan University, Kunming, China
| | - Cui-Xian Xu
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulation, School of Life Sciences, Yunnan University, Kunming, China
- School of Health, Yunnan Technology and Business University, Kunming, China
| | - Yan Hu
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulation, School of Life Sciences, Yunnan University, Kunming, China
| | - Ya-Ping Liang
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulation, School of Life Sciences, Yunnan University, Kunming, China
| | - Jie Jin
- School of Urban and Environmental Sciences, Yunnan University of Finance and Economics, Kunming, China
| | - Ming Li
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulation, School of Life Sciences, Yunnan University, Kunming, China
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32
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Koyasu S, Horita S, Saito K, Kobayashi M, Ishikita H, Chow CCT, Kambe G, Nishikawa S, Menju T, Morinibu A, Okochi Y, Tabuchi Y, Onodera Y, Takeda N, Date H, Semenza GL, Hammond EM, Harada H. ZBTB2 links p53 deficiency to HIF-1-mediated hypoxia signaling to promote cancer aggressiveness. EMBO Rep 2023; 24:e54042. [PMID: 36341521 PMCID: PMC9827547 DOI: 10.15252/embr.202154042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Aberrant activation of the hypoxia-inducible transcription factor HIF-1 and dysfunction of the tumor suppressor p53 have been reported to induce malignant phenotypes and therapy resistance of cancers. However, their mechanistic and functional relationship remains largely unknown. Here, we reveal a mechanism by which p53 deficiency triggers the activation of HIF-1-dependent hypoxia signaling and identify zinc finger and BTB domain-containing protein 2 (ZBTB2) as an important mediator. ZBTB2 forms homodimers via its N-terminus region and increases the transactivation activity of HIF-1 only when functional p53 is absent. The ZBTB2 homodimer facilitates invasion, distant metastasis, and growth of p53-deficient, but not p53-proficient, cancers. The intratumoral expression levels of ZBTB2 are associated with poor prognosis in lung cancer patients. ZBTB2 N-terminus-mimetic polypeptides competitively inhibit ZBTB2 homodimerization and significantly suppress the ZBTB2-HIF-1 axis, leading to antitumor effects. Our data reveal an important link between aberrant activation of hypoxia signaling and loss of a tumor suppressor and provide a rationale for targeting a key mediator, ZBTB2, to suppress cancer aggressiveness.
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Affiliation(s)
- Sho Koyasu
- Laboratory of Cancer Cell Biology, Graduate School of BiostudiesKyoto UniversityKyotoJapan
- Department of Genome Repair Dynamics, Radiation Biology Center, Graduate School of BiostudiesKyoto UniversityKyotoJapan
- Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of MedicineKyoto UniversityKyotoJapan
- Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shoichiro Horita
- Department of Bioregulation and Pharmacological MedicineFukushima Medical UniversityFukushimaJapan
| | - Keisuke Saito
- Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Minoru Kobayashi
- Laboratory of Cancer Cell Biology, Graduate School of BiostudiesKyoto UniversityKyotoJapan
- Department of Genome Repair Dynamics, Radiation Biology Center, Graduate School of BiostudiesKyoto UniversityKyotoJapan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Christalle CT Chow
- Laboratory of Cancer Cell Biology, Graduate School of BiostudiesKyoto UniversityKyotoJapan
| | - Gouki Kambe
- Laboratory of Cancer Cell Biology, Graduate School of BiostudiesKyoto UniversityKyotoJapan
| | - Shigeto Nishikawa
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Toshi Menju
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Akiyo Morinibu
- Laboratory of Cancer Cell Biology, Graduate School of BiostudiesKyoto UniversityKyotoJapan
- Department of Genome Repair Dynamics, Radiation Biology Center, Graduate School of BiostudiesKyoto UniversityKyotoJapan
| | - Yasushi Okochi
- Laboratory of Cancer Cell Biology, Graduate School of BiostudiesKyoto UniversityKyotoJapan
- Faculty of MedicineKyoto UniversityKyotoJapan
| | - Yoshiaki Tabuchi
- Division of Molecular Genetics Research, Life Science Research CenterUniversity of ToyamaToyamaJapan
| | - Yasuhito Onodera
- Global Center for Biomedical Science and Engineering, Faculty of MedicineHokkaido UniversitySapporoJapan
| | - Norihiko Takeda
- Division of Cardiology and Metabolism, Center for Molecular MedicineJichi Medical UniversityTochigiJapan
| | - Hiroshi Date
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Gregg L Semenza
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Ester M Hammond
- MRC Oxford Institute for Radiation Oncology, Department of OncologyUniversity of OxfordOxfordUK
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Graduate School of BiostudiesKyoto UniversityKyotoJapan
- Department of Genome Repair Dynamics, Radiation Biology Center, Graduate School of BiostudiesKyoto UniversityKyotoJapan
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33
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Chen X, Liu T, Wu J, Zhu C, Guan G, Zou C, Guo Q, Ren X, Li C, Cheng P, Cheng W, Wu A. Molecular profiling identifies distinct subtypes across TP53 mutant tumors. JCI Insight 2022; 7:156485. [PMID: 36256461 PMCID: PMC9746906 DOI: 10.1172/jci.insight.156485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 10/14/2022] [Indexed: 01/12/2023] Open
Abstract
Tumor protein 53 mutation (TP53mut) is one of the most important driver events facilitating tumorigenesis, which could induce a series of chain reactions to promote tumor malignant transformation. However, the malignancy progression patterns under TP53 mutation remain less known. Clarifying the molecular landscapes of TP53mut tumors will help us understand the process of tumor development and aid precise treatment. Here, we distilled genetic and epigenetic features altered in TP53mut cancers for cluster-of-clusters analysis. Using integrated classification, we derived 5 different subtypes of TP53mut patients. These subtypes have distinct features in genomic alteration, clinical relevance, microenvironment dysregulation, and potential therapeutics. Among the 5 subtypes, COCA3 was identified as the subtype with worst prognosis, causing an immunosuppressive microenvironment and immunotherapeutic resistance. Further drug efficacy research highlighted olaparib as the most promising therapeutic agents for COCA3 tumors. Importantly, the therapeutic efficacy of olaparib in COCA3 and immunotherapy in non-COCA3 tumors was validated via in vivo experimentation. Our study explored the important molecular events and developed a subtype classification system with distinct targeted therapy strategies for different subtypes of TP53mut tumors. These multiomics classification systems provide a valuable resource that significantly expands the knowledge of TP53mut tumors and may eventually benefit in clinical practice.
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Affiliation(s)
- Xin Chen
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tianqi Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianqi Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Gefei Guan
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Cunyi Zou
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Qing Guo
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaolin Ren
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China.,Department of Neurosurgery, Shenyang Red Cross Hospital, Shenyang, Liaoning, China
| | - Chen Li
- Department of Orthodontics, Stomatological Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peng Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wen Cheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.,Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Anhua Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.,Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
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34
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Patil MR, Bihari A. A comprehensive study of p53 protein. J Cell Biochem 2022; 123:1891-1937. [PMID: 36183376 DOI: 10.1002/jcb.30331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 01/10/2023]
Abstract
The protein p53 has been extensively investigated since it was found 43 years ago and has become a "guardian of the genome" that regulates the division of cells by preventing the growth of cells and dividing them, that is, inhibits the development of tumors. Initial proof of protein existence by researchers in the mid-1970s was found by altering and regulating the SV40 big T antigen termed the A protein. Researchers demonstrated how viruses play a role in cancer by employing viruses' ability to create T-antigens complex with viral tumors, which was discovered in 1979 following a viral analysis and cancer analog research. Researchers later in the year 1989 explained that in Murine Friend, a virus-caused erythroleukemia, commonly found that p53 was inactivated to suggest that p53 could be a "tumor suppressor gene." The TP53 gene, encoding p53, is one of human cancer's most frequently altered genes. The protein-regulated biological functions of all p53s include cell cycles, apoptosis, senescence, metabolism of the DNA, angiogenesis, cell differentiation, and immunological response. We tried to unfold the history of the p53 protein, which was discovered long back in 1979, that is, 43 years of research on p53, and how p53's function has been developed through time in this article.
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Affiliation(s)
- Manisha R Patil
- Department of Computer-Applications, School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Bihari
- Department of Computational Intelligence, School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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35
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Hamed BA, Ibrahim OAS, Abd El‐Hafeez T. A survey on improving pattern matching algorithms for biological sequences. CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE 2022; 34. [DOI: 10.1002/cpe.7292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/09/2022] [Indexed: 09/12/2023]
Abstract
SummaryPattern matching is a highly useful procedure in several stages of the computational pipelines. Furthermore, some research trends in this research domain contributed to growing biological databases and updated them throughout time. This article proposes an comparison and analysis of different algorithms for match equivalent pattern matching like complexity, efficiency, and techniques. Which algorithm is best for which DNA sequence and why? This describes the different algorithms for various activities that include pattern matching as an important aspect of functionality. This article shows that BM, Horspool, ZT, QS, FS, Smith, and SSABS methods employ the bad character preprocessing function. In addition, BM, SSABS, TVSBS, and BRFS methods are using two approaches in the preprocessing stage, which decreases the preprocessing time. Furthermore, KR, QS, SSABS, BRFS, and Shift‐Or are not recommended for the long pattern, whereas ZT, FS, d‐BM, Raita, and Smith are not recommended for the short pattern. This is because they are time‐consuming and certain algorithms, such as ZT and DCPM, use a lot of time and space during the matching and search process, while others, such as d‐BM and TSW, save space and time. Although DCPM, BRFS, and QS are quicker than other algorithms, FLPM, PAPM, and LFPM rank highest in terms of complexity time.
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Affiliation(s)
- Belal A. Hamed
- Department of Computer Science, Faculty of Science Minia University Minia Egypt
| | | | - Tarek Abd El‐Hafeez
- Department of Computer Science, Faculty of Science Minia University Minia Egypt
- Computer Science Unit Deraya University Minia Egypt
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36
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Yang R, Han Y, Yi W, Long Q. Autoantibodies as biomarkers for breast cancer diagnosis and prognosis. Front Immunol 2022; 13:1035402. [PMID: 36451832 PMCID: PMC9701846 DOI: 10.3389/fimmu.2022.1035402] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/28/2022] [Indexed: 10/07/2023] Open
Abstract
Breast cancer is the most common cancer in women worldwide and is a substantial public health problem. Screening for breast cancer mainly relies on mammography, which leads to false positives and missed diagnoses and is especially non-sensitive for patients with small tumors and dense breasts. The prognosis of breast cancer is mainly classified by tumor, node, and metastasis (TNM) staging, but this method does not consider the molecular characteristics of the tumor. As the product of the immune response to tumor-associated antigens, autoantibodies can be detected in peripheral blood and can be used as noninvasive, presymptomatic, and low-cost biomarkers. Therefore, autoantibodies can provide a possible supplementary method for breast cancer screening and prognosis classification. This article introduces the methods used to detect peripheral blood autoantibodies and the research progress in the screening and prognosis of breast cancer made in recent years to provide a potential direction for the examination and treatment of breast cancer.
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Affiliation(s)
| | | | | | - Qian Long
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
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Brown DW, Beatty PH, Lewis JD. Molecular Targeting of the Most Functionally Complex Gene in Precision Oncology: p53. Cancers (Basel) 2022; 14:5176. [PMID: 36358595 PMCID: PMC9654076 DOI: 10.3390/cancers14215176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/16/2022] [Accepted: 10/20/2022] [Indexed: 09/29/2023] Open
Abstract
While chemotherapy is a key treatment strategy for many solid tumors, it is rarely curative, and most tumor cells eventually become resistant. Because of this, there is an unmet need to develop systemic treatments that capitalize on the unique mutational landscape of each patient's tumor. The most frequently mutated protein in cancer, p53, has a role in nearly all cancer subtypes and tumorigenesis stages and therefore is one of the most promising molecular targets for cancer treatment. Unfortunately, drugs targeting p53 have seen little clinical success despite promising preclinical data. Most of these drug compounds target specific aspects of p53 inactivation, such as through inhibiting negative regulation by the mouse double minute (MDM) family of proteins. These treatment strategies fail to address cancer cells' adaptation mechanisms and ignore the impact that p53 loss has on the entire p53 network. However, recent gene therapy successes show that targeting the p53 network and cellular dysfunction caused by p53 inactivation is now possible and may soon translate into successful clinical responses. In this review, we discuss p53 signaling complexities in cancer that have hindered the development and use of p53-targeted drugs. We also describe several current therapeutics reporting promising preclinical and clinical results.
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Affiliation(s)
- Douglas W. Brown
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Entos Pharmaceuticals, Unit 4550, 10230 Jasper Avenue, Edmonton, AB T5J 4P6, Canada
| | - Perrin H. Beatty
- Entos Pharmaceuticals, Unit 4550, 10230 Jasper Avenue, Edmonton, AB T5J 4P6, Canada
| | - John D. Lewis
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Entos Pharmaceuticals, Unit 4550, 10230 Jasper Avenue, Edmonton, AB T5J 4P6, Canada
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van den Bosch T, Derks S, Miedema DM. Chromosomal Instability, Selection and Competition: Factors That Shape the Level of Karyotype Intra-Tumor Heterogeneity. Cancers (Basel) 2022; 14:cancers14204986. [PMID: 36291770 PMCID: PMC9600040 DOI: 10.3390/cancers14204986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Each cancer consists of billions of cells. These cells are far from identical; hence, the population of cells that constitute a tumor is heterogeneous. A salient property that varies between cells in a tumor is their karyotype, the number and configuration of the chromosomes. The level of karyotype heterogeneity can be used to predict the survival of a patient. In this review, we describe the processes that shape the level of karyotype heterogeneity in a cancer. Abstract Intra-tumor heterogeneity (ITH) is a pan-cancer predictor of survival, with high ITH being correlated to a dismal prognosis. The level of ITH is, hence, a clinically relevant characteristic of a malignancy. ITH of karyotypes is driven by chromosomal instability (CIN). However, not all new karyotypes generated by CIN are viable or competitive, which limits the amount of ITH. Here, we review the cellular processes and ecological properties that determine karyotype ITH. We propose a framework to understand karyotype ITH, in which cells with new karyotypes emerge through CIN, are selected by cell intrinsic and cell extrinsic selective pressures, and propagate through a cancer in competition with other malignant cells. We further discuss how CIN modulates the cell phenotype and immune microenvironment, and the implications this has for the subsequent selection of karyotypes. Together, we aim to provide a comprehensive overview of the biological processes that shape the level of karyotype heterogeneity.
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Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
| | - Sarah Derks
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam University Medical Centers—Location VUmc, 1081 HV Amsterdam, The Netherlands
- Correspondence: (S.D.); (D.M.M.)
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Correspondence: (S.D.); (D.M.M.)
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Mori T. Involvement of the p53-p16/RB pathway control mechanism in early-stage carcinogenesis in head and neck squamous cell carcinoma. Pathol Int 2022; 72:577-588. [PMID: 36218243 DOI: 10.1111/pin.13279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/16/2022] [Indexed: 11/28/2022]
Abstract
Head and neck squamous cell carcinoma develops through a heterogeneous process involving human papillomavirus infection, smoking, and alcohol consumption. A comprehensive genomic analysis of head and neck squamous cell carcinomas to date has identified a few single driver gene mutations, the most frequent of which involve TP53 and CDKN2A/p16. To investigate the involvement of the tumorigenesis mechanism in early-stage carcinogenesis, HPV-derived genomes E6 and E7, which are carcinogens, and stem/progenitor-associated, polycomb (PcG) genes Bmi1 and TERT were induced into human stromal cells and immortalized as the head and neck squamous cell carcinoma model. We found that Bmi1 suppressed both the p16INK4a and p16/Rb-p53 pathway cross-talks. The E7 group showed that endogenous p53 is highly expressed and eludes chromosome number aberration, even on long-term observation. Bmi1 was predominantly expressed in early head and neck squamous cell carcinoma, and PcG was essential in early cancer development. Additionally, TP53 whole exon analysis revealed categories useful for estimating malignant potential, such as poor prognosis and high recurrence at the transection site. Therefore, understanding the p53-p16/RB pathway in head and neck squamous cell carcinoma is an essential factor to elucidate the early carcinogenesis of head and neck squamous cell carcinoma.
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Affiliation(s)
- Taisuke Mori
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
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Liu Y, Gu W. The complexity of p53-mediated metabolic regulation in tumor suppression. Semin Cancer Biol 2022; 85:4-32. [PMID: 33785447 PMCID: PMC8473587 DOI: 10.1016/j.semcancer.2021.03.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023]
Abstract
Although the classic activities of p53 including induction of cell-cycle arrest, senescence, and apoptosis are well accepted as critical barriers to cancer development, accumulating evidence suggests that loss of these classic activities is not sufficient to abrogate the tumor suppression activity of p53. Numerous studies suggest that metabolic regulation contributes to tumor suppression, but the mechanisms by which it does so are not completely understood. Cancer cells rewire cellular metabolism to meet the energetic and substrate demands of tumor development. It is well established that p53 suppresses glycolysis and promotes mitochondrial oxidative phosphorylation through a number of downstream targets against the Warburg effect. The role of p53-mediated metabolic regulation in tumor suppression is complexed by its function to promote both cell survival and cell death under different physiological settings. Indeed, p53 can regulate both pro-oxidant and antioxidant target genes for complete opposite effects. In this review, we will summarize the roles of p53 in the regulation of glucose, lipid, amino acid, nucleotide, iron metabolism, and ROS production. We will highlight the mechanisms underlying p53-mediated ferroptosis, AKT/mTOR signaling as well as autophagy and discuss the complexity of p53-metabolic regulation in tumor development.
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Affiliation(s)
- Yanqing Liu
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, 1130 Nicholas Ave, New York, NY, 10032, USA
| | - Wei Gu
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, 1130 Nicholas Ave, New York, NY, 10032, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, 1130 Nicholas Ave, New York, NY, 10032, USA.
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Basta DW, Vong M, Beshimova A, Nakamura BN, Rusu I, Kattah MG, Shao L. A20 Restricts NOS2 Expression and Intestinal Tumorigenesis in a Mouse Model of Colitis-Associated Cancer. GASTRO HEP ADVANCES 2022; 2:96-107. [PMID: 36636264 PMCID: PMC9833806 DOI: 10.1016/j.gastha.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS Colon cancer can occur sporadically or in the setting of chronic inflammation, such as in patients with inflammatory bowel disease. We previously showed that A20, a critical negative regulator of tumor necrosis factor signal transduction, could regulate sporadic colon cancer development. In this report, we investigate whether A20 also acts as a tumor suppressor in a model of colitis-associated cancer. METHODS Colitis and colitis-associated tumors were induced in wild-type and A20 intestinal epithelial cell-specific knockout (A20dIEC) mice using dextran sodium sulfate and azoxymethane. Clinicopathologic markers of inflammation were assessed in conjunction with colonic tumor burden. Gene expression analyses and immunohistochemistry were performed on colonic tissue and intestinal enteroids. Nitric oxide (NO) production and activity were assessed in whole colonic lysates and mouse embryonic fibroblasts. RESULTS A20dIEC mice develop larger tumors after treatment with dextran sodium sulfate and azoxymethane than wild-type mice. In addition to elevated markers of inflammation, A20dIEC mice have significantly enhanced expression of inducible nitric oxide synthase (iNOS), a well-known driver of neoplasia. Enhanced iNOS expression is associated with the formation of reactive nitrogen species and DNA damage. Loss of A20 also enhances NO-dependent cell death directly. CONCLUSION Mechanistically, we propose that A20 normally restricts tumor necrosis factor-induced nuclear factor kappa B-dependent production of iNOS in intestinal epithelial cells, thereby protecting against colitis-associated tumorigenesis. We also propose that A20 plays a direct role in regulating NO-dependent cell death.
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Affiliation(s)
- David W Basta
- Division of Gastroenterology and Liver Disease, Department of Medicine, University of Southern California, Keck School of Medicine, Los Angeles, California
| | - Mandy Vong
- Division of Gastroenterology and Liver Disease, Department of Medicine, University of Southern California, Keck School of Medicine, Los Angeles, California
| | - Adolat Beshimova
- Division of Gastroenterology and Liver Disease, Department of Medicine, University of Southern California, Keck School of Medicine, Los Angeles, California
| | - Brooke N Nakamura
- Division of Gastroenterology and Liver Disease, Department of Medicine, University of Southern California, Keck School of Medicine, Los Angeles, California
| | - Iulia Rusu
- Division of Gastroenterology and Liver Disease, Department of Medicine, University of Southern California, Keck School of Medicine, Los Angeles, California
| | - Michael G Kattah
- Division of Gastroenterology and Liver Disease, Department of Medicine, University of Southern California, Keck School of Medicine, Los Angeles, California
| | - Ling Shao
- Division of Gastroenterology and Liver Disease, Department of Medicine, University of Southern California, Keck School of Medicine, Los Angeles, California
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p53: From Fundamental Biology to Clinical Applications in Cancer. BIOLOGY 2022; 11:biology11091325. [PMID: 36138802 PMCID: PMC9495382 DOI: 10.3390/biology11091325] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022]
Abstract
Simple Summary p53 tumour suppressor gene is the most altered in cancer. Several decades of research have established that it is of pivotal importance in prompting neoplastic phenomena, including cancer initiation and progression. However, it has crucial functions for cellular life. Knowledge and awareness about these multifaceted properties should be part of the cultural background of all scientists. In this review, we describe and discuss the multifaceted roles of p53, from its discovery to clinical applications in cancer therapy. Abstract p53 tumour suppressor gene is our major barrier against neoplastic transformation. It is involved in many cellular functions, including cell cycle arrest, senescence, DNA repair, apoptosis, autophagy, cell metabolism, ferroptosis, immune system regulation, generation of reactive oxygen species, mitochondrial function, global regulation of gene expression, miRNAs, etc. Its crucial importance is denounced by the high percentage of amino acid sequence identity between very different species (Homo sapiens, Drosophila melanogaster, Rattus norvegicus, Danio rerio, Canis lupus familiaris, Gekko japonicus). Many of its activities allowed life on Earth (e.g., repair from radiation-induced DNA damage) and directly contribute to its tumour suppressor function. In this review, we provide paramount information on p53, from its discovery, which is an interesting paradigm of science evolution, to potential clinical applications in anti-cancer treatment. The description of the fundamental biology of p53 is enriched by specific information on the structure and function of the protein as well by tumour/host evolutionistic perspectives of its role.
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Ran R, Li L, Shi Z, Liu G, Jiang H, Fang L, Xu T, Huang J, Chen W, Chen Y. Disruption of
tp53
leads to cutaneous nevus and melanoma formation in
Xenopus tropicalis. Mol Oncol 2022; 16:3554-3567. [PMID: 35981147 PMCID: PMC9533689 DOI: 10.1002/1878-0261.13301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/22/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
In humans, germline TP53 mutations predispose carriers to a wide spectrum of cancers, which is known as Li–Fraumeni syndrome (LFS). To date, the association of melanomas with LFS remains unestablished. No melanomas have been reported in any P53‐modified mouse models either. In this study, we show that targeted disruption of P53 at the DNA‐binding domain in Xenopus tropicalis recapitulates LFS, with the formation of soft‐tissue sarcomas and pancreatic ductal adenocarcinoma. Interestingly, 19% of the 14‐month‐old tp53Δ7/Δ7 homozygotes and 18% of tp53+/Δ7 heterozygotes spontaneously developed small nevi and non‐invasive melanomas. Large invasive melanomas were also observed in other older homozygous mutants, with about 7.9% penetrance. Our data suggest that more dermatologic investigation of LFS patients should be able to settle the association of melanoma with LFS in epidemiology. Our model is also valuable for further investigation of the molecular mechanism underlying melanoma progression upon germline alteration of the tp53 locus.
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Affiliation(s)
- Rensen Ran
- School of Life Science and Technology Harbin Institute of Technology Harbin China
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
| | - Lanxin Li
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
| | - Zhaoying Shi
- School of Life Science and Technology Harbin Institute of Technology Harbin China
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
| | - Guanghui Liu
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
| | - Hao Jiang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
| | - Liangchen Fang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
| | - Tingting Xu
- School of Medical Technology and Engineering Fujian Medical University Fuzhou China
| | - Jixuan Huang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
| | - Weiqi Chen
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
| | - Yonglong Chen
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology Shenzhen China
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Interdiction in the Early Folding of the p53 DNA-Binding Domain Leads to Its Amyloid-Like Misfolding. Molecules 2022; 27:molecules27154810. [PMID: 35956758 PMCID: PMC9370011 DOI: 10.3390/molecules27154810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/18/2022] [Accepted: 07/23/2022] [Indexed: 11/17/2022] Open
Abstract
In this article, we investigate two issues: (a) the initial contact formation events along the folding pathway of the DNA-binding domain of the tumor suppressor protein p53 (core p53); and (b) the intermolecular events leading to its conversion into a prion-like form upon incubation with peptide P8(250-257). In the case of (a), the calculations employ the sequential collapse model (SCM) to identify the segments involved in the initial contact formation events that nucleate the folding pathway. The model predicts that there are several possible initial non-local contacts of comparative stability. The most stable of these possible initial contacts involve the protein segments 159AMAIY163 and 251ILTII255, and it is the only native-like contact. Thus, it is predicted to constitute “Nature’s shortcut” to the native structure of the core domain of p53. In the case of issue (b), these findings are then combined with experimental evidence showing that the incubation of the core domain of p53 with peptide P8(250-257), which is equivalent to the native protein segment 250PILTIITL257, leads to an amyloid conformational transition. It is explained how the SCM predicts that P8(250-257) effectively interdicts in the formation of the most stable possible initial contact and, thereby, disrupts the subsequent normal folding. Interdiction by polymeric P8(250-257) seeds is also studied. It is then hypothesized that enhanced folding through one or several of the less stable contacts could play a role in P8(250-257)-promoted core p53 amyloid misfolding. These findings are compared to previous results obtained for the prion protein. Experiments are proposed to test the hypothesis presented regarding core p53 amyloid misfolding.
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Jiang M, Wu X, Bao S, Wang X, Qu F, Liu Q, Huang X, Li W, Tang J, Yin Y. Immunometabolism characteristics and a potential prognostic risk model associated with TP53 mutations in breast cancer. Front Immunol 2022; 13:946468. [PMID: 35935965 PMCID: PMC9353309 DOI: 10.3389/fimmu.2022.946468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
TP53, a gene with high-frequency mutations, plays an important role in breast cancer (BC) development through metabolic regulation, but the relationship between TP53 mutation and metabolism in BC remains to be explored. Our study included 1,066 BC samples from The Cancer Genome Atlas (TCGA) database, 415 BC cases from the Gene Expression Omnibus (GEO) database, and two immunotherapy cohorts. We identified 92 metabolic genes associated with TP53 mutations by differential expression analysis between TP53 mutant and wild-type groups. Univariate Cox analysis was performed to evaluate the prognostic effects of 24 TP53 mutation-related metabolic genes. By unsupervised clustering and other bioinformatics methods, the survival differences and immunometabolism characteristics of the distinct clusters were illustrated. In a training set from TCGA cohort, we employed the least absolute shrinkage and selection operator (LASSO) regression method to construct a metabolic gene prognostic model associated with TP53 mutations, and the GEO cohort served as an external validation set. Based on bioinformatics, the connections between risk score and survival prognosis, tumor microenvironment (TME), immunotherapy response, metabolic activity, clinical characteristics, and gene characteristics were further analyzed. It is imperative to note that our model is a powerful and robust prognosis factor in comparison to other traditional clinical features and also has high accuracy and clinical usefulness validated by receiver operating characteristic (ROC) and decision curve analysis (DCA). Our findings deepen our understanding of the immune and metabolic characteristics underlying the TP53 mutant metabolic gene profile in BC, laying a foundation for the exploration of potential therapies targeting metabolic pathways. In addition, our model has promising predictive value in the prognosis of BC.
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Affiliation(s)
- Mengping Jiang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Xiangyan Wu
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, China
| | - Shengnan Bao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Fei Qu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Qian Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Jinhai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yongmei Yin, ; Jinhai Tang,
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Yongmei Yin, ; Jinhai Tang,
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Role of p53 in Regulating Radiation Responses. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071099. [PMID: 35888186 PMCID: PMC9319710 DOI: 10.3390/life12071099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 12/12/2022]
Abstract
p53 is known as the guardian of the genome and plays various roles in DNA damage and cancer suppression. The p53 gene was found to express multiple p53 splice variants (isoforms) in a physiological, tissue-dependent manner. The various genes that up- and down-regulated p53 are involved in cell viability, senescence, inflammation, and carcinogenesis. Moreover, p53 affects the radioadaptive response. Given that several studies have already been published on p53, this review presents its role in the response to gamma irradiation by interacting with MDM2, NF-κB, and miRNA, as well as in the inflammation processes, senescence, carcinogenesis, and radiation adaptive responses. Finally, the potential of p53 as a biomarker is discussed.
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Fukusada S, Shimura T, Iwasaki H, Okuda Y, Katano T, Ozeki T, Kitagawa M, Nishie H, Tanaka M, Ozeki K, Kubota E, Tanida S, Kataoka H. Relationship between gene mutations and clinicopathological features in nonampullary duodenal epithelial tumors. Dig Liver Dis 2022; 54:905-910. [PMID: 34961702 DOI: 10.1016/j.dld.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Molecular features of nonampullary duodenal epithelial tumors (NADETs) remain unclear. AIM The aim of this study is to determine the association between the genetic features and clinicopathological findings of NADETs. METHODS In total, 75 NADETs were enrolled in this study, and was performed targeted DNA sequencing of the GNAS, KRAS, TP53, and APC genes. Histological grade was classified as category 3 or category 4/5 according to the Vienna classification, and the immunophenotype was categorized as the gastric phenotype (G type), gastrointestinal phenotype (GI type), or the intestinal phenotype (I type). RESULTS The prevalence of GNAS and KRAS mutations was significantly higher in the G type than in the GI/I type (GNAS, P = 0.027; KRAS, P = 0.005). In contrast, the frequency of TP53 mutations was significantly higher in the GI/I type than in the G type (P = 0.049). Notably, APC mutations, excluding c.4479 G>A which was synonymous mutation, were more frequently identified in category 4/5 tumors than in category 3 tumors (50% vs. 24.5%; P = 0.039). CONCLUSION G-type NADETs harbored frequent GNAS and KRAS mutations, whereas TP53 mutations are common in NADETs with intestinal features. APC mutations were significantly associated with high-grade neoplasia and invasive carcinoma.
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Affiliation(s)
- Shigeki Fukusada
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Takaya Shimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan.
| | - Hiroyasu Iwasaki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Yusuke Okuda
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Takahito Katano
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Takanori Ozeki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Mika Kitagawa
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Hirotada Nishie
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Mamoru Tanaka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Keiji Ozeki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Eiji Kubota
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Satoshi Tanida
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Hiromi Kataoka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1-Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
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Isotypic analysis of anti-p53 serum autoantibodies and p53 protein tissue phenotypes in colorectal cancer. Hum Pathol 2022; 128:1-10. [PMID: 35750247 DOI: 10.1016/j.humpath.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022]
Abstract
The presence of IgA- and IgM-specific autoantibody (AAb) isotypes and their relationship to p53 tissue expression patterns are not well understood. This study aims to investigate the clinical utility of the anti-p53 AAb isotypes and tissue positivity in colorectal cancer (CRC). We analysed anti-p53 IgG, IgM, and IgA AAbs in sera of 99 CRC patients and 99 non-cancer control subjects. Corresponding tissue expression of the p53 protein was evaluated by immunohistochemistry (IHC). Anti-p53 AAbs of the IgG isotype were present in the sera of 21 out of 99 patients (21%), while IgM AAbs were observed in 9 (9%) and IgA in 2 (2%) CRC patients. Anti-p53 AAbs of all three isotypes were generally associated with IHC staining indicative of mutated TP53. Seropositive anti-p53 IgM cases in the absence of anti-p53 IgG were linked to wild-type p53. Anti-p53 IgA in the absence of IgG AAbs was detected in two non-cancer controls indicating a potential p53 epitope mimicry. Although seropositivity was not associated with patient survival (P = 0.650), mutant-pattern p53 tissue expression was associated with reduced 5-year overall survival (P = 0.032), however, it was not an independent prognostic marker (Multivariate Cox regression, P = 0.193). In conclusion, immunoglobulin isotyping revealed that anti-p53 IgM and IgA AAbs were predominantly concurrent with anti-p53 serum IgG and the mutant-pattern p53 tissue phenotype. IgM and IgA seropositive cases in absence of anti-p53 IgG were linked to wild-type p53 tissue phenotype indicating early anti-p53 immune responses preceding isotype class-switch (IgM) or p53 antigen mimicry (IgA).
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Xiao X, Guo L, Dai W, Yan B, Zhang J, Yuan Q, Zhou L, Shan L, Efferth T. Green tea-derived theabrownin suppresses human non-small cell lung carcinoma in xenograft model through activation of not only p53 signaling but also MAPK/JNK signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2022; 291:115167. [PMID: 35271947 DOI: 10.1016/j.jep.2022.115167] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/19/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE According to the theory and practice of traditional Chinese medicine (TCM), the pathogenesis of lung carcinoma is associated with many syndromes, such as "sputum stasis", "cough", "lung fever", "lung toxin", and "hemoptysis", which should be removed for therapeutic purpose. Tea is not only a world-wide beverage, but also a TCM herb, possessing activities against the above syndromes. Recently, green tea extract exerted inhibitory effects on a variety of tumor cells. As a pigment active substance of green tea, theabrownin (TB) has been found to inhibit many cancer cells. AIM OF THE STUDY This study focused on the efficacy and mechanism of TB on non-small cell lung cancer (NSCLC) cell lines. The in vivo efficacy of TB on p53-deficient NSCLC (H1299) cells and p53-wild type NSCLC (A549) cells NSCLC cells were determined, and its mechanism of action was explored. MATERIALS AND METHODS In vivo, two lung cancer cell lines, H1299 (p53-deficient) and A549 (p53-wild type) were selected to establish xenograft models of larval zebrafish, respectively. For in vitro experiments, wound healing assay, DAPI staining, TUNEL assay, immunofluorescence assay, and flow cytometry were conducted in these two cell lines. RNA sequencing (RNAseq), real time PCR (qPCR) and Western blot (WB) were performed for the mechanism study. RESULTS The in vivo results showed that TB significantly inhibited the H1299 and the A549 xenograft tumor growth in larval zebrafish (dosage ranged from 2.13 to 21.3 μg/ml). Wound healing assay results showed that TB suppressed the migration of H1299 cells. DAPI staining, TUNEL assay, and immunofluorescence assay results showed that TB inhibited the growth of H1299 cells by inducing apoptosis. RNAseq, qPCR and WB data showed that TB significantly up-regulated the MAPK/JNK pathway-related proteins (ASK-1, JNK and c-JUN) through phosphorylation activation, accompanying with down-regulation of the epithelial-mesenchymal transition (EMT)-associated genes (N-CADHERIN, SLUG, FIBROWNECTIN and ZEB1) and anti-apoptotic molecules (BCL-2), and up-regulation of the metastasis-related gene HSPA6 and the pro-apoptotic molecules (BIM, BAX, PARP, c-PARP, γ-H2A.X, c-CASP3, c-CASP8, c-CASP9, DDIT3 and DUSP8). CONCLUSION This study determined the in vivo efficacy of green tea-derived TB on p53-deficient NSCLC (H1299) cells and p53-wild type NSCLC (A549) cells and clarified its p53-independent mechanism mediated by the activation of MAPK/JNK signaling pathway.
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Affiliation(s)
- Xiujuan Xiao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China; The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Le Guo
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China; Cell Resource Bank and Integrated Cell Preparation Center of Xiaoshan District, Hangzhou Regional Cell Preparation Center (Shangyu Biotechnology Co., Ltd), Hangzhou, China
| | - Weiyou Dai
- School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Bo Yan
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China; The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jin Zhang
- Theabio Co., Ltd, Hangzhou, 310000, China
| | - Qiang Yuan
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Li Zhou
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Letian Shan
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, 310053, China; Cell Resource Bank and Integrated Cell Preparation Center of Xiaoshan District, Hangzhou Regional Cell Preparation Center (Shangyu Biotechnology Co., Ltd), Hangzhou, China.
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
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Yang Y, Qu Y, Li Z, Tan Z, Lei Y, Bai S. Identification of Novel Characteristics in TP53-Mutant Hepatocellular Carcinoma Using Bioinformatics. Front Genet 2022; 13:874805. [PMID: 35651938 PMCID: PMC9149291 DOI: 10.3389/fgene.2022.874805] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background: TP53 mutations are the most frequent mutations in hepatocellular carcinoma (HCC) and affect the occurrence and development of this cancer type. Therefore, it is essential to clarify the function and mechanism of TP53 mutations in HCC. Methods: We performed a sequence of bioinformatic analyses to elucidate the characteristics of TP53 mutations in HCC. We downloaded the data of hepatocellular carcinoma from The Cancer Genome Atlas database and used different R packages for serial analyses, including gene mutation analysis, copy number variation analysis, analysis of the tumor mutational burden and microsatellite instability, differential gene expression analysis, and functional enrichment analysis of TP53 mutations, and performed gene set enrichment analysis. We established a protein-protein interaction network using the STRING online database and used the Cytoscape software for network visualization, and hub gene screening. In addition, we performed anticancer drug sensitivity analysis using data from the Genomics of Drug Sensitivity in Cancer. Immune infiltration and prognosis analyses were also performed. Results: Missense mutations accounted for a great proportion of HCC mutations, the frequency of single nucleotide polymorphisms was high, and C > T was the most common form of single nucleotide variations. TP53 had a mutation rate of 30% and was the most commonly mutated gene in HCC. In the TP53 mutant group, the tumor mutational burden (p < 0.001), drug sensitivity (p < 0.05), ESTIMATE score (p = 0.038), and stromal score (p < 0.001) dramatically decreased. The Cytoscape software screened ten hub genes, including CT45A1, XAGE1B, CT55, GAGE2A, PASD1, MAGEA4, CTAG2, MAGEA10, MAGEC1, and SAGE1. The prognostic model showed a poor prognosis in the TP53 mutation group compared with that in the wild-type group (overall survival, p = 0.023). Univariate and multivariate cox regression analyses revealed that TP53 mutation was an independent risk factor for the prognosis of HCC patients (p <0.05). The constructed prognostic model had a favorable forecast value for the prognosis of HCC patients at 1 and 3 years (1-year AUC = 0.752, 3-years AUC = 0.702). Conclusion: This study further deepened our understanding of TP53-mutated HCC, provided new insights into a precise individualized therapy for HCC, and has particular significance for prognosis prediction.
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Affiliation(s)
- Yang Yang
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yajuan Qu
- Department of Rehabilitation Medicine, Qujing Second People's Hospital, Qujing, China
| | - Zhaopeng Li
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhiyong Tan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Youming Lei
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Song Bai
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
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