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Sokolowski D, Mai M, Verma A, Morgenshtern G, Subasri V, Naveed H, Yampolsky M, Wilson M, Goldenberg A, Erdman L. iModEst: disentangling -omic impacts on gene expression variation across genes and tissues. NAR Genom Bioinform 2025; 7:lqaf011. [PMID: 40041206 PMCID: PMC11879402 DOI: 10.1093/nargab/lqaf011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/16/2025] [Accepted: 02/17/2025] [Indexed: 03/06/2025] Open
Abstract
Many regulatory factors impact the expression of individual genes including, but not limited, to microRNA, long non-coding RNA (lncRNA), transcription factors (TFs), cis-methylation, copy number variation (CNV), and single-nucleotide polymorphisms (SNPs). While each mechanism can influence gene expression substantially, the relative importance of each mechanism at the level of individual genes and tissues is poorly understood. Here, we present the integrative Models of Estimated gene expression (iModEst), which details the relative contribution of different regulators to the gene expression of 16,000 genes and 21 tissues within The Cancer Genome Atlas (TCGA). Specifically, we derive predictive models of gene expression using tumour data and test their predictive accuracy in cancerous and tumour-adjacent tissues. Our models can explain up to 70% of the variance in gene expression across 43% of the genes within both tumour and tumour-adjacent tissues. We confirm that TF expression best predicts gene expression in both tumour and tumour-adjacent tissue whereas methylation predictive models in tumour tissues does not transfer well to tumour adjacent tissues. We find new patterns and recapitulate previously reported relationships between regulator and gene-expression, such as CNV-predicted FGFR2 expression and SNP-predicted TP63 expression. Together, iModEst offers an interactive, comprehensive atlas of individual regulator-gene-tissue expression relationships as well as relationships between regulators.
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Affiliation(s)
- Dustin J Sokolowski
- Department of Molecular Genetics, University of Toronto, ON M5S 3K3, Canada
- Department of Computer Science, University of Toronto, ON M5S 2E4, Canada
| | - Mingjie Mai
- Department of Computer Science, University of Toronto, ON M5S 2E4, Canada
- SickKids Research Institute, Program in Genetics and Genome Biology, ON M5G 0A4, Canada
- Vector Institute
| | - Arnav Verma
- Department of Computer Science, University of Toronto, ON M5S 2E4, Canada
| | - Gabriela Morgenshtern
- Department of Computer Science, University of Toronto, ON M5S 2E4, Canada
- SickKids Research Institute, Program in Genetics and Genome Biology, ON M5G 0A4, Canada
- Vector Institute
| | - Vallijah Subasri
- SickKids Research Institute, Program in Genetics and Genome Biology, ON M5G 0A4, Canada
- Department of Medical Biophysics, University of Toronto, ON M5G 2C4, Canada
| | - Hareem Naveed
- Department of Computer Science, University of Toronto, ON M5S 2E4, Canada
- SickKids Research Institute, Program in Genetics and Genome Biology, ON M5G 0A4, Canada
| | - Maria Yampolsky
- SickKids Research Institute, Program in Genetics and Genome Biology, ON M5G 0A4, Canada
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, ON M5S 3K3, Canada
- SickKids Research Institute, Program in Genetics and Genome Biology, ON M5G 0A4, Canada
| | - Anna Goldenberg
- Department of Computer Science, University of Toronto, ON M5S 2E4, Canada
- SickKids Research Institute, Program in Genetics and Genome Biology, ON M5G 0A4, Canada
- Vector Institute
- CIFAR: Child and Brain Development, Toronto, ON M5G 1M1, Canada
| | - Lauren Erdman
- Department of Computer Science, University of Toronto, ON M5S 2E4, Canada
- SickKids Research Institute, Program in Genetics and Genome Biology, ON M5G 0A4, Canada
- Vector Institute
- James M. Anderson Center for Health Systems Excellence, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- College of Medicine, University of Cincinnati, OH 45267, United States
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Perica K, Jain N, Scordo M, Patel R, Eren OC, Patel U, Gundem G, Domenico D, Mitra S, Socci ND, Everett JK, Roche AM, Petrichenko A, Shah GL, Arcila ME, Borsu L, Park JH, Horwitz SM, Giralt SA, Dogan A, Leslie C, Papaemmanuil E, Bushman FD, Usmani SZ, Sadelain M, Mailankody S. CD4+ T-Cell Lymphoma Harboring a Chimeric Antigen Receptor Integration in TP53. N Engl J Med 2025; 392:577-583. [PMID: 39908432 PMCID: PMC11801235 DOI: 10.1056/nejmoa2411507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2025]
Abstract
Malignant T-cell transformation after chimeric antigen receptor (CAR) T-cell therapy has been described, but the contribution of CAR integration to oncogenesis is not clear. Here we report a case of a T-cell lymphoma harboring a lentiviral integration in a known tumor suppressor, TP53, which developed in a patient with multiple myeloma after B-cell maturation antigen (BCMA) CAR T-cell therapy.
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Affiliation(s)
- Karlo Perica
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nayan Jain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Scordo
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ruchi Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ozgur Can Eren
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Utsav Patel
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunes Gundem
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dylan Domenico
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sneha Mitra
- Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas D. Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John K. Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Aoife M. Roche
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Angelina Petrichenko
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gunjan L. Shah
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Maria E. Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laetitia Borsu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jae H. Park
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven M. Horwitz
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sergio A. Giralt
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christina Leslie
- Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Saad Z. Usmani
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sham Mailankody
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Zheng X, Cao J, Wang H, Liu L, Jin B, Zhang H, Li M, Nian S, Li H, He R, Wang N, Li X, Wang K. Effects of tauroursodeoxycholate on arsenic-induced hepatic injury in mice: A comparative transcriptomic analysis. J Trace Elem Med Biol 2024; 86:127512. [PMID: 39232337 DOI: 10.1016/j.jtemb.2024.127512] [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: 03/18/2024] [Revised: 07/19/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Prolonged exposure to excessive arsenic (As) and its compounds can cause damage to multiple systems, including respiratory, cardiovascular, immune, nervous, and endocrine systems. Manifestations include changes in skin pigmentation, excessive keratosis on palms and soles, gastrointestinal symptoms, and anemia. The liver as an important detoxification organ of the body, is a significant target organ for arsenic toxicity, and liver diseases are common. So far, the molecular mechanism has not been fully elucidated. Evidence suggests that taurodeoxycholic acid (TUDCA) has a protective role in arsenic-induced liver injury. This study aims to reveal potential target genes at the transcriptional level following TUDCA intervention, providing insights for the intervention of arsenic-induced liver injury. METHODS The TUDCA intervention model of arsenic liver injury in C57BL/6 N mice was established. The experiment was divided into two phases and lasted for 24 weeks. The phase I trial (12 weeks) was divided into control, low, middle and high groups according to the dose of As. The phaseⅡtrial (12 weeks) was administered in combination with 10 mg/L sodium arsenite (the first stage high arsenic group) and TUDCA, so subsequent groups was named with H indicating high arsenic. Divide into four groups: control group(C), TUDCA solvent control group(H-Vehicle), TUDCA combined with As group(H-TUDCA), arsenic group (As). As was ingested through free water and TUDCA was administered to mice by gavage at a dose of 0.1 mL/10 g.b.w (100 mg/kg) once a day for 12 weeks. The differential expression gene (DEG) profile was obtained from the second batch of mouse liver tissues by RNA sequencing technology. Comparative transcriptomic analysis methods were used to identify co-varying DEGs between arsenic induction and TUDCA intervention, along with their associated pathways. QRT-PCR was utilized for validation. RESULTS Transcriptome results showed that 487 DEGs were identified after arsenic induction. TUDCA intervention identified 231 DEGs (p-values < 0.05 and | log2(fold change) | > 1). The comparison of "AS vs C" and "H_TUDCA vs AS" identified 65 covariant DEGs, and further screened the TUDCA pathways and related genes among these genes,six pathways and 11 genes (Ccl21a, Ccr7, Mdm2, Slc2a4, Akr1b7, Pnpla3, Dusp8, Hspa1a, Cyp7a1, Cybrd1, Trpm6) were obtained. Next, we screened for covariant DEGs among the top 50 potential hub genes in arsenic-induced DEGS, and obtained 7 (Hbb-bs, Hspa1a, Mdm2, Slc2a4, Ptk6, Egr1, and Dusp8). Finally, the intersection of Hub gene and pathway gene was selected as the target genes Dusp8, Hspa1a, Mdm2 and Slc2a4. The sequencing results showed that the mRNA expressions of Dusp8, Hspa1a and Mdm2 were significantly increased after arsenic induction, while the expression of Slc2a4 was significantly decreased (P<0.05). Conversely, TUDCA intervention reversed these DEGs changes, consistent with QRT-PCR validation results. CONCLUSION This study contributes to understanding the potential health effects of arsenic-induced liver injury, identifying new potential targets, and providing references for TUDCA intervention.
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Affiliation(s)
- Xiujuan Zheng
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China; Harbin Municipal Center for Disease Control and Prevention, Harbin 150056, PR China.
| | - Jianbin Cao
- Harbin Municipal Center for Disease Control and Prevention, Harbin 150056, PR China.
| | - He Wang
- Department of Medical, The Fourth Hospital of Harbin Medical University, Harbin 150001, PR China.
| | - Lele Liu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China; The first psychological hospital of Harbin, Harbin 150081, PR China.
| | - Baiming Jin
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China; Department of Preventive Medicine, Qiqihar Medical University, Qiqihar 161006, PR China.
| | - Hua Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Mingqi Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Shijing Nian
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Haonan Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Rui He
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Ningning Wang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China; Department of Preventive Medicine, Qiqihar Medical University, Qiqihar 161006, PR China.
| | - Xuying Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
| | - Kewei Wang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin 150081, PR China; National Health Commission & Education Bureau of Heilongjiang Province, Key Laboratory of Etiology and Epidemiology, Harbin Medical University (23618504), Harbin 150081, PR China; Heilongjiang Provincial Key Laboratory of Trace Elements and Human Health, Harbin Medical University, Harbin 150081, PR China; Institute of Cell Biotechnology, China and Russia Medical Research Center, Harbin Medical University, Harbin 150081, PR China.
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Wang Z, Han H, Zhang C, Wu C, Di J, Xing P, Qiao X, Weng K, Hao H, Yang X, Hou Y, Jiang B, Su X. Copy number amplification-induced overexpression of lncRNA LOC101927668 facilitates colorectal cancer progression by recruiting hnRNPD to disrupt RBM47/p53/p21 signaling. J Exp Clin Cancer Res 2024; 43:274. [PMID: 39350250 PMCID: PMC11440719 DOI: 10.1186/s13046-024-03193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Somatic copy number alterations (SCNAs) are pivotal in cancer progression and patient prognosis. Dysregulated long non-coding RNAs (lncRNAs), modulated by SCNAs, significantly impact tumorigenesis, including colorectal cancer (CRC). Nonetheless, the functional significance of lncRNAs induced by SCNAs in CRC remains largely unexplored. METHODS The dysregulated lncRNA LOC101927668, induced by copy number amplification, was identified through comprehensive bioinformatic analyses utilizing multidimensional data. Subsequent in situ hybridization was employed to ascertain the subcellular localization of LOC101927668, and gain- and loss-of-function experiments were conducted to elucidate its role in CRC progression. The downstream targets and signaling pathway influenced by LOC101927668 were identified and validated through a comprehensive approach, encompassing RNA sequencing, RT-qPCR, Western blot analysis, dual-luciferase reporter assay, evaluation of mRNA and protein degradation, and rescue experiments. Analysis of AU-rich elements (AREs) within the mRNA 3' untranslated region (UTR) of the downstream target, along with exploration of putative ARE-binding proteins, was conducted. RNA pull-down, mass spectrometry, RNA immunoprecipitation, and dual-luciferase reporter assays were employed to elucidate potential interacting proteins of LOC101927668 and further delineate the regulatory mechanism between LOC101927668 and its downstream target. Moreover, subcutaneous xenograft and orthotopic liver xenograft tumor models were utilized to evaluate the in vivo impact of LOC101927668 on CRC cells and investigate its correlation with downstream targets. RESULTS Significantly overexpressed LOC101927668, driven by chr7p22.3-p14.3 amplification, was markedly correlated with unfavorable clinical outcomes in our CRC patient cohort, as well as in TCGA and GEO datasets. Moreover, we demonstrated that enforced expression of LOC101927668 significantly enhanced cell proliferation, migration, and invasion, while its depletion impeded these processes in a p53-dependent manner. Mechanistically, nucleus-localized LOC101927668 recruited hnRNPD and translocated to the cytoplasm, accelerating the destabilization of RBM47 mRNA, a transcription factor of p53. As a nucleocytoplasmic shuttling protein, hnRNPD mediated RBM47 destabilization by binding to the ARE motif within RBM47 3'UTR, thereby suppressing the p53 signaling pathway and facilitating CRC progression. CONCLUSIONS The overexpression of LOC101927668, driven by SCNAs, facilitates CRC proliferation and metastasis by recruiting hnRNPD, thus perturbing the RBM47/p53/p21 signaling pathway. These findings underscore the pivotal roles of LOC101927668 and highlight its therapeutic potential in anti-CRC interventions.
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Affiliation(s)
- Zaozao Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
| | - Haibo Han
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Clinical Laboratory, Peking University Cancer Hospital and Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Chenghai Zhang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Chenxin Wu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Jiabo Di
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Pu Xing
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xiaowen Qiao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Kai Weng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Hao Hao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xinying Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Yifan Hou
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Beihai Jiang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xiangqian Su
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
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5
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Kumar A, Singh VK, Singh V, Singh MK, Shrivastava A, Sahu DK. Evaluation of Fibroblast Growth Factor Receptor 3 (FGFR3) and Tumor Protein P53 (TP53) as Independent Prognostic Biomarkers in High-Grade Non-muscle Invasive Bladder Cancer. Cureus 2024; 16:e65816. [PMID: 39219882 PMCID: PMC11362872 DOI: 10.7759/cureus.65816] [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] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Bladder cancer is a significant health issue with an increased recurrence and progression rate, requiring invasive follow-up, which shows a poor prognosis. In addition, the prognostic role of mutant fibroblast growth factor receptor 3 (FGFR3) and tumor protein P53 (TP53) is controversial; therefore, we investigated the methylation status and their altered gene expression in low- and high-grade non-muscle-invasive bladder cancer (NMIBC) subjects. Materials and methods This case-control study was conducted between 2020 and 2023, in which n = 115 tumor tissues (NMIBC n = 85) and (controls n = 30) were examined for FGFR3 and FGFR promoter methylation and expression using methylation-specific PCR (MSP) and real-time PCR. The multivariate regression analysis and Kaplan-Meier (KM) plots were used to establish the association of FGFR3 and TP53 with clinicopathological features and survival outcomes of NMIBC patients. Results High-grade NMIBC tumors showed substantial methylation patterns, with TP53 hypomethylated (p = 0.034) and FGFR3 hypermethylated (p = 0.046), as well as significant mRNA expression of Tp53 and FGFR3 (p = 0.001). The multivariate analysis shows FGFR3 and Tp53 were associated with recurrence-free survival with sensitivity (p = 0.045 (78%); 0.034 (70.7%)) and progression-free survival (p = 0.022(61.5%); 0.038 (69.2%)). Conclusion The findings of this investigation indicate that FGFR3 hypermethylation and TP53 hypomethylation are independent prognostic indicators that aid in the evaluation of disease outcomes in high-grade NMIBC tumors.
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Affiliation(s)
- Anil Kumar
- Urology, King George's Medical University, Lucknow, IND
| | - Vivek K Singh
- Urology, King George's Medical University, Lucknow, IND
| | | | - Mukul K Singh
- Urology, King George's Medical University, Lucknow, IND
| | - Ashutosh Shrivastava
- Center for Advance Research, Faculty of Medicine, King George's Medical University, Lucknow, IND
| | - Dinesh K Sahu
- Central Research Facility/Molecular Biology, Post Graduate Institute of Child Health, Noida, IND
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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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Yan H, Wu W, Hu Y, Li J, Xu J, Chen X, Xu Z, Yang X, Yang B, He Q, Luo P. Regorafenib inhibits EphA2 phosphorylation and leads to liver damage via the ERK/MDM2/p53 axis. Nat Commun 2023; 14:2756. [PMID: 37179400 PMCID: PMC10182995 DOI: 10.1038/s41467-023-38430-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
The hepatotoxicity of regorafenib is one of the most noteworthy concerns for patients, however the mechanism is poorly understood. Hence, there is a lack of effective intervention strategies. Here, by comparing the target with sorafenib, we show that regorafenib-induced liver injury is mainly due to its nontherapeutic target Eph receptor A2 (EphA2). EphA2 deficiency attenuated liver damage and cell apoptosis under regorafenib treatment in male mice. Mechanistically, regorafenib inhibits EphA2 Ser897 phosphorylation and reduces ubiquitination of p53 by altering the intracellular localization of mouse double minute 2 (MDM2) by affecting the extracellular signal-regulated kinase (ERK)/MDM2 axis. Meanwhile, we found that schisandrin C, which can upregulate the phosphorylation of EphA2 at Ser897 also has protective effect against the toxicity in vivo. Collectively, our findings identify the inhibition of EphA2 Ser897 phosphorylation as a key cause of regorafenib-induced hepatotoxicity, and chemical activation of EphA2 Ser897 represents a potential therapeutic strategy to prevent regorafenib-induced hepatotoxicity.
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Affiliation(s)
- Hao Yan
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wentong Wu
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuhuai Hu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, 310018, China
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, 310058, China
| | - Jinjin Li
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiangxin Xu
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xueqin Chen
- Department of Oncology, Affiliated Hangzhou Cancer Hospital, Zhejiang University School of Medicine, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou, 310002, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Zhifei Xu
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaochun Yang
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiaojun He
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, 310018, China
| | - Peihua Luo
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- Department of Pharmacology and Toxicology, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310018, China.
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou Cancer Hospital, Zhejiang University School of Medicine, Hangzhou, 310002, China.
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8
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Epstein RJ, Lin FPY, Brink RA, Blackburn J. Synonymous alterations of cancer-associated Trp53 CpG mutational hotspots cause fatal developmental jaw malocclusions but no tumors in knock-in mice. PLoS One 2023; 18:e0284327. [PMID: 37053216 PMCID: PMC10101519 DOI: 10.1371/journal.pone.0284327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Intragenic CpG dinucleotides are tightly conserved in evolution yet are also vulnerable to methylation-dependent mutation, raising the question as to why these functionally critical sites have not been deselected by more stable coding sequences. We previously showed in cell lines that altered exonic CpG methylation can modify promoter start sites, and hence protein isoform expression, for the human TP53 tumor suppressor gene. Here we extend this work to the in vivo setting by testing whether synonymous germline modifications of exonic CpG sites affect murine development, fertility, longevity, or cancer incidence. We substituted the DNA-binding exons 5-8 of Trp53, the mouse ortholog of human TP53, with variant-CpG (either CpG-depleted or -enriched) sequences predicted to encode the normal p53 amino acid sequence; a control construct was also created in which all non-CpG sites were synonymously substituted. Homozygous Trp53-null mice were the only genotype to develop tumors. Mice with variant-CpG Trp53 sequences remained tumor-free, but were uniquely prone to dental anomalies causing jaw malocclusion (p < .0001). Since the latter phenotype also characterises murine Rett syndrome due to dysfunction of the trans-repressive MeCP2 methyl-CpG-binding protein, we hypothesise that CpG sites may exert non-coding phenotypic effects via pre-translational cis-interactions of 5-methylcytosine with methyl-binding proteins which regulate mRNA transcript initiation, expression or splicing, although direct effects on mRNA structure or translation are also possible.
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Affiliation(s)
- Richard J Epstein
- University of New South Wales, St Vincent's Hospital Campus, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Frank P Y Lin
- University of New South Wales, St Vincent's Hospital Campus, Sydney, Australia
- Centre for Clinical Genomics, The Kinghorn Cancer Centre, Sydney, Australia
| | - Robert A Brink
- University of New South Wales, St Vincent's Hospital Campus, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - James Blackburn
- University of New South Wales, St Vincent's Hospital Campus, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
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9
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Hassanen EI, Ebedy YA, Ibrahim MA, Farroh KY, Elshazly MO. Insights overview on the possible protective effect of chitosan nanoparticles encapsulation against neurotoxicity induced by carbendazim in rats. Neurotoxicology 2022; 91:31-43. [PMID: 35513110 DOI: 10.1016/j.neuro.2022.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
Carbendazim (CBZ) contamination of food and water is a principal factor in many negative impacts on public health. Nanoencapsulation of agrochemicals by nontoxic polymers as chitosan nanoparticles (CS-NPs) is one of the most applications of nanotechnology in agriculture. Despite its many advantages, such as it provides controlled release property, more stability and solubility of the active ingredient, it is not authorized to be used in the market because there are no adequate studies on the nano pesticides induced toxicity on experimental animals. So, we aim to study the possible impacts of CBZ-loading CS-NPs on the whole brain of rats and to explain its mechanism of action. 20 male Wistar rats were partitioned into 4 groups as follows: Group (1), normal saline; group (2), 5 mg/kg CS-NPs; group (3), 300 mg/kg CBZ; group (4) 300 mg/kg CS/CBZ-NCs. After 28 days, some neurobehavioral parameters were assessed to all rats then euthanization was done to collect the brain. Our results revealed that CBZ prompted neurotoxicity manifested by severe neurobehavioral changes and a significant increase of MDA with a decrease of GSH and CAT in brain tissue. In addition, there were severe neuropathological alterations confirmed by immunohistochemistry which showed strong bax, GFAP, and TNF-ὰ protein expression in some brain areas. CBZ also induced apoptosis manifested by up-regulation of JNK and P53 with down-regulation of Bcl-2 in brain tissue. Otherwise, encapsulation of CBZ with CS-NPs could reduce CBZ-induced neurotoxicity and improve all studied toxicological parameters. We recommend using CBZ-loading CS-NPs as an alternative approach for fungicide application in agricultural and veterinary practices but further studies are needed to ensure its safety on other organs.
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Affiliation(s)
- Eman I Hassanen
- Pathology Department, Faculty of Veterinary Medicine, Cairo University, Egypt.
| | - Yasmin A Ebedy
- Pathology Department, Faculty of Veterinary Medicine, Cairo University, Egypt
| | - Marwa A Ibrahim
- Biochemistry and Molecular Biology Department, Faculty of Veterinary Medicine, Cairo University, Egypt
| | - Khaled Y Farroh
- Nanotechnology and Advanced Materials Central Lab, Agricultural Research Center, Egypt
| | - M O Elshazly
- Pathology Department, Faculty of Veterinary Medicine, Cairo University, Egypt
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10
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Li Z, Zhou X, Cai S, Fan J, Wei Z, Chen Y, Cao G. Key roles of CCCTC-binding factor in cancer evolution and development. EXPLORATION OF MEDICINE 2021. [DOI: 10.37349/emed.2021.00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The processes of cancer and embryonic development have a partially overlapping effect. Several transcription factor families, which are highly conserved in the evolutionary history of biology, play a key role in the development of cancer and are often responsible for the pivotal developmental processes such as cell survival, expansion, senescence, and differentiation. As an evolutionary conserved and ubiquitously expression protein, CCCTC-binding factor (CTCF) has diverse regulatory functions, including gene regulation, imprinting, insulation, X chromosome inactivation, and the establishment of three-dimensional (3D) chromatin structure during human embryogenesis. In various cancers, CTCF is considered as a tumor suppressor gene and plays homeostatic roles in maintaining genome function and integrity. However, the mechanisms of CTCF in tumor development have not been fully elucidated. Here, this review will focus on the key roles of CTCF in cancer evolution and development (Cancer Evo-Dev) and embryogenesis.
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Affiliation(s)
- Zishuai Li
- Department of Epidemiology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Xinyu Zhou
- Department of Epidemiology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Shiliang Cai
- Department of Epidemiology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Junyan Fan
- Department of Epidemiology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Zhimin Wei
- Department of Epidemiology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Yifan Chen
- Department of Epidemiology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Guangwen Cao
- Department of Epidemiology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
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11
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Machida Y, Imai T. Different properties of mammary carcinogenesis induced by two chemical carcinogens, DMBA and PhIP, in heterozygous BALB/c Trp53 knockout mice. Oncol Lett 2021; 22:738. [PMID: 34466150 PMCID: PMC8387855 DOI: 10.3892/ol.2021.12999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/02/2021] [Indexed: 12/31/2022] Open
Abstract
Chemical carcinogens, such as 7,12-dimethylbenz[a]anthracene (DMBA) and 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP), are known to induce mammary carcinomas in mice and rats. In the present study, the phenotypic and genotypic characteristics of carcinogen-induced mammary carcinogenesis in heterozygous BALB/c tumor protein p53 (Trp53) knockout mice were examined with reference to published data surrounding human breast cancer. A significantly accelerated induction of mammary carcinomas was observed following a single dose of DMBA (50 mg/kg of body weight at 7 weeks of age), and a modest acceleration was induced by PhIP (50 mg/kg of body weight) administered by gavage 6 times/2 weeks from 7 weeks of age. DMBA-induced mammary carcinomas were histopathologically characterized by distinct biphasic structures with luminal and myoepithelial cells, as well as a frequent estrogen receptor expression, and PhIP-induced carcinomas with solid/microacinar structures consisted of pleomorphic cells. Of note, DMBA-induced mammary carcinomas were characterized by a HRas proto-oncogene (Hras) mutation at codon 61, and gene/protein expression indicating MAPK stimulation. PhIP-induced lesions were suspected to be caused by different molecular mechanisms, including Wnt/β-catenin signaling and/or gene mutation-independent PI3K/AKT signaling activation. In conclusion, the present mouse mammary carcinogenesis models, induced by a combination of genetic and exogenous factors, may be utilized (such as the DMBA-induced model with Trp53 gene function deficiency as a model of adenomyoepithelioma, characterized by distinct biphasic cell constituents and Hras mutations), but PhIP-induced models are required to further analyze the genetic/epigenetic mechanisms promoting mammary carcinomas.
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Affiliation(s)
- Yukino Machida
- Central Animal Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,Department of Veterinary Pathology, Nippon Veterinary and Life Science University, Tokyo 180-8602, Japan
| | - Toshio Imai
- Central Animal Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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12
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Ottaiano A, Santorsola M, Caraglia M, Circelli L, Gigantino V, Botti G, Nasti G. Genetic regressive trajectories in colorectal cancer: A new hallmark of oligo-metastatic disease? Transl Oncol 2021; 14:101131. [PMID: 34034007 PMCID: PMC8144733 DOI: 10.1016/j.tranon.2021.101131] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) originates as consequence of multiple genetic alterations. Some of the involved genes have been extensively studied (APC, TP53, KRAS, SMAD4, PIK3CA, MMR genes) in highly heterogeneous and poly-metastatic cohorts. However, about 10% of metastatic CRC patients presents with an indolent oligo-metastatic disease differently from other patients with poly-metastatic and aggressive clinical course. Which are the genetic dynamics underlying the differences between oligo- and poly-metastatic CRC? The understanding of the genetic trajectories (primary→metastatic) of CRC, in patients selected to represent homogenous clinical models, is crucial to make genotype/phenotype correlations and to identify the molecular events pushing the disease towards an increasing malignant phenotype. This information is crucial to plan innovative therapeutic strategies aimed to reverse or inhibit these phenomena. In the present study, we review the genetic evolution of CRC with the intent to give a developmental perspective on the border line between oligo- and poly-metastatic diseases.
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Affiliation(s)
- Alessandro Ottaiano
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy.
| | - Mariachiara Santorsola
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via L. De Crecchio, 7 80138, Naples, Italy; Biogem Scarl, Institute of Genetic Research, Laboratory of Precision and Molecular Oncology, 83031, Ariano Irpino, Italy
| | - Luisa Circelli
- AMES-Centro Polidiagnostico Strumentale, 80013, Casalnuovo di Napoli, Italy
| | - Valerio Gigantino
- Innovalab scarl, Molecular Biology, Centro Direzionale, isola A2, 80143, Naples, Italy
| | - Gerardo Botti
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
| | - Guglielmo Nasti
- Istituto Nazionale Tumori di Napoli, IRCCS "G. Pascale", Via M. Semmola, 80131, Naples, Italy
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13
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The Anti-Tumor Activity of the NEDD8 Inhibitor Pevonedistat in Neuroblastoma. Int J Mol Sci 2021; 22:ijms22126565. [PMID: 34207315 PMCID: PMC8234433 DOI: 10.3390/ijms22126565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/01/2022] Open
Abstract
Pevonedistat is a neddylation inhibitor that blocks proteasomal degradation of cullin–RING ligase (CRL) proteins involved in the degradation of short-lived regulatory proteins, including those involved with cell-cycle regulation. We determined the sensitivity and mechanism of action of pevonedistat cytotoxicity in neuroblastoma. Pevonedistat cytotoxicity was assessed using cell viability assays and apoptosis. We examined mechanisms of action using flow cytometry, bromodeoxyuridine (BrDU) and immunoblots. Orthotopic mouse xenografts of human neuroblastoma were generated to assess in vivo anti-tumor activity. Neuroblastoma cell lines were very sensitive to pevonedistat (IC50 136–400 nM). The mechanism of pevonedistat cytotoxicity depended on p53 status. Neuroblastoma cells with mutant (p53MUT) or reduced levels of wild-type p53 (p53si-p53) underwent G2-M cell-cycle arrest with rereplication, whereas p53 wild-type (p53WT) cell lines underwent G0-G1 cell-cycle arrest and apoptosis. In orthotopic neuroblastoma models, pevonedistat decreased tumor weight independent of p53 status. Control mice had an average tumor weight of 1.6 mg + 0.8 mg versus 0.5 mg + 0.4 mg (p < 0.05) in mice treated with pevonedistat. The mechanism of action of pevonedistat in neuroblastoma cell lines in vitro appears p53 dependent. However, in vivo studies using mouse neuroblastoma orthotopic models showed a significant decrease in tumor weight following pevonedistat treatment independent of the p53 status. Novel chemotherapy agents, such as the NEDD8-activating enzyme (NAE) inhibitor pevonedistat, deserve further study in the treatment of neuroblastoma.
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14
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Wang JJ, Tian Y, Li MH, Feng YQ, Kong L, Zhang FL, Shen W. Single-cell transcriptome dissection of the toxic impact of Di (2-ethylhexyl) phthalate on primordial follicle assembly. Am J Cancer Res 2021; 11:4992-5009. [PMID: 33754040 PMCID: PMC7978297 DOI: 10.7150/thno.55006] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Rationale: Accumulated evidence indicates that environmental plasticizers are a threat to human and animal fertility. Di (2-ethylhexyl) phthalate (DEHP), a plasticizer to which humans are exposed daily, can trigger reproductive toxicity by acting as an endocrine-disrupting chemical. In mammals, the female primordial follicle pool forms the lifetime available ovarian reserve, which does not undergo regeneration once it is established during the fetal and neonatal period. It is therefore critical to examine the toxicity of DEHP regarding the establishment of the ovarian reserve as it has not been well investigated. Methods: The ovarian cells of postnatal pups, following maternal DEHP exposure, were prepared for single cell-RNA sequencing, and the effects of DEHP on primordial follicle formation were revealed using gene differential expression analysis and single-cell developmental trajectory. In addition, further biochemical experiments, including immunohistochemical staining, apoptosis detection, and Western blotting, were performed to verify the dataset results. Results: Using single-cell RNA sequencing, we revealed the gene expression dynamics of female germ cells and granulosa cells following exposure to DEHP in mice. Regarding germ cells: DEHP impeded the progression of follicle assembly and interfered with their developmental status, while key genes such as Lhx8, Figla, and others, strongly evidenced the reduction. As for granulosa cells: DEHP likely inhibited their proliferative activity, and activated the regulation of cell death. Furthermore, the interaction between ovarian cells mediated by transforming growth factor-beta signaling, was disrupted by DEHP exposure, since the expression of GDF9, BMPR1A, and SMAD3 was affected. In addition, DNA damage and apoptosis were elevated in germ cells and/or somatic cells. Conclusion: These findings offer substantial novel insights into the reproductive toxicity of DEHP exposure during murine germ cell cyst breakdown and primordial follicle formation. These results may enhance the understanding of DEHP exposure on reproductive health.
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Schoop I, Maleki SS, Behrens HM, Krüger S, Haag J, Röcken C. p53 immunostaining cannot be used to predict TP53 mutations in gastric cancer: results from a large Central European cohort. Hum Pathol 2020; 105:53-66. [PMID: 32971129 DOI: 10.1016/j.humpath.2020.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 12/26/2022]
Abstract
Four molecular subgroups of gastric cancer (GC) have been proposed, ie, Epstein-Barr virus (EBV)-positive, microsatellite instable, chromosomal instable (CIN), and genomically stable GC. Based on the complex relationship between chromosomal instability and TP53 mutational status, we hypothesized that the typical clinicopathological characteristics caused by chromosomal instability are correlated with the p53 expression that is detected by immunohistochemistry. Four hundred sixty-seven whole-tissue sections of patients with therapy-naive GC were stained with anti-p53 antibody. The histoscore and staining pattern were analyzed for each slide. Different algorithms of immunohistochemistry evaluation were formed and correlated with clinicopathological characteristics. The algorithms were validated by assessing the mutational status of TP53 in 111 cases. Four hundred forty-two GCs were p53 positive, and 25 were negative, including 414 GCs with a homogeneous pattern and 53 GCs with a heterogeneous staining pattern. There was no correlation with overall or tumor-specific survival. In comparison with clinicopathological characteristics, the algorithm high versus low showed correlations with microsatellite instability, hepatocyte growth factor receptor (MET), and TP53 mutational status. The algorithm Q1/Q4 versus Q2/Q3 appeared to be correlated with the phenotype as per the Laurén classification, microsatellite instability, EBV status, and p53 expression pattern. The algorithm <90% = 0 and <50% = 3+ versus ≥90% = 0 or ≥50% = 3+ showed correlations with the EBV status, microsatellite instability, grading, and p53 expression pattern. The algorithm homogeneous versus heterogeneous did not correlate with any clinicopathological characteristic. Our results showed that the immunohistochemistry of p53, TP53 mutational status, and CIN subtype were connected. However, different algorithms for p53 immunohistochemical evaluation cannot be used to predict TP53 mutations in CIN GCs in individual cases.
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Affiliation(s)
- Isabelle Schoop
- Department of Pathology, Christian-Albrechts-University, D-24105 Kiel, Germany
| | - Saffiyeh Saboor Maleki
- Department of Pathology, Christian-Albrechts-University, D-24105 Kiel, Germany; Institute for Cardiovascular Prevention, Ludwig Maximilians University, D-80336 Munich, Germany
| | | | - Sandra Krüger
- Department of Pathology, Christian-Albrechts-University, D-24105 Kiel, Germany
| | - Jochen Haag
- Department of Pathology, Christian-Albrechts-University, D-24105 Kiel, Germany
| | - Christoph Röcken
- Department of Pathology, Christian-Albrechts-University, D-24105 Kiel, Germany.
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16
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Qiao C, Liu W, Jiang H, He M, Yang Q, Xing Y. Integrated analysis of miRNA and mRNA expression profiles in p53-edited PFF cells. Cell Cycle 2020; 19:949-959. [PMID: 32213107 DOI: 10.1080/15384101.2020.1742852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
p53 is the most frequently mutated gene in human cancers, with over half of all tumors harboring mutation at this locus. R248 and R249 (corresponding to porcine R241 and R242), are among the hotspot mutations frequently mutated in liver, lung, breast, and some other cancers. In this study, p53 gene was knocked out or point-edited (R241 and R242 were converted to 241W and 242S) in porcine fetal fibroblast (PFF) cells via CRISPR-Cas9 technique. High throughput sequencing of miRNA and mRNA uncovered a total of 225 differentially expressed miRNAs (DEMs) and 738 differentially expressed genes (DEGs) in the p53 knockout (p53-KO) cells, and a total of 211 DEMs and 722 DEGs in the point-modified (p53-241W242S) cells. Totally 28 annotated DEMs were found to overlap between p53-KO/p53-WT and p53-241W242S/p53-WT miRNAs datasets, of which miR-34 c, miR-218, miR-205, miR-105-1, miR-105-2, miR-206, miR-224 and miR-429 play important roles in p53 regulatory network. Among the top 10 DEGs in p53-KO and p53-241W242S cells, most genes were reported to be involved in tumors, cell proliferation or cell migration. p53-KO and p53-241W242S cells showed a significantly higher (P < 0.01) proliferation rate compared with p53-WT cells. In conclusion, genetic modifications of p53 gene significantly affect the expression levels of a large number of genes and miRNAs in the PFF cells. The p53-edited PFF cells could be used as non-tumor cell models for investigating the p53 signaling network, and as donor cells for somatic nuclear transfer, with the aim to develop porcine models with the corresponding p53 mutations.Abbreviations: CRISPR-Cas9: Clustered regularly interspaced short palindromic repeats-associated protein 9; PFF: porcine fetal fibroblasts; SCNT: somatic cell nuclear transfer; RNA sequencing: small RNA sequencing and mRNA sequencing; DEGs: differentially expressed mRNAs; DEMs: differentially expressed miRNAs.
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Affiliation(s)
- Chuanmin Qiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Weiwei Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Haoyun Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Maozhang He
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qiang Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuyun Xing
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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17
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Kurbegovic A, Trudel M. The master regulators Myc and p53 cellular signaling and functions in polycystic kidney disease. Cell Signal 2020; 71:109594. [PMID: 32145315 DOI: 10.1016/j.cellsig.2020.109594] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 01/08/2023]
Abstract
The transcription factors Myc and p53 associated with oncogenesis play determinant roles in a human genetic disorder, autosomal dominant polycystic kidney disease (ADPKD), that was coined early in ADPKD etiology a «neoplasia in disguise ». These factors are interdependent master cell regulators of major biological processes including proliferation, apoptosis, cell growth, metabolism, inflammation, fibrosis and differentiation that are all modulated in ADPKD. Myc and p53 proteins evolved to respond and carry out overlapping functions via opposing mechanisms of action. Studies in human ADPKD kidneys, caused by mutations in the PKD1 or PKD2 genes, reveal reduced p53 expression and high expression of Myc in the cystic tubular epithelium. Myc and p53 via direct interaction act respectively, as transcriptional activator and repressor of PKD1 gene expression, consistent with increased renal PKD1 levels in ADPKD. Mouse models generated by Pkd1 and Pkd2 gene dosage dysregulation reproduce renal cystogenesis with activation of Myc expression and numerous signaling pathways, strikingly similar to those determined in human ADPKD. In fact, upregulation of renal Myc expression is also detected in virtually all non-orthologous animal models of PKD. A definitive causal connection of Myc with cystogenesis was established by renal overexpression of Myc in transgenic mice that phenocopies human ADPKD. The network of activated signaling pathways in human and mouse cystogenesis individually or in combination can target Myc as a central node of PKD pathogenesis. One or many of the multiple functions of Myc upon activation can play a role in every phases of ADPKD development and lend credence to the notion of "Myc addiction" for cystogenesis. We propose that the residual p53 levels are conducive to an ADPKD biological program without cancerogenesis while a "p53 dependent annihilation" mechanism would be permissive to oncogenesis. Of major importance, Myc ablation in orthologous mouse models or direct inhibition in non-orthologous mouse model significantly delays cystogenesis consistent with pharmacologic or genetic inhibition of Myc upstream regulator or downstream targets in the mouse. Together, these studies on PKD proteins upon dysregulation not only converged on Myc as a focal point but also attribute to Myc upregulation a causal and « driver » role in pathogenesis. This review will present and discuss our current knowledge on Myc and p53, focused on PKD mouse models and ADPKD.
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Affiliation(s)
- Almira Kurbegovic
- Institut de Recherches Cliniques de Montréal, Molecular Genetics and Development, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Marie Trudel
- Institut de Recherches Cliniques de Montréal, Molecular Genetics and Development, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.
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Reichrath J, Reichrath S, Vogt T, Römer K. Crosstalk Between Vitamin D and p53 Signaling in Cancer: An Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1268:307-318. [PMID: 32918225 DOI: 10.1007/978-3-030-46227-7_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It has now been convincingly shown that vitamin D and p53 signaling protect against spontaneous or carcinogen-induced malignant transformation of cells. The vitamin D receptor (VDR) and the p53/p63/p73 proteins (the p53 family hereafter) exert their effects as receptors/sensors that turn into transcriptional regulators upon stimulus. While the p53 clan, mostly in the nucleoplasm, responds to a large and still growing number of alterations in cellular homeostasis commonly referred to as stress, the nuclear VDR is transcriptionally activated after binding its naturally occurring biologically active ligand 1,25-dihydroxyvitamin D with high affinity. Interestingly, a crosstalk between vitamin D and p53 signaling has been demonstrated that occurs at different levels, has genome-wide implications, and is of high importance for many malignancies, including non-melanoma skin cancer. These interactions include the ability of p53 to upregulate skin pigmentation via POMC derivatives including alpha-MSH and ACTH. Increased pigmentation protects the skin against UV-induced DNA damage and skin photocarcinogenesis, but also inhibits cutaneous synthesis of vitamin D. A second level of interaction is characterized by binding of VDR and p53 protein, an observation that may be of relevance for the ability of 1,25-dihydroxyvitamin D to increase the survival of skin cells after UV irradiation. UV irradiation-surviving cells show significant reductions in thymine dimers in the presence of 1,25-dihydroxyvitamin D that are associated with increased nuclear p53 protein expression and significantly reduced NO products. A third level of interaction is documented by the ability of vitamin D compounds to regulate the expression of the murine double minute (MDM2) gene in dependence of the presence of wild-type p53. MDM2 has a well-established role as a key negative regulator of p53 activity. Finally, p53 and its family members have been implicated in the direct regulation of the VDR. This review gives an update on some of the implications of the crosstalk between vitamin D and p53 signaling for carcinogenesis in the skin and other tissues, focusing on a genome-wide perspective.
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Affiliation(s)
- Jörg Reichrath
- Center for Clinical and Experimental Photodermatology and Department of Dermatology, Saarland University Medical Center, Homburg, Germany.
| | - Sandra Reichrath
- Department of Dermatology, The Saarland University Hospital, Homburg, Germany
| | - Thomas Vogt
- Department of Dermatology, The Saarland University Hospital, Homburg, Germany
| | - Klaus Römer
- José Carreras Centre and Internal Medicine I, University of Saarland Medical Centre, Homburg (Saar), Germany
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Alanis-Lobato G, Schaefer MH. Generation and Interpretation of Context-Specific Human Protein-Protein Interaction Networks with HIPPIE. Methods Mol Biol 2020; 2074:135-144. [PMID: 31583636 DOI: 10.1007/978-1-4939-9873-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput techniques for the detection of protein-protein interactions (PPIs) have enabled a systems approach for the study of the living cell. However, the increasing amount of protein interaction data, the varying quality of these measurements, and the lack of context information make it difficult to construct meaningful and reliable protein networks.The Human Integrated Protein-Protein Interaction rEference (HIPPIE) is a web tool that integrates and annotates experimentally supported human PPIs from a heterogeneous set of data sources. In HIPPIE, one can query for the interactors of one or more proteins and generate high-quality and context-specific networks. This chapter highlights HIPPIE's most important features and exemplifies its functionality through a proposed use case.
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Affiliation(s)
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.
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20
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Fujita K. p53 Isoforms in Cellular Senescence- and Ageing-Associated Biological and Physiological Functions. Int J Mol Sci 2019; 20:ijms20236023. [PMID: 31795382 PMCID: PMC6928910 DOI: 10.3390/ijms20236023] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022] Open
Abstract
Cellular senescence, a term originally used to define the characteristics of normal human fibroblasts that reached their replicative limit, is an important factor for ageing, age-related diseases including cancer, and cell reprogramming. These outcomes are mediated by senescence-associated changes in gene expressions, which sometimes lead to the secretion of pro-inflammatory factors, or senescence-associated secretory phenotype (SASP) that contribute to paradoxical pro-tumorigenic effects. p53 functions as a transcription factor in cell-autonomous responses such as cell-cycle control, DNA repair, apoptosis, and cellular senescence, and also non-cell-autonomous responses to DNA damage by mediating the SASP function of immune system activation. The human TP53 gene encodes twelve protein isoforms, which provides an explanation for the pleiotropic p53 function on cellular senescence. Recent reports suggest that some short isoforms of p53 may modulate gene expressions in a full-length p53-dependent and -independent manner, in other words, some p53 isoforms cooperate with full-length p53, whereas others operate independently. This review summarizes our current knowledge about the biological activities and functions of p53 isoforms, especially Δ40p53, Δ133p53α, and p53β, on cellular senescence, ageing, age-related disorder, reprogramming, and cancer. Numerous cellular and animal model studies indicate that an unbalance in p53 isoform expression in specific cell types causes age-related disorders such as cancer, premature ageing, and degenerative diseases.
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Affiliation(s)
- Kaori Fujita
- Cell Induction and Regulation Field, Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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Abstract
Background The knowledge about specific mechanisms generating TP53 dysfunction in diffuse large B-cell lymphoma is limited. The aim of the current study was to comprehensively explore TP53 gene variability resulting from somatic mutations, promoter methylation, and allelic imbalance in tumorous tissue of diffuse large B-cell lymphoma (DLBCL). Methods DNA samples from 74 patients with DLBCL were used. Genomic DNA was isolated from paraffin blocks of lymph nodes or from extranodal biopsies of tumors by the phenol–chloroform extraction method with guanidine. Analysis of coding sequences of the TP53 gene was based on Sanger’s direct sequencing method. The methylation status of the TP53 promoter was analyzed using by methylation-specific PCR on bisulfite-converted DNA. Assessment of the detected mutations was carried out in the IARC TP53 Database and the TP53 UMD mutation database of human cancer. Results The mutations in regions coding for the DNA-binding domain were prevalent (95%). In the analyzed sample of patients, codons 275, 155, 272, and 212 were hotspots of mutations in the TP53 gene. In addition, functionally significant intron mutations (IVS6-36G > C and IVS5 + 43G > T) were detected. Instances of TP53 promoter methylation were observed only in a few samples of diffuse large B-cell lymphoma tissue. Furthermore, loss of heterozygosity was revealed only in the subgroup of patients with altered status of the gene (mutations were detected in five patients and promoter methylation in one case). Conclusions Thus, the results suggest that there are two sequential events in the formation of diffuse large B-cell lymphoma in at least some cases. The first event is mutation or methylation of the TP53 promoter, leading to appearance of a cell with increased risk of malignant transformation. The second event is the loss of an intact allele of the gene; this change is necessary for tumorigenesis. We identified TP53 mutation patterns in a Russian cohort of patients with de novo DLBCL who were treated with R-CHOP and R-CHOP-like regimens and confirmed that TP53 mutation status is a valuable prognostic biomarker.
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22
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Wu M, Sun Y, Xu F, Liang Y, Liu H, Yi Y. Annexin A2 Silencing Inhibits Proliferation and Epithelial-to-mesenchymal Transition through p53-Dependent Pathway in NSCLCs. J Cancer 2019; 10:1077-1085. [PMID: 30854114 PMCID: PMC6400676 DOI: 10.7150/jca.29440] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/15/2018] [Indexed: 12/11/2022] Open
Abstract
Annexin A2 has been involved in cancer cell adhesion, invasion and metastasis. However, the exact function and mechanism of Annexin A2 in tumor progression of NSCLCs have not been elucidated. In this study, we showed that Annexin A2 was evidently overexpressed in human NSCLCs cell lines and NSCLCs tissues. Clinicopathologic analysis showed that Annexin A2 expression was significantly correlated with clinical stage, and lymph node metastasis. Kaplan-Meier analysis revealed that patients with high Annexin A2 expression had poorer overall survival rates than those with low Annexin A2 expression. Moreover, we found that knockdown of Annexin A2 significantly suppressed cell proliferation and invasion of NSCLCs cells. Mechanistically, our studies showed that knockdown of Annexin A2 increased the expression of p53, which in turn, induced cell cycle G2 arrest and inhibited epithelial-to-mesenchymal transition (EMT). Taken together, these data suggest that Annexin A2 plays an important role in NSCLCs progression, which could serve as a potential prognosis marker and a novel therapeutic target for NSCLCs.
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Affiliation(s)
- Minhua Wu
- Department of Histology and Embryology, Guangdong Medical University, Zhanjiang 524023, Guangdong, China
| | - Yanqin Sun
- Department of Pathology, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Feipeng Xu
- Department of Gastrointestinal Surgery, Affiliated hospital of Guangdong Medical University, Zhanjiang 524000, Guangdong, China
| | - Yanqing Liang
- Department of Histology and Embryology, Guangdong Medical University, Zhanjiang 524023, Guangdong, China
| | - Hao Liu
- Cancer Hospital and Cancer Research Institute, Guangzhou Medical University, Guangzhou 510095, Guangdong, China
| | - Yanmei Yi
- Department of Histology and Embryology, Guangdong Medical University, Zhanjiang 524023, Guangdong, China
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The oncoprotein HBXIP promotes human breast cancer growth through down-regulating p53 via miR-18b/MDM2 and pAKT/MDM2 pathways. Acta Pharmacol Sin 2018; 39:1787-1796. [PMID: 30181579 DOI: 10.1038/s41401-018-0034-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Mammalian hepatitis B X-interacting protein (HBXIP) is an 18-kDa protein that regulates a large number of transcription factors such as TF-IID, E2F1, SP1, STAT3, c-Myc, and LXR by serving as an oncogenic transcription coactivator and plays an important role in the development of breast cancer. We previously showed that HBXIP as an oncoprotein could enhance the promoter activity of MDM2 through coactivating p53, promoting the MDM2 transcription in breast cancer. In this study we investigated the molecular mechanisms underlying the modulation of MDM2/p53 interaction by HBXIP in human breast cancer MCF-7 cells in vitro and in vivo. We showed that HBXIP could up-regulate MDM2 through inducing DNA methylation of miR-18b, thus suppressing the miR-18b expression, leading to the attenuation of p53 in breast cancer cells. In addition, HBXIP could promote the phosphorylation of MDM2 by increasing the level of pAKT and bind to pMDM2, subsequently enhancing the interaction between MDM2 and p53 for the down-regulation of p53 in breast cancer cells. In MCF-7 breast cancer xenograft nude mice, we also observed that overexpression of HBXIP promoted breast cancer growth through the miR-18b/MDM2 and pAKT/MDM2 pathways. In conclusion, oncoprotein HBXIP suppresses miR-18b to elevate MDM2 and activates pAKT to phosphorylate MDM2 for enhancing the interaction between MDM2 and p53, leading to p53 degradation in promotion of breast cancer growth. Our findings shed light on a novel mechanism of p53 down-regulation during the development of breast cancer.
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24
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p53 mediated transcriptional regulation of long non-coding RNA by 1-hydroxy-1-norresistomycin triggers intrinsic apoptosis in adenocarcinoma lung cancer. Chem Biol Interact 2018; 287:1-12. [DOI: 10.1016/j.cbi.2018.03.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/06/2018] [Accepted: 03/25/2018] [Indexed: 12/20/2022]
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25
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Wawrzynow B, Zylicz A, Zylicz M. Chaperoning the guardian of the genome. The two-faced role of molecular chaperones in p53 tumor suppressor action. Biochim Biophys Acta Rev Cancer 2018; 1869:161-174. [DOI: 10.1016/j.bbcan.2017.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 12/17/2022]
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26
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Tano K, Onoguchi-Mizutani R, Yeasmin F, Uchiumi F, Suzuki Y, Yada T, Akimitsu N. Identification of Minimal p53 Promoter Region Regulated by MALAT1 in Human Lung Adenocarcinoma Cells. Front Genet 2018; 8:208. [PMID: 29632545 PMCID: PMC5879451 DOI: 10.3389/fgene.2017.00208] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
The MALAT1 long noncoding RNA is strongly linked to cancer progression. Here we report a MALAT1 function in repressing the promoter of p53 (TP53) tumor suppressor gene. p21 and FAS, well-known p53 targets, were upregulated by MALAT1 knockdown in A549 human lung adenocarcinoma cells. We found that these upregulations were mediated by transcriptional activation of p53 through MALAT1 depletion. In addition, we identified a minimal MALAT1-responsive region in the P1 promoter of p53 gene. Flow cytometry analysis revealed that MALAT1-depleted cells exhibited G1 cell cycle arrest. These results suggest that MALAT1 affects the expression of p53 target genes through repressing p53 promoter activity, leading to influence the cell cycle progression.
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Affiliation(s)
- Keiko Tano
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | | | - Fouzia Yeasmin
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Fumiaki Uchiumi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kitakyushu, Japan
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27
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Schipp R, Varga J, Bátor J, Vecsernyés M, Árvai Z, Pap M, Szeberényi J. Partial p53-dependence of anisomycin-induced apoptosis in PC12 cells. Mol Cell Biochem 2017; 434:41-50. [PMID: 28432551 DOI: 10.1007/s11010-017-3035-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/12/2017] [Indexed: 01/25/2023]
Abstract
The bacterial antibiotic anisomycin is known to induce apoptosis by activating several mitogen-activated protein kinases and by inhibiting protein synthesis. In this study, the influence of p53 protein on the apoptosis-inducing effect of anisomycin was investigated. The effect of protein synthesis-inhibiting concentration of anisomycin on apoptotic events was analyzed using Western blot, DNA fragmentation, and cell viability assays in wild-type PC12 and in mutant p53 protein expressing p143p53PC12 cells. Anisomycin stimulated the main apoptotic pathways in both cell lines, but p143p53PC12 cells showed lower sensitivity to the drug than their wild-type counterparts. Anisomycin caused the activation of the main stress kinases, phosphorylation of the p53 protein and the eukaryotic initiation factor eIF2α, proteolytic cleavage of protein kinase R, Bid, caspase-9 and -3. Furthermore, anisomycin treatment led to the activation of TRAIL and caspase-8, two proteins involved in the extrinsic apoptotic pathway. All these changes were stronger and more sustained in wtPC12 cells. In the presence of the dominant inhibitory p53 protein, p53- dependent genes involved in the regulation of apoptosis may be less transcribed and this can lead to the decrease of apoptotic processes in p143p53PC12 cells.
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Affiliation(s)
- R Schipp
- Department of Medical Biology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.,Signal Transduction Research Group, Szentágothai Research Centre, Ifjúság útja 20, Pécs, 7624, Hungary
| | - J Varga
- Department of Medical Biology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.,Signal Transduction Research Group, Szentágothai Research Centre, Ifjúság útja 20, Pécs, 7624, Hungary
| | - J Bátor
- Department of Medical Biology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.,Signal Transduction Research Group, Szentágothai Research Centre, Ifjúság útja 20, Pécs, 7624, Hungary
| | - M Vecsernyés
- Department of Medical Biology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.,Signal Transduction Research Group, Szentágothai Research Centre, Ifjúság útja 20, Pécs, 7624, Hungary
| | - Z Árvai
- Department of Medical Biology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.,Signal Transduction Research Group, Szentágothai Research Centre, Ifjúság útja 20, Pécs, 7624, Hungary
| | - M Pap
- Department of Medical Biology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.,Signal Transduction Research Group, Szentágothai Research Centre, Ifjúság útja 20, Pécs, 7624, Hungary
| | - József Szeberényi
- Department of Medical Biology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary. .,Signal Transduction Research Group, Szentágothai Research Centre, Ifjúság útja 20, Pécs, 7624, Hungary.
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28
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Voropaeva EN, Pospelova TI, Voevoda MI, Maksimov VN. Frequency, spectrum, and functional significance of TP53 mutations in patients with diffuse large B-cell lymphoma. Mol Biol 2017. [DOI: 10.1134/s0026893316060224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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29
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Molecular mechanisms involved in gliomagenesis. Brain Tumor Pathol 2017; 34:1-7. [DOI: 10.1007/s10014-017-0278-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
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30
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Pavel AB, Vasile CI. Identifying cancer type specific oncogenes and tumor suppressors using limited size data. J Bioinform Comput Biol 2016; 14:1650031. [PMID: 27712196 DOI: 10.1142/s0219720016500311] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cancer is a complex and heterogeneous genetic disease. Different mutations and dysregulated molecular mechanisms alter the pathways that lead to cell proliferation. In this paper, we explore a method which classifies genes into oncogenes (ONGs) and tumor suppressors. We optimize this method to identify specific (ONGs) and tumor suppressors for breast cancer, lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and colon adenocarcinoma (COAD), using data from the cancer genome atlas (TCGA). A set of genes were previously classified as ONGs and tumor suppressors across multiple cancer types (Science 2013). Each gene was assigned an ONG score and a tumor suppressor score based on the frequency of its driver mutations across all variants from the catalogue of somatic mutations in cancer (COSMIC). We evaluate and optimize this approach within different cancer types from TCGA. We are able to determine known driver genes for each of the four cancer types. After establishing the baseline parameters for each cancer type, we identify new driver genes for each cancer type, and the molecular pathways that are highly affected by them. Our methodology is general and can be applied to different cancer subtypes to identify specific driver genes and improve personalized therapy.
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Affiliation(s)
- Ana B Pavel
- 1 Graduate Program in Bioinformatics, Boston University, 24 Cummington Mall, MA 02215, Boston, USA
| | - Cristian I Vasile
- 2 Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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31
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Wang S, Zhang Y, Wang Y, Ye P, Li J, Li H, Ding Q, Xia J. Amphiregulin Confers Regulatory T Cell Suppressive Function and Tumor Invasion via the EGFR/GSK-3β/Foxp3 Axis. J Biol Chem 2016; 291:21085-21095. [PMID: 27432879 DOI: 10.1074/jbc.m116.717892] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 11/06/2022] Open
Abstract
Previous studies mainly focused on the role of the epidermal growth factor receptor (EGFR) in tumor cells, whereas the effects of the EGFR on immune responses has not been determined. Our study shows that the EGFR signaling pathway play a role in the regulation of regulatory T cells (Treg cells) in cancer patients. The EGF-like growth factor Amphiregulin (AREG) protein was frequently up-regulated in a tissue microarray, which was associated with worse overall survival. Additionally, in sera, tissue specimens, and effusions of lung or gastric cancer patients, up-regulated AREG protein enhanced the suppressive function of Treg cells. AREG maintained the Treg cell suppressive function via the EGFR/GSK-3β/Foxp3 axis in vitro and in vivo Furthermore, inhibition of EGFR by the tyrosine kinase inhibitor gefitinib restored the activity of GSK-3β and attenuated Treg cell function. β-TrCP was involved in GSK-3β-mediated Foxp3 degradation, and mass spectrometry identified Lys356 as the ubiquitination site of Foxp3 by β-TrCP. These findings demonstrate the posttranslational regulation of Foxp3 expression by AREG in cancer patients through AREG/EGFR/GSK-3β signaling, which could lead to Foxp3 protein degradation in Treg cells and a potential therapeutic target for cancer treatment.
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Affiliation(s)
- Sihua Wang
- From the Departments of Thoracic Surgery
| | | | - Yan Wang
- the Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, and
| | - Ping Ye
- the Department of Cardiovascular Surgery, Central Hospital of Wuhan, Wuhan 430022, China
| | - Jun Li
- the Department of Cardiovascular Surgery, Central Hospital of Wuhan, Wuhan 430022, China
| | - Huabin Li
- the Department of Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Qingqing Ding
- the Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, and
| | - Jiahong Xia
- Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China,
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Nuttall P, Lee K, Ciccarella P, Carminati M, Ferrari G, Kim KB, Albrecht T. Single-Molecule Studies of Unlabeled Full-Length p53 Protein Binding to DNA. J Phys Chem B 2016; 120:2106-14. [DOI: 10.1021/acs.jpcb.5b11076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Philippa Nuttall
- Imperial College London, Department of Chemistry, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Kidan Lee
- Department
of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Pietro Ciccarella
- Dipartimento
di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, P.za Leonardo da Vinci 32, Milano, Italy
| | - Marco Carminati
- Dipartimento
di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, P.za Leonardo da Vinci 32, Milano, Italy
| | - Giorgio Ferrari
- Dipartimento
di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, P.za Leonardo da Vinci 32, Milano, Italy
| | - Ki-Bum Kim
- Department
of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Tim Albrecht
- Imperial College London, Department of Chemistry, Exhibition Road, London SW7 2AZ, United Kingdom
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Krais AM, Speksnijder EN, Melis JP, Singh R, Caldwell A, Gamboa da Costa G, Luijten M, Phillips DH, Arlt VM. Metabolic activation of 2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine and DNA adduct formation depends on p53: Studies in Trp53(+/+),Trp53(+/-) and Trp53(-/-) mice. Int J Cancer 2016; 138:976-82. [PMID: 26335255 PMCID: PMC4832306 DOI: 10.1002/ijc.29836] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/20/2015] [Indexed: 11/07/2022]
Abstract
The expression of the tumor suppressor p53 can influence the bioactivation of, and DNA damage induced by, the environmental carcinogen benzo[a]pyrene, indicating a role for p53 in its cytochrome P450 (CYP)-mediated biotransformation. The carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), which is formed during the cooking of food, is also metabolically activated by CYP enzymes, particularly CYP1A2. We investigated the potential role of p53 in PhIP metabolism in vivo by treating Trp53(+/+), Trp53(+/-) and Trp53(-/-) mice with a single oral dose of 50 mg/kg body weight PhIP. N-(Deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP-C8-dG) levels in DNA, measured by liquid chromatography-tandem mass spectrometry, were significantly lower in liver, colon, forestomach and glandular stomach of Trp53(-/-) mice compared to Trp53(+/+) mice. Lower PhIP-DNA adduct levels in the livers of Trp53(-/-) mice correlated with lower Cyp1a2 enzyme activity (measured by methoxyresorufin-O-demethylase activity) in these animals. Interestingly, PhIP-DNA adduct levels were significantly higher in kidney and bladder of Trp53(-/-) mice compared to Trp53(+/+) mice, which was accompanied by higher sulfotransferase (Sult) 1a1 protein levels and increased Sult1a1 enzyme activity (measured by 2-naphthylsulfate formation from 2-naphthol) in kidneys of these animals. Our study demonstrates a role for p53 in the metabolism of PhIP in vivo, extending previous results on a novel role for p53 in xenobiotic metabolism. Our results also indicate that the impact of p53 on PhIP biotransformation is tissue-dependent and that in addition to Cyp1a enzymes, Sult1a1 can contribute to PhIP-DNA adduct formation.
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Affiliation(s)
- Annette M. Krais
- Analytical and Environmental Sciences Division, MRC‐PHE Centre for Environment and HealthKing's College LondonLondonSE1 9NHUnited Kingdom
- Annette M. Krais current address is: Division of Occupational and Environmental MedicineLund University221 85LundSweden
| | - Ewoud N. Speksnijder
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM)BilthovenMA3721The Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeiden2300The NetherlandsRC
| | - Joost P.M. Melis
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM)BilthovenMA3721The Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeiden2300The NetherlandsRC
| | - Rajinder Singh
- Department of Cancer Studies and Molecular MedicineUniversity of LeicesterLeicesterLE2 7LXUnited Kingdom
| | - Anna Caldwell
- Mass Spectrometry Facility, King's College LondonLondonSE1 9NHUnited Kingdom
| | - Gonçalo Gamboa da Costa
- Division of Biochemical ToxicologyNational Center for Toxicological ResearchJeffersonAR72079
| | - Mirjam Luijten
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM)BilthovenMA3721The Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeiden2300The NetherlandsRC
| | - David H. Phillips
- Analytical and Environmental Sciences Division, MRC‐PHE Centre for Environment and HealthKing's College LondonLondonSE1 9NHUnited Kingdom
| | - Volker M. Arlt
- Analytical and Environmental Sciences Division, MRC‐PHE Centre for Environment and HealthKing's College LondonLondonSE1 9NHUnited Kingdom
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Pavel AB, Sonkin D, Reddy A. Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity. BMC SYSTEMS BIOLOGY 2016; 10:16. [PMID: 26864072 PMCID: PMC4750289 DOI: 10.1186/s12918-016-0260-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 01/25/2016] [Indexed: 01/06/2023]
Abstract
Background High throughput technologies have been used to profile genes in multiple different dimensions, such as genetic variation, copy number, gene and protein expression, epigenetics, metabolomics. Computational analyses often treat these different data types as independent, leading to an explosion in the number of features making studies under-powered and more importantly do not provide a comprehensive view of the gene’s state. We sought to infer gene activity by integrating different dimensions using biological knowledge of oncogenes and tumor suppressors. Results This paper proposes an integrative model of oncogene and tumor suppressor activity in cells which is used to identify cancer drivers and compute patient-specific gene activity scores. We have developed a Fuzzy Logic Modeling (FLM) framework to incorporate biological knowledge with multi-omics data such as somatic mutation, gene expression and copy number measurements. The advantage of using a fuzzy logic approach is to abstract meaningful biological rules from low-level numerical data. Biological knowledge is often qualitative, thus combining it with quantitative numerical measurements may leverage new biological insights about a gene’s state. We show that the oncogenic and altered tumor suppressing state of a gene can be better characterized by integrating different molecular measurements with biological knowledge than by each data type alone. We validate the gene activity score using data from the Cancer Cell Line Encyclopedia and drug sensitivity data for five compounds: BYL719 (PIK3CA inhibitor), PLX4720 (BRAF inhibitor), AZD6244 (MEK inhibitor), Erlotinib (EGFR inhibitor), and Nutlin-3 (MDM2 inhibitor). The integrative score improves prediction of drug sensitivity for the known drug targets of these compounds compared to each data type alone. The gene activity scores are also used to cluster colorectal cancer cell lines. Two subtypes of CRCs were found and potential cancer drivers and therapeutic targets for each of the subtypes were identified. Conclusions We propose a fuzzy logic based approach to infer gene activity in cancer by integrating numerical data with descriptive biological knowledge. We compute general patient-specific gene-level scores useful to determine the oncogenic or tumor suppressor status of cancer gene drivers and to cluster or classify patients. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0260-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana B Pavel
- Graduate Program in Bioinformatics, Boston University, 24 Cummington Mall, Boston, 02215, MA, USA. .,Section of Computational Biomedicine, Boston University School of Medicine, 72 East Concord Street, Boston, 02118, MA, USA.
| | - Dmitriy Sonkin
- Novartis Institutes for Biomedical Research, 250 Massachusetts Ave, Cambridge, 02139, MA, USA.
| | - Anupama Reddy
- Duke University Medical Center, Durham, 27708, NC, USA.
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Pronsato L, Milanesi L. Effect of testosterone on the regulation of p53 and p66Shc during oxidative stress damage in C2C12 cells. Steroids 2016; 106:41-54. [PMID: 26703444 DOI: 10.1016/j.steroids.2015.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 11/10/2015] [Accepted: 12/10/2015] [Indexed: 12/12/2022]
Abstract
Accumulating evidence indicates that apoptosis is activated in the aged skeletal muscle, contributing to sarcopenia. We have previously demonstrated that testosterone protects against hydrogen peroxide (H2O2)-induced apoptosis in C2C12 muscle cells, at different levels: morphological, physiological, biochemical and molecular. In the present study we observed that H2O2 induces the mitochondrial permeability transition pore (mPTP) opening and exerts p53 activation in a time-dependent way, with a maximum response after 1-2h of treatment. Testosterone treatment, prior to H2O2, reduces not only p53 phosphorylation but also p66Shc expression, activation and its mitochondrial localization, at the same time that it prevents the mPTP opening. Furthermore, testosterone diminishes JNK and PKCβI phosphorylation induced by H2O2 and probably contributing thus, to reduce the activation of p66Shc. Thus, the mPTP opening, p53, JNK and PKCβI activation, as well as p66Shc mRNA increase, induced by oxidative stress, were reduced by testosterone pretreatment. The data presented in this work show some of the components upstream of the classical apoptotic pathway, that are activated during oxidative stress and that are points where testosterone exerts its protective action against apoptosis, exposing some of the puzzle pieces of the intricate network that aged skeletal muscle apoptosis represents.
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Affiliation(s)
- Lucía Pronsato
- Instituto de Investigaciones Biológicas y Biomédicas del Sur (INBIOSUR-CONICET), 8000 Bahía Blanca, Argentina
| | - Lorena Milanesi
- Instituto de Investigaciones Biológicas y Biomédicas del Sur (INBIOSUR-CONICET), 8000 Bahía Blanca, Argentina.
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Fleck JL, Pavel AB, Cassandras CG. Integrating mutation and gene expression cross-sectional data to infer cancer progression. BMC SYSTEMS BIOLOGY 2016; 10:12. [PMID: 26810975 PMCID: PMC4727329 DOI: 10.1186/s12918-016-0255-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/11/2016] [Indexed: 01/21/2023]
Abstract
Background A major problem in identifying the best therapeutic targets for cancer is the molecular heterogeneity of the disease. Cancer is often caused by an accumulation of mutations which produce irreversible damage to the cell’s control mechanisms of survival and proliferation. Different mutations may affect these cellular anachronisms through a combination of molecular interactions which may be dynamically changing during cancer progression. It has been previously shown that cancer accumulates mutations over time. In this paper we address the problem of cancer heterogeneity by modeling cancer progression using somatic mutation and gene expression cross-sectional data. Results We propose a novel formulation of integrating somatic mutation and gene expression data to infer the temporal sequence of events from cross-sectional data. Using a mixed integer linear program we model the interaction between groups of different mutated genes and the resulting modifications at the gene expression level. Our approach identifies a partition of mutation events which gradually produce gene expression changes to a partition of genes over time. The proposed formulation is tested using both simulated data and real breast cancer data with matched somatic mutations and gene expression measurements from The Cancer Genome Atlas. First, we classify the genes as oncogenes or tumor suppressors based on the frequency of driver mutations. As expected, the most frequently mutated genes in breast cancer are PIK3CA and TP53 genes. Then, we select those genes with most frequent driver mutations and a set of genes known to play roles in cancer development. Furthermore, we apply the proposed mixed integer linear program to identify the temporal order in which genes mutate and, simultaneously, the changes they produce at the gene expression level during cancer progression. In addition, we are able to identify known causal relationships between mutations and gene expression changes in PI3K/AKT and TP53 pathways. Conclusions This paper proposes a new model to infer the temporal sequence in which mutations occur and lead to changes at the gene expression level during cancer progression. The approach is general and can be applied to any data sets with available somatic mutations and gene expression measurements. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0255-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia L Fleck
- Division of Systems Engineering, Boston University, 15 Saint Mary's Street, Brookline, MA 02446, USA.
| | - Ana B Pavel
- Graduate Program in Bioinformatics, Boston University, 24 Cummington Mall, Boston, MA 02215, USA. .,Section of Computational Biomedicine, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA.
| | - Christos G Cassandras
- Division of Systems Engineering, Boston University, 15 Saint Mary's Street, Brookline, MA 02446, USA.
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Roh SH, Kasembeli M, Bakthavatsalam D, Chiu W, Tweardy DJ. Contribution of the Type II Chaperonin, TRiC/CCT, to Oncogenesis. Int J Mol Sci 2015; 16:26706-20. [PMID: 26561808 PMCID: PMC4661834 DOI: 10.3390/ijms161125975] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 02/07/2023] Open
Abstract
The folding of newly synthesized proteins and the maintenance of pre-existing proteins are essential in sustaining a living cell. A network of molecular chaperones tightly guides the folding, intracellular localization, and proteolytic turnover of proteins. Many of the key regulators of cell growth and differentiation have been identified as clients of molecular chaperones, which implies that chaperones are potential mediators of oncogenesis. In this review, we briefly provide an overview of the role of chaperones, including HSP70 and HSP90, in cancer. We further summarize and highlight the emerging the role of chaperonin TRiC (T-complex protein-1 ring complex, also known as CCT) in the development and progression of cancer mediated through its critical interactions with oncogenic clients that modulate growth deregulation, apoptosis, and genome instability in cancer cells. Elucidation of how TRiC modulates the folding and function of oncogenic clients will provide strategies for developing novel cancer therapies.
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Affiliation(s)
- Soung-Hun Roh
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Moses Kasembeli
- Division of Internal Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | | | - Wah Chiu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - David J Tweardy
- Division of Internal Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Matamala N, Martínez MT, Lara B, Pérez L, Vázquez I, Jimenez A, Barquín M, Ferrarotti I, Blanco I, Janciauskiene S, Martinez-Delgado B. Alternative transcripts of the SERPINA1 gene in alpha-1 antitrypsin deficiency. J Transl Med 2015; 13:211. [PMID: 26141700 PMCID: PMC4490674 DOI: 10.1186/s12967-015-0585-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/25/2015] [Indexed: 12/14/2022] Open
Abstract
Background SERPINA1 is the gene for alpha-1 antitrypsin (AAT), an acute phase protein with anti-protease and immunoregulatory activities. Mutations in SERPINA1 gene cause AAT deficiency and predispose individuals to early-onset emphysema and liver diseases. Expression of the SERPINA1 gene is regulated by different promoters and alternative splicing events among non-coding exons 1A, 1B and 1C. Methods We have developed three quantitative PCR (QT-PCR) assays (1A, 1B and 1C). These assays were applied for the analysis of SERPINA1 alternative transcripts in: (1) 16 human tissues and (2) peripheral blood leukocytes from 33 subjects with AAT mutations and 7 controls. Results Tissue-specific expression was found for the SERPINA1 transcripts. The 1A transcripts were mainly expressed in leukocytes and lung tissue while those detected with the 1B assay were highly restricted to leukocytes. Only 1B transcripts significantly correlated with serum AAT levels. The 1C transcripts were specifically found in lung, liver, kidney and pancreas. Furthermore, the expression of transcripts was related to AAT genotypes. While deficient variants of AAT had no pronounced effect on the transcript expression, null alleles were associated with significant reduction of different transcripts. Conclusions The possibility to discriminate between SERPINA1 alternative splicing products will help us to understand better the regulation of SERPINA1 gene and its association with SERPINA1 mutations-related diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0585-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nerea Matamala
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | | | - Beatriz Lara
- Respiratory Medicine Department, Royal Exeter and Devon Hospital, Exeter, Devon, UK.
| | - Laura Pérez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | - Irene Vázquez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | - Azucena Jimenez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | - Miguel Barquín
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | - Ilaria Ferrarotti
- Section of Pneumology, Department of Molecular Medicine, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Hospital Foundation, University of Pavia, Pavia, Italy.
| | - Ignacio Blanco
- Alpha1-Antitrypsin Deficiency Spanish Registry, Lung Foundation RESPIRA, Spanish Society of Pneumology (SEPAR), Barcelona, Spain.
| | - Sabina Janciauskiene
- Department of Respiratory Medicine, Hannover Medical School, Hanover, Germany. .,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30626, Hanover, Germany.
| | - Beatriz Martinez-Delgado
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
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Kruiswijk F, Labuschagne CF, Vousden KH. p53 in survival, death and metabolic health: a lifeguard with a licence to kill. Nat Rev Mol Cell Biol 2015; 16:393-405. [PMID: 26122615 DOI: 10.1038/nrm4007] [Citation(s) in RCA: 805] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The function of p53 as a tumour suppressor has been attributed to its ability to promote cell death or permanently inhibit cell proliferation. However, in recent years, it has become clear that p53 can also contribute to cell survival. p53 regulates various metabolic pathways, helping to balance glycolysis and oxidative phosphorylation, limiting the production of reactive oxygen species, and contributing to the ability of cells to adapt to and survive mild metabolic stresses. Although these activities may be integrated into the tumour suppressive functions of p53, deregulation of some elements of the p53-induced response might also provide tumours with a survival advantage.
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Affiliation(s)
- Flore Kruiswijk
- 1] Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK. [2]
| | | | - Karen H Vousden
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
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Yang SD, Cai YL, Jiang P, Li W, Tang JX. Association of a miR-502-binding site single nucleotide polymorphism in the 3'-untranslated region of SET8 and the TP53 codon 72 polymorphism with cervical cancer in the Chinese population. Asian Pac J Cancer Prev 2015; 15:6505-10. [PMID: 25169478 DOI: 10.7314/apjcp.2014.15.16.6505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE This study was conducted to identify whether polymorphic variants of set domain-containing protein 8 (SET8) and tumor protein p53 (TP53) codon 72, either independently or jointly, might be associated with increased risk for cervical cancer. METHODS We genotyped SET8 and TP53 codon 72 polymorphisms of peripheral blood DNA from 114 cervical cancer patients and 200 controls using the polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) and direct DNA sequencing. RESULTS The frequency of SET8 CC (odds ratios (OR) = 2.717, 95% CI=1.436-5.141) or TP53 GG (OR=2.168, 95% CI=1.149-4.089) genotype was associated with an increased risk of cervical cancer on comparison with the SET8 TT or TP53 CC genotypes, respectively. In additional, interaction between the SET8 and TP53 polymorphisms increased the risk of cervical cancer in a synergistic manner, with the OR being 9.913 (95% CI=2.028-48.459) for subjects carrying both SET8 CC and TP53 GG genotypes. CONCLUSION These data suggest that there are significant associations between the miR-502-binding site SNP in the 3'-UTR of SET8 and the TP53 codon 72 polymorphism with cervical cancer in Chinese, and there is a gene-gene interaction.
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Affiliation(s)
- Shao-Di Yang
- Key Laboratory of Green Packaging and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, China E-mail :
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He X, Xie Z, Dong Q, Chen P, Li W, Wang T. Dynamic p53 protein expression and phosphorylation in the kidneys of rats that experienced intrauterine growth restriction. Ren Fail 2015; 37:896-902. [DOI: 10.3109/0886022x.2015.1015428] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Quintens R, Verreet T, Janssen A, Neefs M, Leysen L, Michaux A, Verslegers M, Samari N, Pani G, Verheyde J, Baatout S, Benotmane MA. Identification of novel radiation-induced p53-dependent transcripts extensively regulated during mouse brain development. Biol Open 2015; 4:331-44. [PMID: 25681390 PMCID: PMC4359739 DOI: 10.1242/bio.20149969] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ionizing radiation is a potent activator of the tumor suppressor gene p53, which itself regulates the transcription of genes involved in canonical pathways such as the cell cycle, DNA repair and apoptosis as well as other biological processes like metabolism, autophagy, differentiation and development. In this study, we performed a meta-analysis on gene expression data from different in vivo and in vitro experiments to identify a signature of early radiation-responsive genes which were predicted to be predominantly regulated by p53. Moreover, we found that several genes expressed different transcript isoforms after irradiation in a p53-dependent manner. Among this gene signature, we identified novel p53 targets, some of which have not yet been functionally characterized. Surprisingly, in contrast to genes from the canonical p53-regulated pathways, our gene signature was found to be highly enriched during embryonic and post-natal brain development and during in vitro neuronal differentiation. Furthermore, we could show that for a number of genes, radiation-responsive transcript variants were upregulated during development and differentiation, while radiation non-responsive variants were not. This suggests that radiation exposure of the developing brain and immature cortical neurons results in the p53-mediated activation of a neuronal differentiation program. Overall, our results further increase the knowledge of the radiation-induced p53 network of the embryonic brain and provide more evidence concerning the importance of p53 and its transcriptional targets during mouse brain development.
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Affiliation(s)
- Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
| | - Tine Verreet
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology Section, Department of Biology, KU Leuven, B-3000 Leuven, Belgium
| | - Ann Janssen
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
| | - Mieke Neefs
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
| | - Liselotte Leysen
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
| | - Arlette Michaux
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
| | - Nada Samari
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
| | - Giuseppe Pani
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium Present address: Nutritional Biochemistry and Space Biology Lab, Department of Pharmacology and Bio-molecular Sciences, Università degli Studi di Milano, 20122 Milano, Italy
| | - Joris Verheyde
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium Cell Systems and Imaging Research Group (CSI), Department of Molecular Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - Mohammed A Benotmane
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK•CEN, B-2400 Mol, Belgium
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Wang X, Docanto MM, Sasano H, Lo C, Simpson ER, Brown KA. Prostaglandin E2 inhibits p53 in human breast adipose stromal cells: a novel mechanism for the regulation of aromatase in obesity and breast cancer. Cancer Res 2015; 75:645-55. [PMID: 25634217 DOI: 10.1158/0008-5472.can-14-2164] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Obesity is a risk factor for postmenopausal breast cancer and the majority of these cancers are estrogen dependent. Aromatase converts androgens into estrogens and its increased expression in breast adipose stromal cells (ASC) is a major driver of estrogen receptor-positive breast cancer. In particular, obesity-associated and tumor-derived factors, such as prostaglandin E2 (PGE2), have been shown to drive the expression of aromatase by stimulating the activity of the proximal promoter II (PII). The tumor-suppressor p53 is a key regulator of cell-cycle arrest and apoptosis and is frequently mutated in breast cancer. Mutations in p53 are rare in tumor-associated ASCs. Therefore, it was hypothesized that p53 is regulated by PGE2 and involved in the PGE2-mediated regulation of aromatase. Results demonstrate that PGE2 causes a significant decrease in p53 transcript and nuclear protein expression, as well as phosphorylation at Ser15 in primary human breast ASCs. Stabilization of p53 with RITA leads to a significant decrease in the PGE2-stimulated aromatase mRNA expression and activity, and PII activity. Interaction of p53 with PII was demonstrated and this interaction is decreased in the presence of PGE2. Moreover, mutation of the identified p53 response element leads to an increase in the basal activity of the promoter. Immunofluorescence on clinical samples demonstrates that p53 is decreased in tumor-associated ASCs compared with ASCs from normal breast tissue, and that there is a positive association between perinuclear (inactive) p53 and aromatase expression in these cells. Furthermore, aromatase expression is increased in breast ASCs from Li-Fraumeni patients (germline TP53 mutations) compared with non-Li-Fraumeni breast tissue. Overall, our results demonstrate that p53 is a negative regulator of aromatase in the breast and its inhibition by PGE2 provides a novel mechanism for aromatase regulation in obesity and breast cancer.
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Affiliation(s)
- Xuyi Wang
- Metabolism and Cancer Laboratory, Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria, Australia. Department of Physiology, Monash University, Clayton, Victoria, Australia
| | - Maria M Docanto
- Metabolism and Cancer Laboratory, Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria, Australia
| | - Hironobu Sasano
- Department of Pathology, Tohoku University School of Medicine, Sendai, Japan
| | - Camden Lo
- Monash Micro Imaging, Monash University, Clayton, Victoria, Australia
| | - Evan R Simpson
- Metabolism and Cancer Laboratory, Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria, Australia. Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Kristy A Brown
- Metabolism and Cancer Laboratory, Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria, Australia. Department of Physiology, Monash University, Clayton, Victoria, Australia.
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Nakanishi A, Minami A, Kitagishi Y, Ogura Y, Matsuda S. BRCA1 and p53 tumor suppressor molecules in Alzheimer's disease. Int J Mol Sci 2015; 16:2879-92. [PMID: 25636033 PMCID: PMC4346871 DOI: 10.3390/ijms16022879] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 11/20/2014] [Accepted: 01/20/2015] [Indexed: 12/16/2022] Open
Abstract
Tumor suppressor molecules play a pivotal role in regulating DNA repair, cell proliferation, and cell death, which are also important processes in the pathogenesis of Alzheimer’s disease. Alzheimer’s disease is the most common neurodegenerative disorder, however, the precise molecular events that control the death of neuronal cells are unclear. Recently, a fundamental role for tumor suppressor molecules in regulating neurons in Alzheimer’s disease was highlighted. Generally, onset of neurodegenerative diseases including Alzheimer’s disease may be delayed with use of dietary neuro-protective agents against oxidative stresses. Studies suggest that dietary antioxidants are also beneficial for brain health in reducing disease-risk and in slowing down disease-progression. We summarize research advances in dietary regulation for the treatment of Alzheimer’s disease with a focus on its modulatory roles in BRCA1 and p53 tumor suppressor expression, in support of further therapeutic research in this field.
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Affiliation(s)
- Atsuko Nakanishi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Akari Minami
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Yasuko Kitagishi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Yasunori Ogura
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
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Ståhlberg A, Kåbjörn Gustafsson C, Engtröm K, Thomsen C, Dolatabadi S, Jonasson E, Li CY, Ruff D, Chen SM, Åman P. Normal and functional TP53 in genetically stable myxoid/round cell liposarcoma. PLoS One 2014; 9:e113110. [PMID: 25393000 PMCID: PMC4231113 DOI: 10.1371/journal.pone.0113110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/20/2014] [Indexed: 12/30/2022] Open
Abstract
Myxoid/round-cell liposarcoma (MLS/RCLS) is characterized by either the fusion gene FUS-DDIT3 or the less commonly occurring EWSR1-DDIT3 and most cases carry few or no additional cytogenetic changes. There are conflicting reports concerning the status and role of TP53 in MLS/RCLS. Here we analysed four MLS/RCLS derived cell lines for TP53 mutations, expression and function. Three SV40 transformed cell lines expressed normal TP53 proteins. Irradiation caused normal posttranslational modifications of TP53 and induced P21 expression in two of these cell lines. Transfection experiments showed that the FUS-DDIT3 fusion protein had no effects on irradiation induced TP53 responses. Ion Torrent AmpliSeq screening, using the Cancer Hotspot panel, showed no dysfunctional or disease associated alleles/mutations. In conclusion, our results suggest that most MLS/RCLS cases carry functional TP53 genes and this is consistent with the low numbers of secondary mutations observed in this tumor entity.
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Affiliation(s)
- Anders Ståhlberg
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Christina Kåbjörn Gustafsson
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Katarina Engtröm
- Department of Oncology, Institute of Medical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Christer Thomsen
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Soheila Dolatabadi
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Jonasson
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Chieh-Yuan Li
- Genetic, Medical and Applied Sciences division, Life Science Group, Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - David Ruff
- Genetic, Medical and Applied Sciences division, Life Science Group, Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Shiaw-Min Chen
- Genetic, Medical and Applied Sciences division, Life Science Group, Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Pierre Åman
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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Varga J, Bátor J, Péter M, Árvai Z, Pap M, Sétáló G, Szeberényi J. The role of the p53 protein in nitrosative stress-induced apoptosis of PC12 rat pheochromocytoma cells. Cell Tissue Res 2014; 358:65-74. [DOI: 10.1007/s00441-014-1932-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/22/2014] [Indexed: 01/30/2023]
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Reichrath J, Reichrath S, Heyne K, Vogt T, Roemer K. Tumor suppression in skin and other tissues via cross-talk between vitamin D- and p53-signaling. Front Physiol 2014; 5:166. [PMID: 24917821 PMCID: PMC4042062 DOI: 10.3389/fphys.2014.00166] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/10/2014] [Indexed: 01/12/2023] Open
Abstract
P53 and its family members have been implicated in the direct regulation of the vitamin D receptor (VDR). Vitamin D- and p53-signaling pathways have a significant impact on spontaneous or carcinogen-induced malignant transformation of cells, with VDR and p53 representing important tumor suppressors. VDR and the p53/p63/p73 proteins all function typically as receptors or sensors that turn into transcriptional regulators upon stimulus, with the main difference being that the nuclear VDR is activated as a transcription factor after binding its naturally occurring ligand 1,25-dihydroxyvitamin D with high affinity while the p53 family of transcription factors, mostly in the nucleoplasm, responds to a large number of alterations in cell homeostasis commonly referred to as stress. An increasing body of evidence now convincingly demonstrates a cross-talk between vitamin D- and p53-signaling that occurs at different levels, has genome-wide implications and that should be of high importance for many malignancies, including non-melanoma skin cancer. One interaction involves the ability of p53 to increase skin pigmentation via POMC derivatives including alpha-MSH and ACTH. Pigmentation protects the skin against UV-induced DNA damage and skin carcinogenesis, yet on the other hand reduces cutaneous synthesis of vitamin D. A second level of interaction may be through the ability of 1,25-dihydroxyvitamin D to increase the survival of skin cells after UV irradiation. UV irradiation-surviving cells show significant reductions in thymine dimers in the presence of 1,25-dihydroxyvitamin D that are associated with increased nuclear p53 protein expression, and significantly reduced NO products. A third level of interaction is documented by the ability of vitamin D compounds to regulate the expression of the murine double minute 2 (MDM2) gene in dependence of the presence of wild-type p53. MDM2 has a well-established role as a key negative regulator of p53 activity. Finally, p53 and family members have been implicated in the direct regulation of VDR. This overview summarizes some of the implications of the cross-talk between vitamin D- and p53-signaling for carcinogenesis in the skin and other tissues.
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Affiliation(s)
- Jörg Reichrath
- Department of Dermatology, The Saarland University Hospital Homburg (Saar), Germany
| | - Sandra Reichrath
- Department of Dermatology, The Saarland University Hospital Homburg (Saar), Germany
| | - Kristina Heyne
- José Carreras Centre and Internal Medicine I, University of Saarland Medical Centre Homburg (Saar), Germany
| | - Thomas Vogt
- Department of Dermatology, The Saarland University Hospital Homburg (Saar), Germany
| | - Klaus Roemer
- José Carreras Centre and Internal Medicine I, University of Saarland Medical Centre Homburg (Saar), Germany
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Ma X, Rousseau V, Sun H, Lantuejoul S, Filipits M, Pirker R, Popper H, Mendiboure J, Vataire AL, Le Chevalier T, Soria JC, Brambilla E, Dunant A, Hainaut P. Significance of TP53 mutations as predictive markers of adjuvant cisplatin-based chemotherapy in completely resected non-small-cell lung cancer. Mol Oncol 2014; 8:555-64. [PMID: 24495481 PMCID: PMC5528648 DOI: 10.1016/j.molonc.2013.12.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/29/2013] [Accepted: 12/23/2013] [Indexed: 01/16/2023] Open
Abstract
Adjuvant cisplatin-based chemotherapy only marginally improves survival in patients with completely resected non-small-cell lung cancer (NSCLC). We have evaluated the predictive value of mutations in TP53, encoding the tumour suppressor p53, in the International Adjuvant Lung Cancer Trial (IALT), a randomized trial of adjuvant cisplatin-based chemotherapy against observation. TP53 (exons 4-8) was sequenced in 524 archived specimens of IALT patients with a median follow-up of 7.5 years. Predictive analyses were based on Cox models adjusted for clinical and pathological variables. P-values ≤ 0.01 were considered as significant. Mutations were detected in 221 patients (42%) and had no predictive value for the effect of chemotherapy (interaction between TP53 and treatment: p = 0.17 for Overall Survival (OS); p = 0.06 for Disease-Free Interval, (DFS)). However, among patients with mutations, outcome appeared worse in treatment compared to observation arms (HR for OS = 1.36 (95% CI [0.97-1.31), p = 0.08; DFS = 1.40 (95% CI [1.01-1.95]), p = 0.04). When grouping mutations into classes according to predicted effects on protein structure, the tendency towards worse outcomes was restricted to "structure" mutations affecting residues of the hydrophobic core that are not located at the p53 protein-DNA interface (HR for death in this class vs wild-type T53 = 1.66; 95% CI [1.10-2.52], p = 0.02). Overall, TP53 mutations are not significant predictors of outcome in this trial of cisplatin-based chemotherapy, although a specific class of structural mutations may be associated with a tendency towards worse outcomes upon treatment.
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Affiliation(s)
- Xiaoli Ma
- International Agency for Research on Cancer, Lyon, France
| | - Vanessa Rousseau
- Biostatistics and Epidemiology Unit, Institut Gustave Roussy, Villejuif, France
| | - Haiji Sun
- International Agency for Research on Cancer, Lyon, France
| | - Sylvie Lantuejoul
- Department of Anatomy and Cytology, Centre Hospitalo-Universitaire, Albert Michallon, Grenoble, France
| | - Martin Filipits
- Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Robert Pirker
- Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Helmut Popper
- Institute of Pathology, Medical University of Graz, Austria
| | - Jean Mendiboure
- Biostatistics and Epidemiology Unit, Institut Gustave Roussy, Villejuif, France
| | - Anne-Lise Vataire
- Biostatistics and Epidemiology Unit, Institut Gustave Roussy, Villejuif, France
| | - Thierry Le Chevalier
- Department of Medicine/Service des Innovations Thérapeutiques Précoces, Institut Gustave Roussy, Villejuif, France
| | - Jean Charles Soria
- Department of Medicine/Service des Innovations Thérapeutiques Précoces, Institut Gustave Roussy, Villejuif, France; Institut National de la Santé et de la Recherche Médicale U981, Villejuif, France; Clinical and Translational Research Division, Institut Gustave Roussy, Villejuif, France
| | - Elisabeth Brambilla
- Department of Anatomy and Cytology, Centre Hospitalo-Universitaire, Albert Michallon, Grenoble, France
| | - Ariane Dunant
- Biostatistics and Epidemiology Unit, Institut Gustave Roussy, Villejuif, France
| | - Pierre Hainaut
- University of Strathclyde School of Global Public Health at iPRI, International Prevention Research Institute, Lyon, France; Institut Albert Bonniot, Institut National de la Santé et de la Recherche Médicale U 823, Grenoble, France.
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Yin J, Liu Z, Li H, Sun J, Chang X, Liu J, He S, Li B. Association of PKCζ expression with clinicopathological characteristics of breast cancer. PLoS One 2014; 9:e90811. [PMID: 24603690 PMCID: PMC3946230 DOI: 10.1371/journal.pone.0090811] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 02/04/2014] [Indexed: 12/16/2022] Open
Abstract
The protein kinase C (PKC) family has been functionally linked to cancer. It has been suggested that atypical PKCs contribute to cell proliferation and cancer progression. With respect to breast cancer, PKCζ has been found to play a key role in intracellular transduction of mitogenic and apoptotic signals using mammary cell lines. However, little is known about its function in vivo. Here we examined the correlation between PKCζ protein levels and important clinicopathologic factors in breast cancer using patient samples. To conduct the study, 30 invasive ductal carcinoma cases and their paired normal tissues were used for tissue microarray analysis (TMA) and 16 were used for western blot analysis. In addition, the correlation between PKCζ expression levels and clinicopathologic characteristics was determined in 176 cases with relevant clinical data. Finally, the correlation between PKCζ and epithelial growth factor receptor 2 (HER2) expressions was determined using three breast cancer cell lines by western blot analysis. Both TMA and western blot results showed that PKCζ protein was highly expressed in primary tumors but not in paired normal tissue. The correlation study indicated that high PKCζ levels were associated with premenopausal patients (p = 0.019) and worse prognostic factors, such as advanced clinical stage, more lymph node involvement and larger tumor size. Both disease-free survival and overall survival rates were lower in the high PKCζ group than those in the low PKCζ group. No correlation was observed between PKCζ levels and age, histological grade, or estrogen or progesterone receptor expression status. A positive correlation between PKCζ and HER2 levels was observed in both tumor samples and cell lines. Our observations link PKCζ expression with factors pointing to worse prognosis, higher HER2 levels and a lower survival rate. This suggests that PKCζ protein levels may serve as a prognostic marker of breast cancer.
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Affiliation(s)
- Jian Yin
- Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
- * E-mail:
| | - Zhipei Liu
- Production and R&D Center, Tianjin Binhai Union Gene Technology Co. LTD, Tianjin, China
- Gene Bank, Union Stem Cell & Gene Engineering Co. LTD, Tianjin, China
| | - Haixin Li
- Tumor Tissue Banking Facility, Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jingyan Sun
- Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Xinzhong Chang
- Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jing Liu
- Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Shanshan He
- Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Binghui Li
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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Kaur JS, Vierkant RA, Hobday T, Visscher D. Regional differences in breast cancer biomarkers in american Indian and Alaska native women. Cancer Epidemiol Biomarkers Prev 2014; 23:409-15. [PMID: 24609850 PMCID: PMC3955020 DOI: 10.1158/1055-9965.epi-13-0738] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Breast cancer is not a homogeneous disease, but several different and unique subtypes defined by gene expression analysis. Incidence and mortality rates vary by almost 3-fold between Alaska (highest) and the Southwestern tribes (lowest). We hypothesized that these differences may be due to, in part, varying levels of biologic tumor aggressiveness. METHODS A biorepository of the North Central Cancer Treatment Group with 95 cases of American Indian and Alaska Native (AIAN) women with adenocarcinoma of the breast surgically treated from 1990 to 2000 was tested for several biomarkers. Comparison distributions of biomarker values across state of residence using t tests for continuous (p53, MIB-1, cyclin D) and ordinally scaled markers [EGF receptor (EGFR), BCL-2, Her2] and χ(2) tests of significance for binary markers [estrogen receptor (ER), progesterone receptor (PR)] were done. RESULTS Significant regional differences in some biomarker expression levels were seen. No increase was observed in "triple-negative" breast cancer or Her2 overexpression in these cases. CONCLUSIONS Despite a 3-fold difference in breast cancer mortality in Alaska Native versus Southwestern American Indians, standard biomarkers such as ER, PR, and Her2 neu expression did not explain the disparity. IMPACT There is a need for research to understand the biologic basis of breast cancer disparities in AIAN women. Potential for a prospective trial will be explored with tribes.
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Affiliation(s)
- Judith S Kaur
- Authors' Affiliations: Divisions of Medical Oncology and Anatomical Pathology; Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
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