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Sophonnithiprasert T, Konjanthet S, Narinnork N, Prompat N, Benjakul S, Saetang J, Chimplee S, Mad-Adam N, Graidist P, Rattanaburee T. B-AP15 inhibited colon cancer cell proliferation by decreasing CDK6, Cyclin A, Cyclin E, c-Myc, and VEGF gene expression. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-03940-3. [PMID: 40156610 DOI: 10.1007/s00210-025-03940-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Accepted: 02/16/2025] [Indexed: 04/01/2025]
Abstract
This study evaluated the screening of novel possible target proteins of B-AP15 (NSC687852) in silico. Through in vitro investigation, the anticancer activity of B-AP15 was examined with respect to gene expression and cell proliferation of SW620 cells (colon cancer cells). Twenty proteins associated with colon cancer were selected to screen possible target proteins of B-AP15 using molecular docking. The binding position of B-AP15 and the top five candidate proteins were investigated using the Discovery Studio 2021 software program. Cytotoxicity, colonization ability, and cell inhibition were evaluated in SW620 cells for 24, 48, and 72 h via MTT assay, colony formation assay, and trypan blue assay. The gene expression was estimated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) at 48 h. B-AP15 showed higher binding to E2F8 (- 10.88 kcal/mol), Ras (- 10.86 kcal/mol), GSK3B (- 10.77 kcal/mol), CDK6 (- 10.75 kcal/mol), and Raf (- 10.12 kcal/mol) than to USP14 (- 7.83 kcal/mol) as a target protein of B-AP15. Interestingly, Ras, GSK3B, and CDK6 shared the binding position between B-AP15 and known inhibitors. The IC50 values of B-AP15 against SW620 cells for 24, 48, and 72 h were 0.89 ± 0.0019 µM, 1.38 ± 0.16 µM, and 1.77 ± 0.0016 µM, respectively. B-AP15 reduced cell viability and the size and number of colonies and increased cell inhibition in a time- and dose-dependent manner. CDK6, Cyclin A, and VEGF expression were inhibited at B-AP15 concentrations of 0.89 and 1.78 µM after treatment for 48 h. Cyclin E and cMyc expression were suppressed only at 1.78 µM. These results suggest that B-AP15 possesses cytotoxicity, reducing the size and number of colonies and increasing cell inhibition via suppression of CDK6, Cyclin A, Cyclin E c-Myc, and VEGF.
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Affiliation(s)
- Thanet Sophonnithiprasert
- Biochemistry Unit, Department of Medical Sciences, Faculty of Science, Rangsit University, Pathum Thani, 12000, Thailand
| | - Sasiwan Konjanthet
- Biochemistry Unit, Department of Medical Sciences, Faculty of Science, Rangsit University, Pathum Thani, 12000, Thailand
| | - Nattanicha Narinnork
- Biochemistry Unit, Department of Medical Sciences, Faculty of Science, Rangsit University, Pathum Thani, 12000, Thailand
| | - Napat Prompat
- Faculty of Medical Technology, Medical Technology Service Center, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Jirakrit Saetang
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Siriphorn Chimplee
- General Education Department, School of Languages and General Education, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Nadeeya Mad-Adam
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 111 Bang Pla, Bang Phli, Samut Prakan, 10540, Thailand
| | - Potchanapond Graidist
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Thidarath Rattanaburee
- Biochemistry Unit, Department of Medical Sciences, Faculty of Science, Rangsit University, Pathum Thani, 12000, Thailand.
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Huang F, Li K, Chen Z, Cui Z, Hankey W, Fang K, Yan J, Wang H, Jin VX, Dong Y, Wang Q. Integrative analysis identifies the atypical repressor E2F8 as a targetable transcriptional activator driving lethal prostate cancer. Oncogene 2025; 44:481-493. [PMID: 39613933 DOI: 10.1038/s41388-024-03239-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 11/12/2024] [Accepted: 11/22/2024] [Indexed: 12/01/2024]
Abstract
Acquired resistance to androgen receptor (AR)-targeted therapies underscores the need to identify alternative therapeutic targets for treating lethal prostate cancer. In this study, we evaluated the prognostic significance of 1635 human transcription factors (TFs) by analyzing castration-resistant prostate cancer (CRPC) datasets from the West and East Stand Up to Cancer (SU2C) cohorts. Through this screening approach, we identified E2F8, a putative transcriptional repressor, as a TF consistently associated with poorer patient outcomes in both cohorts. Notably, E2F8 is highly expressed and active in AR-negative CRPC compared to AR-positive CRPC. Integrative profiling of E2F8 cistromes and transcriptomes in AR-negative CRPC cells revealed that E2F8 directly and non-canonically activates target oncogenes involved in cancer-associated pathways. To target E2F8 in CRPC, we employed the CRISPR/CasRx system to knockdown E2F8 mRNA, resulting in effective and specific downregulation of E2F8 and its target oncogenes, as well as significant growth inhibition in AR-negative CRPC in both cultured cells and xenograft models. Our findings identify and characterize E2F8 as a targetable transcriptional activator driving CRPC, particularly the growth of AR-negative CRPC.
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Affiliation(s)
- Furong Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Kexin Li
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Zhong Chen
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Zhifen Cui
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - William Hankey
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Kun Fang
- Data Science Institute, MCW Cancer Center and Mellowes Center for Genome Science and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jingyue Yan
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Biomedical Engineering and Imaging Institute, Friedman Brain Institute , Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hongyan Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Victor X Jin
- Data Science Institute, MCW Cancer Center and Mellowes Center for Genome Science and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yizhou Dong
- Icahn Genomics Institute, Precision Immunology Institute, Department of Immunology and Immunotherapy, Department of Oncological Sciences, Tisch Cancer Institute, Biomedical Engineering and Imaging Institute, Friedman Brain Institute , Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qianben Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
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Du X, Lin L, Yu Y, Yang N, Gao S, Guo J, Fang L, Su P. The evolution and functional characterization of transcription factors E2Fs in lamprey, Lethenteron reissneri. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2025; 165:105348. [PMID: 40031963 DOI: 10.1016/j.dci.2025.105348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Revised: 02/26/2025] [Accepted: 02/28/2025] [Indexed: 03/05/2025]
Abstract
The E2 promoter binding factors (E2Fs) are a group of transcriptional regulators that govern the cell cycle and play crucial roles in various cellular physiological processes, including proliferation and embryonic development. In this study, we identified four homologous genes-Lr-E2F3, Lr-E2F4, Lr-E2F5, and Lr-E2F8-from the lamprey (Lethenteron reissneri) genome database. Phylogenetic tree analysis was conducted to elucidate the evolutionary relationships within the E2F family across different species. Furthermore, analyses of motifs, domains, gene structures, and 3D structures reinforced the conservation of the E2F family. Notably, synteny analysis revealed that the neighboring genes of the Lr-E2Fs exhibited greater diversity compared to those in jawed vertebrates. Activity assays indicated that Lr-E2Fs may be involved in lamprey innate immunity mediated by NF-кB. Additionally, morphological observations of embryos microinjected with Cas9/sgRNA demonstrated that E2F-deficient lamprey embryos displayed embryonic lethality, suggesting that Lr-E2Fs play a significant role in lamprey embryonic development. In summary, our research not only provides new insights into the evolution of Lr-E2Fs but also offers valuable clues regarding their functional roles.
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Affiliation(s)
- Xinyu Du
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Lin Lin
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Department of Gynaecology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, 116001, China
| | - Yongcheng Yu
- Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China; Department of Computing Science and Artificial Intelligence, Liaoning Normal University, Dalian, 116081, China
| | - Ning Yang
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Si Gao
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Jinyang Guo
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Lingling Fang
- Department of Computing Science and Artificial Intelligence, Liaoning Normal University, Dalian, 116081, China
| | - Peng Su
- College of Life Sciences, Liaoning Normal University, Dalian, 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China.
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Ferrando-Marco M, Barkoulas M. EFL-3/E2F7 modulates Wnt signalling by repressing the Nemo-like kinase LIT-1 during asymmetric epidermal cell division in Caenorhabditis elegans. Development 2025; 152:DEV204546. [PMID: 40026193 PMCID: PMC11925398 DOI: 10.1242/dev.204546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 02/02/2025] [Indexed: 03/04/2025]
Abstract
The E2F family of transcription factors is conserved in higher eukaryotes and plays pivotal roles in controlling gene expression during the cell cycle. Most canonical E2Fs associate with members of the Dimerisation Partner (DP) family to activate or repress target genes. However, atypical repressors, such as E2F7 and E2F8, lack DP interaction domains and their functions are less understood. We report here that EFL-3, the E2F7 homologue of Caenorhabditis elegans, regulates epidermal stem cell differentiation. We show that phenotypic defects in efl-3 mutants depend on the Nemo-like kinase LIT-1. EFL-3 represses lit-1 expression through direct binding to a lit-1 intronic element. Increased LIT-1 expression in efl-3 mutants reduces POP-1/TCF nuclear distribution, and consequently alters Wnt pathway activation. Our findings provide a mechanistic link between an atypical E2F family member and NLK during C. elegans asymmetric cell division, which may be conserved in other animals.
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Morin A, Chu CP, Pavlidis P. Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.02.15.580581. [PMID: 38559016 PMCID: PMC10979919 DOI: 10.1101/2024.02.15.580581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes such as the regulation of gene transcription. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.
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Affiliation(s)
- Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - C. Pan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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Wu T, Jiang F, Wu F, Zheng G, Li Y, Wu L. E2F1 and E2F7 regulate gastric cancer cell proliferation, respectively, through transcriptional activation and transcriptional repression of MYBL2. J Biol Chem 2025; 301:108027. [PMID: 39613162 PMCID: PMC11731210 DOI: 10.1016/j.jbc.2024.108027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 10/22/2024] [Accepted: 11/12/2024] [Indexed: 12/01/2024] Open
Abstract
Gastric cancer (GC) is the most common malignant tumor of the digestive tract. However, the molecular pathogenesis is not well understood. Through bioinformatic analysis and analyzing clinical tissue samples, we found that E2F1 and E2F7 as well as their potential downstream target MYBL2 were all upregulated in GC tissues and that their expressions correlated with patient prognosis. While knockdown of E2F1 or MYBL2 inhibited cell proliferation and promoted apoptosis, knockdown of E2F7 promoted cell proliferation but had no effects on apoptosis. Chromatin immunoprecipitation and dual luciferase reporter assays demonstrated that MYBL2 was transcriptionally activated and repressed by E2F1 and E2F7, respectively. Importantly, in vitro and ex vivo experiments demonstrated that the effects of E2F1 and E2F7 on GC cell proliferation were significantly attenuated by reversely modulating MYBL2 expression, indicating that MYBL2 is a direct and functionally relevant target of E2F1 and E2F7 in GC cells. Furthermore, the effects of E2F1 and E2F7 on GC cell proliferation through transcriptional regulation of MYBL2 can be mediated by the PI3K/AKT signaling pathway. Interestingly, we found differential nucleocytoplasmic distribution of E2F7 in GC cells with functional relevance. Taken together, our data suggest that targeted therapies of GC may be achieved from three different angles, E2F1, E2F7, and MYBL2 themselves, E2F1/E2F7 expression balance, and E2F7 nuclear localization.
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Affiliation(s)
- Tianyi Wu
- Department of Pathophysiology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Fengli Jiang
- Department of Pathophysiology, College of Basic Medical Sciences, China Medical University, Shenyang, China; Department of Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fan Wu
- Department of Pathophysiology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Guoliang Zheng
- Department of Pathophysiology, College of Basic Medical Sciences, China Medical University, Shenyang, China; Department of Gastric Surgery, Cancer Hospital of China Medical University (Liaoning Cancer Hospital and Institute), Shenyang, China
| | - Yang Li
- Department of Pathophysiology, College of Basic Medical Sciences, China Medical University, Shenyang, China; Department of Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lizhao Wu
- Department of Pathophysiology, College of Basic Medical Sciences, China Medical University, Shenyang, China.
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Schaal DL, Amucheazi AA, Jones SC, Nkadi EH, Scott RS. Epstein-Barr virus replication within differentiated epithelia requires pRb sequestration of activator E2F transcription factors. J Virol 2024; 98:e0099524. [PMID: 39291960 PMCID: PMC11494884 DOI: 10.1128/jvi.00995-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/15/2024] [Indexed: 09/19/2024] Open
Abstract
Epstein-Barr virus (EBV) co-infections with human papillomavirus (HPV) have been observed in oropharyngeal squamous cell carcinoma. Modeling EBV/HPV co-infection in organotypic epithelial raft cultures revealed that HPV16 E7 inhibited EBV productive replication through the facilitated degradation of the retinoblastoma protein pRb/p105. To further understand how pRb is required for EBV productive replication, we generated CRISPR-Cas9 pRb knockout (KO) normal oral keratinocytes (NOKs) in the context of wild-type and mutant K120E p53. EBV replication was examined in organotypic rafts as a physiological correlate for epithelial differentiation. In pRb KO rafts, EBV DNA copy number was statistically decreased compared to vector controls, regardless of p53 context. Loss of pRb did not affect EBV binding or internalization of calcium-treated NOKs or early infection of rafts. Rather, the block in EBV replication correlated with impaired immediate early gene expression. An EBV infection time course in rafts with mutant p53 demonstrated that pRb-positive basal cells were initially infected with delayed replication occurring in differentiated layers. Loss of pRb showed increased S-phase progression makers and elevated activator E2F activity in raft tissues. Complementation with a panel of pRb/E2F binding mutants showed that wild type or pRb∆685 mutant capable of E2F binding reduced S-phase marker gene expression, rescued EBV DNA replication, and restored BZLF1 expression in pRb KO rafts. However, pRb KO complemented with pRb661W mutant, unable to bind E2Fs, failed to rescue EBV replication in raft culture. These findings suggest that EBV productive replication in differentiated epithelium requires pRb inhibition of activator E2Fs to restrict S-phase progression.IMPORTANCEA subset of human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma is co-positive for Epstein-Barr virus (EBV). Potential oncogenic viral interactions revealed that HPV16 E7 inhibited productive EBV replication within the differentiated epithelium. As E7 mediates the degradation of pRb, we aimed to establish how pRb is involved in EBV replication. In the context of differentiated epithelium using organotypic raft culture, we evaluated how the loss of pRb affects EBV lytic replication to better comprehend EBV contributions to carcinogenesis. In this study, ablation of pRb interfered with EBV replication at the level of immediate early gene expression. Loss of pRb increased activator E2Fs and associated S-phase gene expression throughout the differentiated epithelium. Complementation studies showed that wild type and pRb mutant capable of binding to E2F rescued EBV replication, while pRb mutant lacking E2F binding did not. Altogether, these studies support that in differentiated tissues, HPV16 E7-mediated degradation of pRb inhibits EBV replication through unregulated E2F activity.
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Affiliation(s)
- Danielle L. Schaal
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
- Center for Applied Immunology and Pathological Processes, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
| | - Akajiugo A. Amucheazi
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
| | - Sarah C. Jones
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
| | - Ebubechukwu H. Nkadi
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
- Center for Applied Immunology and Pathological Processes, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
| | - Rona S. Scott
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
- Center for Applied Immunology and Pathological Processes, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
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Baral S, Yu Y, Sun Q, Jiang M, Li R, Cheng Y, Hussein AM, Shi Y, Jiang Y, Tang D, Wang S, Wang D. Transcription Factor E2F4 Promote Proliferation, Migration, and Invasion of Gastric Cancer Cells by transcriptionally activating DSCC1. Int J Biol Sci 2024; 20:4978-4998. [PMID: 39309429 PMCID: PMC11414385 DOI: 10.7150/ijbs.99590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 09/08/2024] [Indexed: 09/25/2024] Open
Abstract
Gastric cancer (GC) ranks as the fifth most common cancer and the fourth leading cause of cancer-related deaths globally. Despite advancements in molecular profiling, the mechanisms driving GC proliferation and metastasis remain unclear. This study identifies Early 2 Factor 4 (E2F4) as a key transcription factor that promotes GC cell proliferation, migration, and invasion by upregulating DNA Replication and Sister Chromatid Cohesion 1 (DSCC1) expression. Bioinformatics and transcription factor analyses revealed E2F4 as a significant regulator of DSCC1. Functional assays confirmed E2F4's role in enhancing GC cell malignancy in vitro and in vivo. Knockdown and overexpression experiments demonstrated that E2F4 positively regulates DSCC1 at the transcriptional level, with ChIP-qPCR and dual luciferase reporter assays validating the binding sites on the DSCC1 promoter. These findings highlight the E2F4-DSCC1 axis as a potential therapeutic target to mitigate GC progression.
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Affiliation(s)
- Shantanu Baral
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, Jiangsu, 225001, P. R. China
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225001, P. R. China
- General Surgery Institute of Yangzhou, Yangzhou University, Yangzhou, Jiangsu, 225001, P. R. China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
| | - Yantao Yu
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
- The Yangzhou School of Clinical Medicine of Dalian Medical University. Yangzhou, Jiangsu, 225001, P. R. China
| | - Qiannan Sun
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225001, P. R. China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
| | - Mingrui Jiang
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, Jiangsu, 225001, P. R. China
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225001, P. R. China
- General Surgery Institute of Yangzhou, Yangzhou University, Yangzhou, Jiangsu, 225001, P. R. China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
| | - Ruiqi Li
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
- Northern Jiangsu People's Hospital, Clinical Teaching Hospital of Medical School, Nanjing University, Yangzhou, Jiangsu, 225001, P. R. China
| | - Yifan Cheng
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
- Northern Jiangsu People's Hospital, Clinical Teaching Hospital of Medical School, Nanjing University, Yangzhou, Jiangsu, 225001, P. R. China
| | - Arawker Mubeen Hussein
- General Surgery Institute of Yangzhou, Yangzhou University, Yangzhou, Jiangsu, 225001, P. R. China
| | - Youquan Shi
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
| | - Yongjun Jiang
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
| | - Dong Tang
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225001, P. R. China
| | - Sen Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, P. R. China
| | - Daorong Wang
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, Jiangsu, 225001, P. R. China
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, 225001, P. R. China
- General Surgery Institute of Yangzhou, Yangzhou University, Yangzhou, Jiangsu, 225001, P. R. China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, Jiangsu, 225001, P. R. China
- Northern Jiangsu People's Hospital, Clinical Teaching Hospital of Medical School, Nanjing University, Yangzhou, Jiangsu, 225001, P. R. China
- The Yangzhou School of Clinical Medicine of Dalian Medical University. Yangzhou, Jiangsu, 225001, P. R. China
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Gan Z, Abudurexiti A, Hu X, Chen W, Zhang N, Sang W. E2F3/5/8 serve as potential prognostic biomarkers and new therapeutic direction for human bladder cancer. Medicine (Baltimore) 2024; 103:e35722. [PMID: 38215110 PMCID: PMC10783276 DOI: 10.1097/md.0000000000035722] [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: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 01/14/2024] Open
Abstract
OBJECTS Human bladder cancer (BC) is the most common urogenital system malignancy. E2F transcription factors (E2Fs) have been reported to be involved in the growth of various cancers. However, the expression patterns, prognostic value and immune infiltration in the tumor microenvironment of the 8 E2Fs in BC have yet fully to be explored. METHODS AND STRATEGY We investigated the differential expression of E2Fs in BC patients, the prognostic value and correlation with immune infiltration by analyzing a range of databases. RESULTS We found that the mRNA expression levels of E2F1/2/3/4/5/7/8 were significantly higher in BC patients than that of control tissues. And the increased mRNA expression levels of all E2Fs were associated with tumor stage of BC. The survival analysis revealed that the elevated mRNA expression levels of E2F3/5/8 were significantly correlated with the overall survival (OS) of BC patients. And the genetic changes of E2Fs in BC patients were associated with shorter overall survival (OS) and progression-free survival (PFS). In addition, we revealed that the E2F3/5/8 expressions were closely correlated with tumor-infiltrating lymphocytes (TILs). CONCLUSIONS E2F3/5/8 might serve as promising prognostic biomarkers and new therapeutic direction for BC patients.
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Affiliation(s)
- Zhilu Gan
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Alimujiang Abudurexiti
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Xiaogang Hu
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Wenxin Chen
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Ning Zhang
- Surgery Department of Urology, The Third People’s Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, P.R. China
| | - Wei Sang
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, P.R. China
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, P.R. China
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10
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Zhou Y, Nakajima R, Shirasawa M, Fikriyanti M, Zhao L, Iwanaga R, Bradford AP, Kurayoshi K, Araki K, Ohtani K. Expanding Roles of the E2F-RB-p53 Pathway in Tumor Suppression. BIOLOGY 2023; 12:1511. [PMID: 38132337 PMCID: PMC10740672 DOI: 10.3390/biology12121511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The transcription factor E2F links the RB pathway to the p53 pathway upon loss of function of pRB, thereby playing a pivotal role in the suppression of tumorigenesis. E2F fulfills a major role in cell proliferation by controlling a variety of growth-associated genes. The activity of E2F is controlled by the tumor suppressor pRB, which binds to E2F and actively suppresses target gene expression, thereby restraining cell proliferation. Signaling pathways originating from growth stimulative and growth suppressive signals converge on pRB (the RB pathway) to regulate E2F activity. In most cancers, the function of pRB is compromised by oncogenic mutations, and E2F activity is enhanced, thereby facilitating cell proliferation to promote tumorigenesis. Upon such events, E2F activates the Arf tumor suppressor gene, leading to activation of the tumor suppressor p53 to protect cells from tumorigenesis. ARF inactivates MDM2, which facilitates degradation of p53 through proteasome by ubiquitination (the p53 pathway). P53 suppresses tumorigenesis by inducing cellular senescence or apoptosis. Hence, in almost all cancers, the p53 pathway is also disabled. Here we will introduce the canonical functions of the RB-E2F-p53 pathway first and then the non-classical functions of each component, which may be relevant to cancer biology.
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Affiliation(s)
- Yaxuan Zhou
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Rinka Nakajima
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mashiro Shirasawa
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Mariana Fikriyanti
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Lin Zhao
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
| | - Ritsuko Iwanaga
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Andrew P. Bradford
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA; (R.I.); (A.P.B.)
| | - Kenta Kurayoshi
- Division of Molecular Genetics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan;
| | - Keigo Araki
- Department of Morphological Biology, Ohu University School of Dentistry, 31-1 Misumido Tomitamachi, Koriyama, Fukushima 963-8611, Japan;
| | - Kiyoshi Ohtani
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan; (Y.Z.); (R.N.); (M.S.); (M.F.); (L.Z.)
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11
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Fung CW, Chau KY, Tong DCS, Knox C, Tam SST, Tan SY, Loi DSC, Leung Z, Xu Y, Lan Y, Qian PY, Chan KYK, Wu AR. Parentage influence on gene expression under acidification revealed through single-embryo sequencing. Mol Ecol 2023; 32:6796-6808. [PMID: 37888909 DOI: 10.1111/mec.17148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023]
Abstract
The dissolution of anthropogenic carbon dioxide (CO2 ) in seawater has altered its carbonate chemistry in the process of ocean acidification (OA). OA affects the viability of marine species. In particular, calcifying organisms and their early planktonic larval stages are considered vulnerable. These organisms often utilize energy reserves for metabolism rather than growth and calcification as supported by bulk RNA-sequencing (RNA-seq) experiments. Yet, transcriptomic profiling of a bulk sample reflects the average gene expression of the population, neglecting the variations between individuals, which forms the basis for natural selection. Here, we used single-embryo RNA-seq on larval sea urchin Heliocidaris crassispina, which is a commercially and ecologically valuable species in East Asia, to document gene expression changes to OA at an individual and family level. Three paternal half-sibs groups were fertilized and exposed to 3 pH conditions (ambient pH 8.0, 7.7 and 7.4) for 12 h prior to sequencing and oxygen consumption assay. The resulting transcriptomic profile of all embryos can be distinguished into four clusters, with differences in gene expressions that govern biomineralization, cell differentiation and patterning, as well as metabolism. While these responses were influenced by pH conditions, the male identities also had an effect. Specifically, a regression model and goodness of fit tests indicated a significant interaction between sire and pH on the probability of embryo membership in different clusters of gene expression. The single-embryo RNA-seq approach is promising in climate stressor research because not only does it highlight potential impacts before phenotypic changes were observed, but it also highlights variations between individuals and lineages, thus enabling a better determination of evolutionary potential.
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Affiliation(s)
- Cheuk Wang Fung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kin Yung Chau
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Daniel Chun Sang Tong
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Claire Knox
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Sindy Sing Ting Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Sin Yen Tan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Danson Shek Chun Loi
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ziuwin Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ying Xu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kit Yu Karen Chan
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Biology Department, Swarthmore College, Swarthmore, Pennsylvania, USA
| | - Angela Ruohao Wu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Center for Aging Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
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12
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Liu K, Wang L, Lou Z, Guo L, Xu Y, Qi H, Fang Z, Mei L, Chen X, Zhang X, Shao J, Xiang X. E2F8 exerts cancer-promoting effects by transcriptionally activating RRM2 and E2F8 knockdown synergizes with WEE1 inhibition in suppressing lung adenocarcinoma. Biochem Pharmacol 2023; 218:115854. [PMID: 37863324 DOI: 10.1016/j.bcp.2023.115854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023]
Abstract
Ribonucleotide reductase (RR) is a rate-limiting enzyme that facilitates DNA replication and repair by reducing nucleotide diphosphates (NDPs) to deoxyribonucleotide diphosphates (dNDPs) and is thereby crucial for cell proliferation and cancer development. The E2F family of transcription factors includes key regulators of gene expression involved in cell cycle control. In this study, E2F8 expression was significantly increased in most cancer tissues of lung adenocarcinoma (LUAD) patients and was correlated with the expression of RRM2 through database and clinical samples analysis. The protein expression of E2F8 and RRM2 were positively correlated with tumor-node-metastasis (TNM) pathological stage, and high expression of E2F8 and RRM2 predicted a low 5-year overall survival rate in LUAD patients. Overexpression and knockdown experiments showed that E2F8 was essential for LUAD cell proliferation, DNA synthesis, and cell cycle progression, which were RRM2-dependent. Reporter gene, ChIP-qPCR, and DNA pulldown-Western blot assays indicated that E2F8 activated the transcription of the RRM2 gene by directly binding with the RRM2 promoter in LUAD cells. Previous studies indicated that inhibition of WEE1 kinase can suppress the phosphorylation of CDK1/2 and promote the degradation of RRM2. We further showed here that the combination of E2F8 knockdown with MK-1775, an inhibitor of WEE1 being evaluated in clinical trials, synergistically suppressed proliferation and promoted apoptosis of LUAD cells in vitro and in vivo. Thus, this study reveals a novel role of E2F8 as a proto-oncogenic transcription activator by activating RRM2 expression in LUAD, and targeting both the transcription and degradation mechanisms of RRM2 could produce a synergistic inhibitory effect for LUAD treatment in addition to conventional inhibition of RR enzyme activity.
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Affiliation(s)
- Kaiping Liu
- Department of Pathology and Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Department of Pharmacy, Sanmen People's Hospital of Zhejiang, Sanmen, Zhejiang, China
| | - Ling Wang
- Department of Pathology and Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhiyuan Lou
- Department of Pathology and Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lijuan Guo
- Department of Pathology and Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuanling Xu
- Department of Pathology and Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hongyan Qi
- Department of Pathology and Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zejun Fang
- Department of Pharmacy, Sanmen People's Hospital of Zhejiang, Sanmen, Zhejiang, China
| | - Lingming Mei
- Department of Pharmacy, Sanmen People's Hospital of Zhejiang, Sanmen, Zhejiang, China
| | - Xiang Chen
- Department of Pharmacy, Sanmen People's Hospital of Zhejiang, Sanmen, Zhejiang, China
| | - Xiaomin Zhang
- Department of Pharmacy, Sanmen People's Hospital of Zhejiang, Sanmen, Zhejiang, China.
| | - Jimin Shao
- Department of Pathology and Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, China; Cancer Center of Zhejiang University, Hangzhou, China.
| | - Xueping Xiang
- Department of Pathology and Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, China.
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13
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Sapienza MR, Chiaretti S, Cardinali D, Mazzara S, Chiarle R, Foà R, Pileri SA. A five-gene signature may associate with central nervous system dissemination in adult acute lymphoblastic leukemia. Hematol Oncol 2023; 41:789-791. [PMID: 37016899 DOI: 10.1002/hon.3136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Affiliation(s)
| | - Sabina Chiaretti
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Deborah Cardinali
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Saveria Mazzara
- Division of Hematopathology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Roberto Chiarle
- Division of Hematopathology, IEO European Institute of Oncology IRCCS, Milan, Italy
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Stefano A Pileri
- Division of Hematopathology, IEO European Institute of Oncology IRCCS, Milan, Italy
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14
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Wu Z, Su J, Li FL, Chen T, Mayner J, Engler A, Ma S, Li Q, Guan KL. YAP silencing by RB1 mutation is essential for small-cell lung cancer metastasis. Nat Commun 2023; 14:5916. [PMID: 37739954 PMCID: PMC10516997 DOI: 10.1038/s41467-023-41585-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
Small cell lung cancer (SCLC) is highly lethal due to its prevalent metastasis. Most SCLCs have inactivating mutations in TP53 and RB1. We find that loss of YAP expression is key for SCLC cells to acquire rapid ameboid migration and high metastatic potential. YAP functions through its target genes CCN1/CCN2 to inhibit SCLC ameboid migration. RB1 mutation contributes to YAP transcriptional silencing via E2F7, which recruits the RCOR co-repressor complex to YAP promoter. We discover that benzamide family HDAC inhibitors stimulate YAP expression by inhibiting the RCOR-HDAC complex, thereby suppressing SCLC metastasis and improving survival in a mouse model. Our study unveils the molecular and cellular basis underlying SCLC's high metastatic potential, the previously unrecognized role of YAP in suppressing ameboid migration and tumor metastasis, and the mechanism of YAP transcription regulation involving E2F7, RCOR, and Sin3 HDAC. This study reveals a therapeutic potential of benzamides for SCLC treatment.
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Affiliation(s)
- Zhengming Wu
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Junhui Su
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Fu-Long Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Tao Chen
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Jaimie Mayner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Adam Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shenghong Ma
- Wellcome Sanger Institute, Cambridge, CB10 1RQ, UK
| | - Qingquan Li
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China.
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.
- School of Life Sciences, Westlake University, Hangzhou, 310030, China.
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15
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Pang J, Li H, Zhang X, Luo Z, Chen Y, Zhao H, Lv H, Zheng H, Fu Z, Tang W, Sheng M. Application of Novel Transcription Factor Machine Learning Model and Targeted Drug Combination Therapy Strategy in Triple Negative Breast Cancer. Int J Mol Sci 2023; 24:13497. [PMID: 37686305 PMCID: PMC10487460 DOI: 10.3390/ijms241713497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/17/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Transcription factors (TFs) have been shown to play a key role in the occurrence and development of tumors, including triple-negative breast cancer (TNBC), with a worse prognosis. Machine learning is widely used for establishing prediction models and screening key tumor drivers. Current studies lack TF integration in TNBC, so targeted research on TF prognostic models and targeted drugs is beneficial to improve clinical translational application. The purpose of this study was to use the Least Absolute Shrinkage and Selection Operator to build a prognostic TFs model after cohort normalization based on housekeeping gene expression levels. Potential targeted drugs were then screened on the basis of molecular docking, and a multi-drug combination strategy was used for both in vivo and in vitro experimental studies. The machine learning model of TFs built by E2F8, FOXM1, and MYBL2 has broad applicability, with an AUC value of up to 0.877 at one year. As a high-risk clinical factor, its abnormal disorder may lead to upregulation of the activity of pathways related to cell proliferation. This model can also be used to predict the adverse effects of immunotherapy in patients with TNBC. Molecular docking was used to screen three drugs that target TFs: Trichostatin A (TSA), Doxorubicin (DOX), and Calcitriol. In vitro and in vivo experiments showed that TSA + DOX was able to effectively reduce DOX dosage, and TSA + DOX + Calcitriol may be able to effectively reduce the toxic side effects of DOX on the heart. In conclusion, the machine learning model based on three TFs provides new biomarkers for clinical and prognostic diagnosis of TNBC, and the combination targeted drug strategy offers a novel research perspective for TNBC treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Wenru Tang
- Laboratory of Molecular Genetics of Aging & Tumor, Medicine School, Kunming University of Science and Technology, Kunming 650500, China; (J.P.); (H.L.)
| | - Miaomiao Sheng
- Laboratory of Molecular Genetics of Aging & Tumor, Medicine School, Kunming University of Science and Technology, Kunming 650500, China; (J.P.); (H.L.)
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16
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Thong KX, Andriesei P, Luo J, Qin M, Ng J, Tagalakis AD, Hysi P, Yu-Wai-Man C. Adrenaline blocks key cell cycle genes and exhibits antifibrotic and vasoconstrictor effects in glaucoma surgery. Exp Eye Res 2023; 233:109561. [PMID: 37429521 DOI: 10.1016/j.exer.2023.109561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/04/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Adrenaline is a sympathomimetic drug used to maintain pupil dilation and to decrease the risk of bleeding. The aim of this study was to demonstrate if adrenaline could exert antifibrotic effects in glaucoma surgery. Adrenaline was tested in fibroblast-populated collagen contraction assays and there was a dose-response decrease in fibroblast contractility: matrices decreased to 47.4% (P = 0.0002) and 86.6% (P = 0.0036) with adrenaline 0.0005% and 0.01%, respectively. There was no significant decrease in cell viability even at high concentrations. Human Tenon's fibroblasts were also treated with adrenaline (0%, 0.0005%, 0.01%) for 24 h and RNA-Sequencing was performed on the Illumina NextSeq 2000. We carried out detailed gene ontology, pathway, disease and drug enrichment analyses. Adrenaline 0.01% upregulated 26 G1/S and 11 S-phase genes, and downregulated 23 G2 and 17 M-phase genes (P < 0.05). Adrenaline demonstrated similar pathway enrichment to mitosis and spindle checkpoint regulation. Adrenaline 0.05% was also injected subconjunctivally during trabeculectomy, PreserFlo Microshunt and Baerveldt 350 tube surgeries, and patients did not experience any adverse effects. Adrenaline is a safe and cheap antifibrotic drug that significantly blocks key cell cycle genes when used at high concentrations. Unless contraindicated, we recommend subconjunctival injections of adrenaline (0.05%) in all glaucoma bleb-forming surgeries.
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Affiliation(s)
- Kai Xin Thong
- Faculty of Life Sciences & Medicine, King's College London, London, SE1 7EH, UK
| | - Petru Andriesei
- Faculty of Life Sciences & Medicine, King's College London, London, SE1 7EH, UK
| | - Jinyuan Luo
- Faculty of Life Sciences & Medicine, King's College London, London, SE1 7EH, UK
| | - Mengqi Qin
- Faculty of Life Sciences & Medicine, King's College London, London, SE1 7EH, UK
| | - Jia Ng
- Faculty of Life Sciences & Medicine, King's College London, London, SE1 7EH, UK
| | | | - Pirro Hysi
- Faculty of Life Sciences & Medicine, King's College London, London, SE1 7EH, UK
| | - Cynthia Yu-Wai-Man
- Faculty of Life Sciences & Medicine, King's College London, London, SE1 7EH, UK; Department of Ophthalmology, Guy's and St Thomas' NHS Foundation Trust, London, SE1 7EH, UK.
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17
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Lee DY, Chun JN, Cho M, So I, Jeon JH. Emerging role of E2F8 in human cancer. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166745. [PMID: 37164180 DOI: 10.1016/j.bbadis.2023.166745] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023]
Abstract
E2F8 is a multifaceted transcription factor that plays a crucial role in mediating the hallmarks of cancer, including sustaining proliferative signaling, resisting cell death, and activating invasion and metastasis. Aberrant E2F8 expression is associated with poor clinical outcomes in most human cancers. However, E2F8 also exhibits tumor-suppressing activity; thus, the role of E2F8 in cell-fate determination is unclear. In this review, we highlight the recent progress in understanding the role of E2F8 in human cancers, which will contribute to building a conceptual framework and broadening our knowledge pertaining to E2F8. This review provides insight into future challenges and perspectives regarding the translation of biological knowledge into therapeutic strategies for the treatment of cancer.
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Affiliation(s)
- Da Young Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jung Nyeo Chun
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea; Institute of Human-Environment Interface Biology, Seoul National University, Seoul, Republic of Korea
| | - Minsoo Cho
- Independent researcher, Seoul, Republic of Korea
| | - Insuk So
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea; Institute of Human-Environment Interface Biology, Seoul National University, Seoul, Republic of Korea
| | - Ju-Hong Jeon
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea; Institute of Human-Environment Interface Biology, Seoul National University, Seoul, Republic of Korea.
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18
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Papp C, Mukundan VT, Jenjaroenpun P, Winnerdy FR, Ow GS, Phan AT, Kuznetsov VA. Stable bulged G-quadruplexes in the human genome: identification, experimental validation and functionalization. Nucleic Acids Res 2023; 51:4148-4177. [PMID: 37094040 DOI: 10.1093/nar/gkad252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/23/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023] Open
Abstract
DNA sequence composition determines the topology and stability of G-quadruplexes (G4s). Bulged G-quadruplex structures (G4-Bs) are a subset of G4s characterized by 3D conformations with bulges. Current search algorithms fail to capture stable G4-B, making their genome-wide study infeasible. Here, we introduced a large family of computationally defined and experimentally verified potential G4-B forming sequences (pG4-BS). We found 478 263 pG4-BS regions that do not overlap 'canonical' G4-forming sequences in the human genome and are preferentially localized in transcription regulatory regions including R-loops and open chromatin. Over 90% of protein-coding genes contain pG4-BS in their promoter or gene body. We observed generally higher pG4-BS content in R-loops and their flanks, longer genes that are associated with brain tissue, immune and developmental processes. Also, the presence of pG4-BS on both template and non-template strands in promoters is associated with oncogenesis, cardiovascular disease and stemness. Our G4-BS models predicted G4-forming ability in vitro with 91.5% accuracy. Analysis of G4-seq and CUT&Tag data strongly supports the existence of G4-BS conformations genome-wide. We reconstructed a novel G4-B 3D structure located in the E2F8 promoter. This study defines a large family of G4-like sequences, offering new insights into the essential biological functions and potential future therapeutic uses of G4-B.
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Affiliation(s)
- Csaba Papp
- Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Vineeth T Mukundan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Ghim Siong Ow
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Vladimir A Kuznetsov
- Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
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19
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Deregulated E2F Activity as a Cancer-Cell Specific Therapeutic Tool. Genes (Basel) 2023; 14:genes14020393. [PMID: 36833320 PMCID: PMC9956157 DOI: 10.3390/genes14020393] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The transcription factor E2F, the principal target of the tumor suppressor pRB, plays crucial roles in cell proliferation and tumor suppression. In almost all cancers, pRB function is disabled, and E2F activity is enhanced. To specifically target cancer cells, trials have been undertaken to suppress enhanced E2F activity to restrain cell proliferation or selectively kill cancer cells, utilizing enhanced E2F activity. However, these approaches may also impact normal growing cells, since growth stimulation also inactivates pRB and enhances E2F activity. E2F activated upon the loss of pRB control (deregulated E2F) activates tumor suppressor genes, which are not activated by E2F induced by growth stimulation, inducing cellular senescence or apoptosis to protect cells from tumorigenesis. Deregulated E2F activity is tolerated in cancer cells due to inactivation of the ARF-p53 pathway, thus representing a feature unique to cancer cells. Deregulated E2F activity, which activates tumor suppressor genes, is distinct from enhanced E2F activity, which activates growth-related genes, in that deregulated E2F activity does not depend on the heterodimeric partner DP. Indeed, the ARF promoter, which is specifically activated by deregulated E2F, showed higher cancer-cell specific activity, compared to the E2F1 promoter, which is also activated by E2F induced by growth stimulation. Thus, deregulated E2F activity is an attractive potential therapeutic tool to specifically target cancer cells.
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20
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Sun C, Wang J, Xia T, Sun Q, He Y, Wang H, He Q, Liu L. Mitochondrion-Targeted NIR Therapeutic Agent Suppresses Melanoma by Inducing Apoptosis and Cell Cycle Arrest via E2F/Cyclin/CDK Pathway. Pharmaceuticals (Basel) 2022; 15:ph15121589. [PMID: 36559040 PMCID: PMC9786161 DOI: 10.3390/ph15121589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Malignant melanoma is the most fatal form of skin cancer worldwide, and earlier diagnosis and more effective therapies are required to improve prognosis. As a possible solution, near-infrared fluorescent heptamethine cyanine dyes have been shown to be useful for tumor diagnosis and treatment. Here, we synthesized a novel theranostic agent, IR-817, a multifunctional bioactive small-molecule that has near-infrared emission, targets mitochondria in cancer cells, and has selective anti-cancer effects. In in vitro experiments, IR-817 preferentially accumulated in melanoma cells through organic anion transporting polypeptide transporters but also selectively inhibited the growth of tumor cells by inducing mitochondrial-dependent intrinsic apoptosis. Mechanistically, IR-817 caused G0/G1 cell cycle arrest by targeting the E2F/Cyclin/CDK pathway. Finally, IR-817 significantly suppressed the growth of xenograft tumors in zebrafish and mice. Immunohistochemical staining and hematoxylin and eosin staining revealed that IR-817 induced apoptosis and inhibited tumor cell proliferation without notable side effects. Therefore, mitochondrial-targeting theranostic agent IR-817 may be promising for accurate tumor diagnosis, real-time monitoring, and safe anti-cancer treatments.
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Affiliation(s)
- Changzhen Sun
- Drug Research Center of Integrated Traditional Chinese and Western Medicine, National Traditional Chinese Medicine Clinical Research Base, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646610, China
| | - Jianv Wang
- Department of Dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Tong Xia
- Department of Dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Qin Sun
- Drug Research Center of Integrated Traditional Chinese and Western Medicine, National Traditional Chinese Medicine Clinical Research Base, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646610, China
| | - Yijing He
- Department of Science and Technology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Hailan Wang
- Drug Research Center of Integrated Traditional Chinese and Western Medicine, National Traditional Chinese Medicine Clinical Research Base, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646610, China
| | - Qizhou He
- Department of Radiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646610, China
- Correspondence: (Q.H.); (L.L.); Tel.: +86-159-0836-2735 (Q.H.); +86-193-3860-9127 (L.L.)
| | - Li Liu
- Department of Dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Correspondence: (Q.H.); (L.L.); Tel.: +86-159-0836-2735 (Q.H.); +86-193-3860-9127 (L.L.)
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21
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Nazar M, Abdalla IM, Chen Z, Ullah N, Liang Y, Chu S, Xu T, Mao Y, Yang Z, Lu X. Genome-Wide Association Study for Udder Conformation Traits in Chinese Holstein Cattle. Animals (Basel) 2022; 12:2542. [PMID: 36230283 PMCID: PMC9559277 DOI: 10.3390/ani12192542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Udder conformation traits are one of the most economic traits in dairy cows, greatly affecting animal health, milk production, and producer profitability in the dairy industry. Genetic analysis of udder structure and scores have been developed in Holstein cattle. In our research, we conducted a genome-wide association study for five udder traits, including anterior udder attachment (AUA), central suspensory ligament (CSL), posterior udder attachment height (PUAH), posterior udder attachment width (PUAW), and udder depth (UD), in which the fixed and random model circulating probability unification (FarmCPU) model was applied for the association analysis. The heritability and the standard errors of these five udder traits ranged from 0.04 ± 0.00 to 0.49 ± 0.03. Phenotype data were measured from 1000 Holstein cows, and the GeneSeek Genomic Profiler (GGP) Bovine 100 K SNP chip was used to analyze genotypic data in Holstein cattle. For GWAS analysis, 984 individual cows and 84,407 single-nucleotide polymorphisms (SNPs) remained after quality control; a total of 18 SNPs were found at the GW significant threshold (p < 5.90 × 10−7). Many candidate genes were identified within 200kb upstream or downstream of the significant SNPs, which include MGST1, MGST2, MTUS1, PRKN, STXBP6, GRID2, E2F8, CDH11, FOXP1, SLF1, TMEM117, SBF2, GC, ADGRB3, and GCLC. Pathway analysis revealed that 58 Gene Ontology (GO) terms and 18 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched with adjusted p values, and these GO terms and the KEGG pathway analysis were associated with biological information, metabolism, hormonal growth, and development processes. These results could give valuable biological information for the genetic architecture of udder conformation traits in dairy Holstein cattle.
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Affiliation(s)
- Mudasir Nazar
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | | | - Zhi Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Numan Ullah
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yan Liang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shuangfeng Chu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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22
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Lin Q. MicroRNA-1-3p affects lung adenocarcinoma progression through E2F8 and regulating NF-кB pathway. Cytokine 2022; 156:155922. [PMID: 35660716 DOI: 10.1016/j.cyto.2022.155922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/12/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
E2F8 can modulate development and progression of various cancers including cervical cancer, breast cancer and hepatocellular carcinoma. But its mechanism in lung adenocarcinoma (LUAD) remains underexplored. In this study, we conducted a series of experiments including qRT-PCR, western blot, CCK-8, scratch healing assay, Transwell, and flow cytometry. Through these assays, we confirmed the notable overexpression of E2F8 in LUAD and its promoting effects on LUAD cell proliferation, migration and invasion. Subsequently, microRNA-1-3p that was negatively associated with E2F8 expression was identified through bioinformatics analysis. qRT-PCR was then carried out for quantification of microRNA-1-3p expression, which displayed low microRNA-1-3p expression in LUAD cells. In addition, dual-luciferase reporter gene assay was utilized for validating the targeted relationship between microRNA-1-3p and E2F8. The results denoted that microRNA-1-3p could bind to the promoter region of E2F8. Finally, the results of rescue experiment revealed that microRNA-1-3p negatively modulated E2F8 level. It regulated NF-κB pathway to repress LUAD cell proliferative, migratory, and invasive properties, lead to cell cycle arrest in G0/G1 phase, and enhance cell apoptosis level. This study unraveled that microRNA-1-3p/E2F8 constrained LUAD malignant progression through NF-κB pathway, which may provide possible targets for LUAD diagnosis and treatment.
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Affiliation(s)
- Qingsheng Lin
- Cardiothoracic Surgery, Puyang Oilfield General Hospital, China.
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23
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Chu J, Sun N, Hu W, Chen X, Yi N, Shen Y. Bayesian hierarchical lasso Cox model: A 9-gene prognostic signature for overall survival in gastric cancer in an Asian population. PLoS One 2022; 17:e0266805. [PMID: 35421138 PMCID: PMC9009599 DOI: 10.1371/journal.pone.0266805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 03/29/2022] [Indexed: 12/24/2022] Open
Abstract
Objective
Gastric cancer (GC) is one of the most common tumour diseases worldwide and has poor survival, especially in the Asian population. Exploration based on biomarkers would be efficient for better diagnosis, prediction, and targeted therapy.
Methods
Expression profiles were downloaded from the Gene Expression Omnibus (GEO) database. Survival-related genes were identified by gene set enrichment analysis (GSEA) and univariate Cox. Then, we applied a Bayesian hierarchical lasso Cox model for prognostic signature screening. Protein-protein interaction and Spearman analysis were performed. Kaplan–Meier and receiver operating characteristic (ROC) curve analysis were applied to evaluate the prediction performance. Multivariate Cox regression was used to identify prognostic factors, and a prognostic nomogram was constructed for clinical application.
Results
With the Bayesian lasso Cox model, a 9-gene signature included TNFRSF11A, NMNAT1, EIF5A, NOTCH3, TOR2A, E2F8, PSMA5, TPMT, and KIF11 was established to predict overall survival in GC. Protein-protein interaction analysis indicated that E2F8 was likely related to KIF11. Kaplan-Meier analysis showed a significant difference between the high-risk and low-risk groups (P<0.001). Multivariate analysis demonstrated that the 9-gene signature was an independent predictor (HR = 2.609, 95% CI 2.017–3.370), and the C-index of the integrative model reached 0.75. Function enrichment analysis for different risk groups revealed the most significant enrichment pathway/term, including pyrimidine metabolism and respiratory electron transport chain.
Conclusion
Our findings suggested that a novel prognostic model based on a 9-gene signature was developed to predict GC patients in high-risk and improve prediction performance. We hope our model could provide a reference for risk classification and clinical decision-making.
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Affiliation(s)
- Jiadong Chu
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
| | - Na Sun
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
| | - Wei Hu
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
| | - Xuanli Chen
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
| | - Nengjun Yi
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yueping Shen
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
- * E-mail:
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24
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Aibara D, Takahashi S, Yagai T, Kim D, Brocker CN, Levi M, Matsusue K, Gonzalez FJ. Gene repression through epigenetic modulation by PPARA enhances hepatocellular proliferation. iScience 2022; 25:104196. [PMID: 35479397 PMCID: PMC9036120 DOI: 10.1016/j.isci.2022.104196] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 02/22/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022] Open
Abstract
Peroxisome proliferator-activated receptor α (PPARA) is a key mediator of lipid metabolism and inflammation. Activation of PPARA in rodents causes hepatocyte proliferation, but the underlying mechanism is poorly understood. This study focused on genes repressed by PPARA and analyzed the mechanism by which PPARA promotes hepatocyte proliferation in mice. Activation of PPARA by agonist treatment was autoregulated, and induced expression of the epigenetic regulator UHRF1 via activation of the newly described PPARA target gene E2f8, which, in turn, regulates Uhrf1. UHRF1 strongly repressed the expression of CDH1 via methylation of the Cdh1 promoter marked with H3K9me3. Repression of CDH1 by PPARA activation was reversed by PPARA deficiency or knockdown of E2F8 or UHRF1. Furthermore, a forced expression of CDH1 inhibited expression of the Wnt signaling target genes such as Myc after PPARA activation, and suppressed hepatocyte hyperproliferation. These results demonstrate that the PPARA-E2F8-UHRF1-CDH1 axis causes epigenetic regulation of hepatocyte proliferation.
PPARA activation induces the UHRF1 expression via novel PPARA target gene E2f8 Induction of UHRF1 by PPARA activation represses Cdh1 gene marked with H3K9me3 CDH1 suppresses hepatocyte proliferation after PPARA activation Autoinduction of PPARA by agonist enhances cell proliferation via E2F8-UHRF1-CDH1
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Affiliation(s)
- Daisuke Aibara
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Faculty of Pharmaceutical Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shogo Takahashi
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC 20057, USA
- Corresponding author
| | - Tomoki Yagai
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Donghwan Kim
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chad N. Brocker
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Moshe Levi
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - Kimihiko Matsusue
- Faculty of Pharmaceutical Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Corresponding author
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25
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Genome-Wide Association Study Candidate Genes on Mammary System-Related Teat-Shape Conformation Traits in Chinese Holstein Cattle. Genes (Basel) 2021; 12:genes12122020. [PMID: 34946969 PMCID: PMC8701322 DOI: 10.3390/genes12122020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022] Open
Abstract
In the dairy industry, mammary system traits are economically important for dairy animals, and it is important to explain their fundamental genetic architecture in Holstein cattle. Good and stable mammary system-related teat traits are essential for producer profitability in animal fitness and in the safety of dairy production. In this study, we conducted a genome-wide association study on three traits—anterior teat position (ATP), posterior teat position (PTP), and front teat length (FTL)—in which the FarmCPU method was used for association analyses. Phenotypic data were collected from 1000 Chinese Holstein cattle, and the GeneSeek Genomic Profiler Bovine 100K single-nucleotide polymorphisms (SNP) chip was used for cattle genotyping data. After the quality control process, 984 individual cattle and 84,406 SNPs remained for GWAS work analysis. Nine SNPs were detected significantly associated with mammary-system-related teat traits after a Bonferroni correction (p < 5.92 × 10−7), and genes within a region of 200 kb upstream or downstream of these SNPs were performed bioinformatics analysis. A total of 36 gene ontology (GO) terms and 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched (p < 0.05), and these terms and pathways are mainly related to metabolic processes, immune response, and cellular and amino acid catabolic processes. Eleven genes including MMS22L, E2F8, CSRP3, CDH11, PEX26, HAL, TAMM41, HIVEP3, SBF2, MYO16 and STXBP6 were selected as candidate genes that might play roles in the teat traits of cows. These results identify SNPs and candidate genes that give helpful biological information for the genetic architecture of these teat traits, thus contributing to the dairy production, health, and genetic selection of Chinese Holstein cattle.
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26
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Sladky VC, Eichin F, Reiberger T, Villunger A. Polyploidy control in hepatic health and disease. J Hepatol 2021; 75:1177-1191. [PMID: 34228992 DOI: 10.1016/j.jhep.2021.06.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022]
Abstract
A balanced increase in DNA content (ploidy) is observed in some human cell types, including bone-resorbing osteoclasts, platelet-producing megakaryocytes, cardiomyocytes or hepatocytes. The impact of increased hepatocyte ploidy on normal physiology and diverse liver pathologies is still poorly understood. Recent findings suggest swift genetic adaptation to hepatotoxic stress and the protection from malignant transformation as beneficial effects. Herein, we discuss the molecular mechanisms regulating hepatocyte polyploidisation and its implication for different liver diseases and hepatocellular carcinoma. We report on centrosomes' role in limiting polyploidy by activating the p53 signalling network (via the PIDDosome multiprotein complex) and we discuss the role of this pathway in liver disease. Increased hepatocyte ploidy is a hallmark of hepatic inflammation and may play a protective role against liver cancer. Our evolving understanding of hepatocyte ploidy is discussed from the perspective of its potential clinical application for risk stratification, prognosis, and novel therapeutic strategies in liver disease and hepatocellular carcinoma.
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Affiliation(s)
- Valentina C Sladky
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Felix Eichin
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas Reiberger
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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27
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Comprehensive Analysis of the Expression and Prognosis for E2Fs in Human Clear Cell Renal Cell Carcinoma. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:5790416. [PMID: 34531966 PMCID: PMC8440094 DOI: 10.1155/2021/5790416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/15/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
Background E2F transcription factors is a family of transcription factors, and lots of studies have shown that they play a key role in the occurrence and development of many tumors. However, the association between expression, prognostic value, and immune infiltration in the tumor microenvironment of the eight E2Fs members in ccRCC is still unclear. Method s. We used online databases, such as ONCOMINE, UALCAN, Kaplan–Meier plotter, GEPIA, Metascape, TIMER, and cBioPortal, to analyze the effect of mRNA expression of E2Fs family members in ccRCC on the prognosis of patients and the relationship with immune infiltration. Results Except for E2F5, other seven members of the family of E2Fs mRNA expression levels in ccRCC tissues were significantly higher than control tissues. And the high expression of E2Fs mRNA in ccRCC patients was related to cancer stage and tumor grade. Survival analysis results suggested that elevated mRNA expression levels of E2F1/2/3/4/7/8 were significantly related to the shorter overall survival (OS) in ccRCC patients (P = 3.9E – 06), while high mRNA expression of E2F6 is not related to OS (P = 0.061). Mutations of E2Fs were correlated with shorter OS of ccRCC patients (P = 7.094E – 5). In addition, mRNA expression of E2F1/2/3/4/7/8 was positively correlated with infiltration of six types of immune cells, including B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. Conclusions These results indicate that E2F1/2/3/4/7/8 may be used as a prognostic marker for the survival of ccRCC patients and laid the foundation for studying the immune infiltration role of E2Fs family members in tumors.
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28
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Abstract
PURPOSE OF REVIEW Breast cancer frequently metastasizes to the bone and lung, but the ability to treat metastatic tumor cells remains a pressing clinical challenge. Histone deacetylases (HDACs) and histone acetyltransferases (HATs) have emerged as promising targets since these enzymes are aberrantly expressed in numerous cancers and regulate the expression of genes that drive tumorigenesis and metastasis. This review focuses on the abnormal expression of histone-modifying enzymes in cancers that have a high tropism for the bone and lung and explores the clinical use of histone deacetylase inhibitors for the treatment and prevention of metastasis to these sites. RECENT FINDINGS Preclinical studies have demonstrated that the role for HDACs is highly dependent on tumor type and stage of disease progression. HDAC inhibitors can induce apoptosis, senescence, cell differentiation, and tumor dormancy genes and inhibit angiogenesis, making these promising therapeutics for the treatment of metastatic disease. HDAC inhibitors are already FDA approved for hematologic malignancies and are in clinical trials with standard-of-care chemotherapies and targeted agents for several solid tumors, including cases of metastatic disease. However, these drugs can negatively impact bone homeostasis. Although HDAC inhibitors are not currently administered for the treatment of bone and lung metastatic disease, preclinical studies have shown that these drugs can reduce distant metastasis by targeting molecular factors and signaling pathways that drive tumor cell dissemination to these sites. Thus, HDAC inhibitors in combination with bone protective therapies may be beneficial in the treatment of bone metastatic cancers.
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Affiliation(s)
- Courtney M Edwards
- Graduate Program in Cancer Biology, Vanderbilt University, 2215b Garland Ave, 1165C Medical Research Building IV, Nashville, TN, 37232, USA
- Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Rachelle W Johnson
- Graduate Program in Cancer Biology, Vanderbilt University, 2215b Garland Ave, 1165C Medical Research Building IV, Nashville, TN, 37232, USA.
- Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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29
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Zheng C, Yu S. Expression and gene regulatory network of SNHG1 in hepatocellular carcinoma. BMC Med Genomics 2021; 14:28. [PMID: 33499863 PMCID: PMC7836560 DOI: 10.1186/s12920-021-00878-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 01/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Small nucleolar RNA host gene 1 (SNHG1), a long noncoding RNA (lncRNA), is a transcript that negatively regulates tumour suppressor genes, such as p53. Abnormal SNHG1 expression is associated with cell proliferation and cancer. We used sequencing data downloaded from Genomic Data Commons to analyse the expression and interaction networks of SNHG1 in hepatocellular carcinoma (HCC). METHODS Expression was examined using the limma package of R and verified by Gene Expression Profiling Interactive Analysis. We also obtained miRNA expression data from StarBase to determine the lncRNA-miRNA-mRNA-related RNA regulatory network in HCC. Kaplan-Meier (KM) analysis was performed using the survival package of R. Gene Ontology annotation of genes was carried out using Metascape. RESULTS We found that SNHG1 was overexpressed and often amplified in HCC patients. In addition, SNHG1 upregulation was associated with the promotion of several primary biological functions, including cell proliferation, transcription and protein binding. Moreover, we found similar trends of small nucleolar RNA host gene 1 (SNHG1), E2F8 (E2F transcription factor 8), FANCE (FA complementation group E) and LMNB2 (encodes lamin B2) expression. In the SNHG1-associated network, high expression levels of SNHG1 (log-rank P value = 0.0643), E2F8 (log-rank P value = 0.000048), FANCE (log-rank P value = 0.00125) and LMNB2 (log-rank P value = 0.0392) were significantly associated with poor survival. Single-cell analysis showed that E2F8 may play an important role in tumorigenesis or cancer development. CONCLUSIONS Our results highlight the benefit of utilizing multiple datasets to understand the functional potential regulatory networks of SNHG1 and the role of SNHG1 in tumours.
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Affiliation(s)
- Chaoran Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Shicheng Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou, 510530, China.
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Bioland Laboratory, Guangzhou, 510005, China.
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30
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Li Y, Gao J, Kamran M, Harmacek L, Danhorn T, Leach SM, O'Connor BP, Hagman JR, Huang H. GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super-enhancers. Nat Commun 2021; 12:494. [PMID: 33479210 PMCID: PMC7820599 DOI: 10.1038/s41467-020-20766-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors. However, it is unclear whether these lineage-determining factors regulate chromatin accessibility at mast cell enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We find that the number and densities of GATA2- but not MITF-bound sites at the super-enhancers are several folds higher than that at the typical enhancers. Our studies reveal that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key mast cell genes.
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Affiliation(s)
- Yapeng Li
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Junfeng Gao
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Mohammad Kamran
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Laura Harmacek
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Thomas Danhorn
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Sonia M Leach
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Brian P O'Connor
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Hua Huang
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA.
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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31
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Ji M, Ren L, Lv Y, Lao X, Feng Q, Tang W, Zhuang A, Liu T, Zheng P, Xu J. Small Nuclear Ribonucleoprotein Polypeptide N Accelerates Malignant Progression and Poor Prognosis in Colorectal Cancer Transcriptionally Regulated by E2F8. Front Oncol 2020; 10:561287. [PMID: 33224876 PMCID: PMC7669248 DOI: 10.3389/fonc.2020.561287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/04/2020] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer is a major cause of death worldwide, and the identification of new diagnostic and prognostic biomarkers is crucial to develop new strategies to avoid colorectal cancer-related deaths. Small nuclear ribonucleoprotein polypeptide N (SNRPN) is an imprinted gene that plays an important role in various neurodevelopmental disabilities. In this study, SNRPN was highly expressed in colorectal cancer tissues and involved in the progression of this disease. Immunohistochemistry analysis of 1,310 colorectal cancer tissue samples showed that SNRPN highly expressed in cancer tissues than in adjacent tissues and was mainly localized in the nucleus. Clinical pathological factor analysis demonstrated that higher expression of SNRPN was significantly associated with larger tumor size, location of the tumor on the left-sided colon, neural invasion, and distant metastasis. Univariate and multivariate analyses showed that SNRPN expression was an independent risk factor for survival, with high expression levels indicating worse overall survival. Both in vitro and in vivo experiments confirmed that high expression of SNRPN was associated with tumor proliferation, cell cycle, and metastasis. Knocking down SNRPN blocked the cell cycle at the G2/M phase transition and promoted tumor cell apoptosis, inhibiting the progression of colorectal cancer. To explore the up-steam of SNRPN, we found by luciferase reporter assay and chromosomal immunoprecipitation assay that E2F8 was a transcriptional regulator up-steam of SNRPN in colorectal cancer. Systematic studies of SNRPN will help us discover new regulatory molecules and provide a theoretical basis for finding new molecular targets for this disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai, China
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32
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Roelofs PA, Goh CY, Chua BH, Jarvis MC, Stewart TA, McCann JL, McDougle RM, Carpenter MA, Martens JW, Span PN, Kappei D, Harris RS. Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B. eLife 2020; 9:61287. [PMID: 32985974 PMCID: PMC7553775 DOI: 10.7554/elife.61287] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022] Open
Abstract
APOBEC3B (A3B)-catalyzed DNA cytosine deamination contributes to the overall mutational landscape in breast cancer. Molecular mechanisms responsible for A3B upregulation in cancer are poorly understood. Here we show that a single E2F cis-element mediates repression in normal cells and that expression is activated by its mutational disruption in a reporter construct or the endogenous A3B gene. The same E2F site is required for A3B induction by polyomavirus T antigen indicating a shared molecular mechanism. Proteomic and biochemical experiments demonstrate the binding of wildtype but not mutant E2F promoters by repressive PRC1.6/E2F6 and DREAM/E2F4 complexes. Knockdown and overexpression studies confirm the involvement of these repressive complexes in regulating A3B expression. Altogether, these studies demonstrate that A3B expression is suppressed in normal cells by repressive E2F complexes and that viral or mutational disruption of this regulatory network triggers overexpression in breast cancer and provides fuel for tumor evolution.
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Affiliation(s)
- Pieter A Roelofs
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Chai Yeen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Haow Chua
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States
| | - Teneale A Stewart
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Mater Research Institute, The University of Queensland, Faculty of Medicine, Brisbane, Australia
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
| | - Rebecca M McDougle
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Hennepin Healthcare, Minneapolis, United States
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
| | - John Wm Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Paul N Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
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33
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E2F8 Induces Cell Proliferation and Invasion through the Epithelial-Mesenchymal Transition and Notch Signaling Pathways in Ovarian Cancer. Int J Mol Sci 2020; 21:ijms21165813. [PMID: 32823614 PMCID: PMC7460858 DOI: 10.3390/ijms21165813] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/02/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Despite the recent research implicating E2F8 (E2F Transcription Factor 8) in cancer, the role of E2F8 in the progression of ovarian cancer has remained unclear. Hence, we explored the bio-functional effects of E2F8 knockdown on ovarian cancer cell lines in vitro and in vivo. Methods: The expression of E2F8 was compared between ovarian cancer and noncancer tissues, and its association with the progression-free survival of ovarian cancer patients was analyzed. To demonstrate the function of E2F8 in cell proliferation, migration, and invasion, we employed RNA interference to suppress E2F8 expression in ovarian cancer cell lines. Finally, the effect of E2F8 knockdown was investigated in a xenograft mouse model of ovarian cancer. Results: Ovarian cancer tissue exhibited significantly higher E2F8 expression compared to that of normal ovarian tissue. Clinical data showed that E2F8 was a significant predictor of progression-free survival. Moreover, the prognosis of the ovarian cancer patients with high E2F8 expression was poorer than that of the patients with low E2F8 expression. In vitro experiments using E2F8-knockdown ovarian cancer cell lines demonstrated that E2F8 knockdown inhibited cell proliferation, migration, and tumor invasion. Additionally, E2F8 was a potent inducer and modulator of the expression of epithelial–mesenchymal transition and Notch signaling pathway-related markers. We confirmed the function of E2F8 in vivo, signifying that E2F8 knockdown was significantly correlated with reduced tumor size and weight. Conclusions: Our findings indicate that E2F8 is highly correlated with ovarian cancer progression. Hence, E2F8 can be utilized as a prognostic marker and therapeutic target against ovarian malignancy.
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34
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Emanuele MJ, Enrico TP, Mouery RD, Wasserman D, Nachum S, Tzur A. Complex Cartography: Regulation of E2F Transcription Factors by Cyclin F and Ubiquitin. Trends Cell Biol 2020; 30:640-652. [PMID: 32513610 PMCID: PMC7859860 DOI: 10.1016/j.tcb.2020.05.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
The E2F family of transcriptional regulators sits at the center of cell cycle gene expression and plays vital roles in normal and cancer cell cycles. Whereas control of E2Fs by the retinoblastoma family of proteins is well established, much less is known about their regulation by ubiquitin pathways. Recent studies placed the Skp1-Cul1-F-box-protein (SCF) family of E3 ubiquitin ligases with the F-box protein Cyclin F at the center of E2F regulation, demonstrating temporal proteolysis of both activator and atypical repressor E2Fs. Importantly, these E2F members, in particular activator E2F1 and repressors E2F7 and E2F8, form a feedback circuit at the crossroads of cell cycle and cell death. Moreover, Cyclin F functions in a reciprocal circuit with the cell cycle E3 ligase anaphase-promoting complex/cyclosome (APC/C), which also controls E2F7 and E2F8. This review focuses on the complex contours of feedback within this circuit, highlighting the deep crosstalk between E2F, SCF-Cyclin F, and APC/C in regulating the oscillator underlying human cell cycles.
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Affiliation(s)
- Michael J Emanuele
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Taylor P Enrico
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D Mouery
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Genetics and Molecular Biology Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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35
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Pennycook BR, Vesela E, Peripolli S, Singh T, Barr AR, Bertoli C, de Bruin RAM. E2F-dependent transcription determines replication capacity and S phase length. Nat Commun 2020; 11:3503. [PMID: 32665547 PMCID: PMC7360579 DOI: 10.1038/s41467-020-17146-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/04/2020] [Indexed: 01/06/2023] Open
Abstract
DNA replication timing is tightly regulated during S-phase. S-phase length is determined by DNA synthesis rate, which depends on the number of active replication forks and their velocity. Here, we show that E2F-dependent transcription, through E2F6, determines the replication capacity of a cell, defined as the maximal amount of DNA a cell can synthesise per unit time during S-phase. Increasing or decreasing E2F-dependent transcription during S-phase increases or decreases replication capacity, and thereby replication rates, thus shortening or lengthening S-phase, respectively. The changes in replication rate occur mainly through changes in fork speed without affecting the number of active forks. An increase in fork speed does not induce replication stress directly, but increases DNA damage over time causing cell cycle arrest. Thus, E2F-dependent transcription determines the DNA replication capacity of a cell, which affects the replication rate, controlling the time it takes to duplicate the genome and complete S-phase.
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Affiliation(s)
- Betheney R Pennycook
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
- MRC London Institute of Medical Science Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Eva Vesela
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Silvia Peripolli
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Tanya Singh
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Alexis R Barr
- MRC London Institute of Medical Science Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, London, W12 0NN, UK
| | - Cosetta Bertoli
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK.
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK.
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
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36
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Yu H, Zhang D, Li Z, Wang M. E2F transcription factor 8 promotes proliferation and radioresistance in glioblastoma. Pathol Res Pract 2020; 216:153030. [PMID: 32703494 DOI: 10.1016/j.prp.2020.153030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Glioblastoma (GBM) is the most lethal brain tumor that has a median survival of less than 2 years. Tumor heterogeneity and high therapeutic resistance are hallmarks of GBM. Transcription factors (TFs) play a critical role in tumor progression by regulating the transcriptional events associated with tumor cells transition into more malignant cellular phenotypes. The E2 F transcription factor 8 (E2 F8) is a recently identified TF in the E2 F family. Studies have revealed that E2 F8 is involved in tumorigenesis of multiple cancer types; however, the oncogenic role of E2 F8 in GBM was rarely studied and the prognostic value of E2 F8 has not been explored. AIMS In this study, we investigated the expression profile, prognosis correlation and oncogenic role of E2 F8 to explore its potential use as a GBM therapeutic target. RESULTS E2 F8 was significantly enriched in GBM compared with normal brain tissues and low-grade glioma. E2 F8 high expression was strongly associated with worse outcome of GBM patients. E2 F8 silencing significantly attenuated the proliferation of tumor cells in vitro and tumorigenicity in vivo, while its overexpression promoted the proliferation of GBM tumor cells. Bioinformatics analysis revealed that E2 F8 was tightly linked to multiple oncogenic processes in GBM, including aggressive cell cycle, DNA repair, STAT3, TGFRβ and WNT pathways. E2 F8 high expression correlated with the expression of a variety of well-known oncogenes in GBM. E2 F8 was identified as a crucial transcriptional regulator of CHEK1 via its directly binding CHEK1 promoter area. Finally, E2 F8 conferred significant radioresistance to GBM tumor cells in vitro and in vivo. CONCLUSION E2 F8 is highly expressed in GBM and associated with worse outcome in GBM patients. It promotes tumorigenesis and radioresistance of GBM tumor cells and has oncogenic roles via its involvement in multiple oncogenic processes and pathways such as the regulation of CHEK1 transcriptional activity.
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Affiliation(s)
- Hai Yu
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Duanni Zhang
- Department of Endocrinology, Shaanxi People's Hospital, Xi'an, Shaanxi 710061, China
| | - Zhijin Li
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Maode Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
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Oncogenic hijacking of a developmental transcription factor evokes vulnerability toward oxidative stress in Ewing sarcoma. Nat Commun 2020; 11:2423. [PMID: 32415069 PMCID: PMC7228971 DOI: 10.1038/s41467-020-16244-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/23/2020] [Indexed: 01/20/2023] Open
Abstract
Ewing sarcoma (EwS) is an aggressive childhood cancer likely originating from mesenchymal stem cells or osteo-chondrogenic progenitors. It is characterized by fusion oncoproteins involving EWSR1 and variable members of the ETS-family of transcription factors (in 85% FLI1). EWSR1-FLI1 can induce target genes by using GGAA-microsatellites as enhancers. Here, we show that EWSR1-FLI1 hijacks the developmental transcription factor SOX6 – a physiological driver of proliferation of osteo-chondrogenic progenitors – by binding to an intronic GGAA-microsatellite, which promotes EwS growth in vitro and in vivo. Through integration of transcriptome-profiling, published drug-screening data, and functional in vitro and in vivo experiments including 3D and PDX models, we discover that constitutively high SOX6 expression promotes elevated levels of oxidative stress that create a therapeutic vulnerability toward the oxidative stress-inducing drug Elesclomol. Collectively, our results exemplify how aberrant activation of a developmental transcription factor by a dominant oncogene can promote malignancy, but provide opportunities for targeted therapy. Ewing sarcoma is characterized by the fusion of EWSR1 and FLI1. Here, the authors show that EWSR1-FLI1 increases the activity of the developmental transcription factor SOX6, which promotes tumor growth but also increases sensitivity to oxidative stress.
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38
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Lü Y, Zhang J, Li L, Li S, Yang Z. Carcinogenesis effects of E2F transcription factor 8 (E2F8) in hepatocellular carcinoma outcomes: an integrated bioinformatic report. Biosci Rep 2020; 40:BSR20193212. [PMID: 31990034 PMCID: PMC7012657 DOI: 10.1042/bsr20193212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 02/05/2023] Open
Abstract
This report aimed to investigate the carcinogenesis effects of E2F transcription factor 8 (E2F8) in hepatocellular carcinoma (HCC). E2F8 expression level was compared in Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and Oncomine. Survival analysis of E2F8 for HCC were conducted in Kaplan-Meier plotter. Correlations of E2F8 and clinico-pathological features were performed in TCGA. Enrichment of interacted and similar genes with E2F8 was evaluated in Gene Set Enrichment Analysis (GSEA) and Metascape. We found that E2F8 was significantly up-regulated in tumor tissues compared with nontumor tissues (all P < 0.01). Moreover, E2F8 was significantly overexpressed in peripheral blood mononuclear cell (PBMC) in HCC patients than that in healthy individuals (P < 0.001). Meta-analysis in Oncomine database confirmed that E2F8 was significantly higher in HCC tumors (P = 4.28E-08). Additionally, E2F8 elevation significantly correlated with overall survival (OS), recurrence-free survival (RFS), disease-specific survival (DSS) and progression-free survival (PFS) in HCC patients (all P < 0.01). E2F8 level was significantly higher in HCC patients with advanced neoplasm histologic grade, American Joint Committee on Cancer (AJCC) stage and α-fetoprotein (AFP) elevation (all P < 0.05). Cox regression model demonstrated that high E2F8 was an independent risk factor for OS and DFS in HCC patients (HR = 2.16, P = 0.003 and HR = 1.64, P = 0.002, respectively). Enrichment analysis revealed that genes interacted/similar with E2F8 were mainly enriched in cell cycle pathways/biological process. Conclusively, up-regulated in tumors, E2F8 might accelerate tumor progression and result in unfavorable outcomes in HCC patients.
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Affiliation(s)
- Ying Lü
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jing Zhang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Lei Li
- Department of Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Shun Li
- Department of Laboratory Animal, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zongguo Yang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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Wasserman D, Nachum S, Cohen M, Enrico TP, Noach-Hirsh M, Parasol J, Zomer-Polak S, Auerbach N, Sheinberger-Chorni E, Nevenzal H, Levi-Dadon N, Wang X, Lahmi R, Michaely E, Gerber D, Emanuele MJ, Tzur A. Cell cycle oscillators underlying orderly proteolysis of E2F8. Mol Biol Cell 2020; 31:725-740. [PMID: 31995441 PMCID: PMC7185961 DOI: 10.1091/mbc.e19-12-0725] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
E2F8 is a transcriptional repressor that antagonizes E2F1 at the crossroads of the cell cycle, apoptosis, and cancer. Previously, we discovered that E2F8 is a direct target of the APC/C ubiquitin ligase. Nevertheless, it remains unknown how E2F8 is dynamically controlled throughout the entirety of the cell cycle. Here, using newly developed human cell-free systems that recapitulate distinct inter-mitotic and G1 phases and a continuous transition from prometaphase to G1, we reveal an interlocking dephosphorylation switch coordinating E2F8 degradation with mitotic exit and the activation of APC/CCdh1. Further, we uncover differential proteolysis rates for E2F8 at different points within G1 phase, accounting for its accumulation in late G1 while APC/CCdh1 is still active. Finally, we demonstrate that the F-box protein Cyclin F regulates E2F8 in G2-phase. Altogether, our data define E2F8 regulation throughout the cell cycle, illuminating an extensive coordination between phosphorylation, ubiquitination and transcription in mammalian cell cycle.
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Affiliation(s)
- Danit Wasserman
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Sapir Nachum
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Meital Cohen
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Taylor P Enrico
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Meirav Noach-Hirsh
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Jasmin Parasol
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Sarit Zomer-Polak
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Naomi Auerbach
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Evelin Sheinberger-Chorni
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Hadas Nevenzal
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Nofar Levi-Dadon
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Xianxi Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Roxane Lahmi
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Efrat Michaely
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Doron Gerber
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
| | - Michael J Emanuele
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Amit Tzur
- Faculty of Life Sciences and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 5290002, Israel
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40
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Cuitiño MC, Pécot T, Sun D, Kladney R, Okano-Uchida T, Shinde N, Saeed R, Perez-Castro AJ, Webb A, Liu T, Bae SI, Clijsters L, Selner N, Coppola V, Timmers C, Ostrowski MC, Pagano M, Leone G. Two Distinct E2F Transcriptional Modules Drive Cell Cycles and Differentiation. Cell Rep 2019; 27:3547-3560.e5. [PMID: 31130414 PMCID: PMC6673649 DOI: 10.1016/j.celrep.2019.05.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/14/2019] [Accepted: 04/30/2019] [Indexed: 02/05/2023] Open
Abstract
Orchestrating cell-cycle-dependent mRNA oscillations is critical to cell proliferation in multicellular organisms. Even though our understanding of cell-cycle-regulated transcription has improved significantly over the last three decades, the mechanisms remain untested in vivo. Unbiased transcriptomic profiling of G0, G1-S, and S-G2-M sorted cells from FUCCI mouse embryos suggested a central role for E2Fs in the control of cell-cycle-dependent gene expression. The analysis of gene expression and E2F-tagged knockin mice with tissue imaging and deep-learning tools suggested that post-transcriptional mechanisms universally coordinate the nuclear accumulation of E2F activators (E2F3A) and canonical (E2F4) and atypical (E2F8) repressors during the cell cycle in vivo. In summary, we mapped the spatiotemporal expression of sentinel E2F activators and canonical and atypical repressors at the single-cell level in vivo and propose that two distinct E2F modules relay the control of gene expression in cells actively cycling (E2F3A-8-4) and exiting the cycle (E2F3A-4) during mammalian development.
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Affiliation(s)
- Maria C Cuitiño
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Thierry Pécot
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Daokun Sun
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Raleigh Kladney
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Takayuki Okano-Uchida
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Neelam Shinde
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Resham Saeed
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Antonio J Perez-Castro
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Amy Webb
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Tom Liu
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Soo In Bae
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Linda Clijsters
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Nicholas Selner
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Vincenzo Coppola
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Cynthia Timmers
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Michael C Ostrowski
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Gustavo Leone
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA.
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Chang H, Song J, Wu J, Zhang Y. E2F transcription factor 8 promotes cell proliferation via CCND1/p21 in esophageal squamous cell carcinoma. Onco Targets Ther 2018; 11:8165-8173. [PMID: 30532557 PMCID: PMC6241692 DOI: 10.2147/ott.s180938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Purpose E2F transcription factor 8 (E2F8) is a novel member of the E2F family, but its function in esophageal squamous cell carcinoma (ESCC) remains unclear. This study aimed to research the function of E2F8 in ESCC. Materials and methods We used quantitative real-time PCR and Western blot analyses to detect the expression pattern of E2F8 in ESCC. The effects of E2F8 on proliferation were investigated by Cell Counting Kit-8, 5-ethynyl-2′-deoxyuridine, and colony formation assays. We also confirmed the function of E2F8 in vivo. Results E2F8 expression was upregulated in ESCC, and promoted cell proliferation and influenced the expression of CCND1/p21. Downregulation of E2F8 expression inhibited cell proliferation in vivo. Conclusion E2F8 was identified as a new potential oncogene in ESCC.
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Affiliation(s)
- Huiwen Chang
- Department of Cardiothoracic Surgery, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, Yancheng, Jiangsu 224001, PR China,
| | - Jianxiang Song
- Department of Cardiothoracic Surgery, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, Yancheng, Jiangsu 224001, PR China,
| | - Jixiang Wu
- Department of Cardiothoracic Surgery, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, Yancheng, Jiangsu 224001, PR China,
| | - Yajun Zhang
- Department of Cardiothoracic Surgery, Yancheng Third People's Hospital, The Affiliated Yancheng Hospital of Southeast University, Yancheng, Jiangsu 224001, PR China,
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Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma. Sci Rep 2018; 8:16408. [PMID: 30401798 PMCID: PMC6219531 DOI: 10.1038/s41598-018-34636-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/23/2018] [Indexed: 12/14/2022] Open
Abstract
Severe equine asthma is a chronic inflammatory condition of the lower airways similar to adult-onset asthma in humans. Exacerbations are characterized by bronchial and bronchiolar neutrophilic inflammation, mucus hypersecretion and airway constriction. In this study we analyzed the gene expression response of the bronchial epithelium within groups of asthmatic and non-asthmatic animals following exposure to a dusty hay challenge. After challenge we identified 2341 and 120 differentially expressed genes in asthmatic and non-asthmatic horses, respectively. Gene set enrichment analysis of changes in gene expression after challenge identified 587 and 171 significantly enriched gene sets in asthmatic and non-asthmatic horses, respectively. Gene sets in asthmatic animals pertained, but were not limited, to cell cycle, neutrophil migration and chemotaxis, wound healing, hemostasis, coagulation, regulation of body fluid levels, and the hedgehog pathway. Furthermore, transcription factor target enrichment analysis in the asthmatic group showed that transcription factor motifs with the highest enrichment scores for up-regulated genes belonged to the E2F transcription factor family. It is postulated that engagement of hedgehog and E2F pathways in asthmatic horses promotes dysregulated cell proliferation and abnormal epithelial repair. These fundamental lesions may prevent re-establishment of homeostasis and perpetuate inflammation.
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Zhang Z, Li J, Huang Y, Peng W, Qian W, Gu J, Wang Q, Hu T, Ji D, Ji B, Zhang Y, Wang S, Sun Y. Upregulated miR-1258 regulates cell cycle and inhibits cell proliferation by directly targeting E2F8 in CRC. Cell Prolif 2018; 51:e12505. [PMID: 30144184 DOI: 10.1111/cpr.12505] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 06/22/2018] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES MicroRNAs (miRNAs) as small noncoding RNA molecules function by regulating their target genes negatively. MiR-1258 was widely researched in multicancers, but its role remains unclear in colorectal cancer (CRC). METHODS The expression of miR-1258 and its specific target gene were detected in human CRC specimens and cell lines by miRNA RT-PCR, qRT-PCR and Western blot. The effects of miR-1258 on CRC proliferation were evaluated using CCK-8 assays, EdU incorporation, colony formation assays and cell-cycle assays; in vitro and the in vivo effects were investigated using a mouse tumorigenicity model. Luciferase reporter and RIP assays were employed to identify interactions between miR-1258 and its specific target gene. RESULTS MiR-1258 was downregulated in CRC tissues and CRC cell lines, and upregulated miR-1258 was proved to inhibit proliferation and arrest cell cycle at G0/G1 in vitro and vivo. Luciferase reporter, RIP and western blot assays revealed E2F8 to be a direct target of miR-1258. The effects of miR-1258 in proliferation and cell cycle regulation can be abolished by E2F8 through rescue experiments. By directly targeting E2F8, miR-1258 influenced the expression of several cell-cycle factors, including cyclin D1 (CCND1) and cyclin dependent kinase inhibitor 1A (p21). CONCLUSION MiR-1258 may function as a suppressive factor by negatively controlling E2F8, thus, highlighting the potential role of miR-1258 as a therapeutic target for human CRC.
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Affiliation(s)
- Zhiyuan Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuanjian Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wen Peng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wenwei Qian
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiou Gu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qingyuan Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tao Hu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dongjian Ji
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bing Ji
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yue Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shijia Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yueming Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Levenson EA, Martens C, Kanakabandi K, Turner CV, Virtaneva K, Paneru M, Ricklefs S, Sosnovtsev SV, Johnson JA, Porcella SF, Green KY. Comparative Transcriptomic Response of Primary and Immortalized Macrophages to Murine Norovirus Infection. THE JOURNAL OF IMMUNOLOGY 2018; 200:4157-4169. [PMID: 29735480 DOI: 10.4049/jimmunol.1700384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/16/2018] [Indexed: 01/10/2023]
Abstract
Murine norovirus (NoV) is genetically similar to human NoV and offers both an efficient in vitro cell culture system and an animal model by which to investigate the molecular basis of replication. In this study, we present a detailed global view of host alterations to cellular pathways that occur during the progression of a NoV infection. This was accomplished for both Mus musculus BALB/c-derived RAW264.7 (RAW) cells, an immortalized cell line widely used in in vitro replication studies, and primary bone marrow-derived macrophages (BMDM), representing a permissive in vivo target cell in the host. Murine NoV replicated in both cell types, although detected genome copies were approximately one log lower in BMDM compared with RAW cells. RAW and BMDM cells shared an IRF3/7-based IFN response that occurred early in infection. In RAW cells, transcriptional upregulation and INF-β expression were not coupled in that a significant delay in the detection of secreted INF-β was observed. In contrast, primary BMDM showed an early upregulation of transcripts and immediate release of INF-β that might account for lower virus yield. Differences in the transcriptional pathway responses included a marked decrease in expression of key genes in the cell cycle and lipid pathways in RAW cells compared with that of BMDM. Our comparative analysis indicates the existence of varying host responses to virus infection in populations of permissive cells. Awareness of these differences at the gene level will be important in the application of a given permissive culture system to the study of NoV immunity, pathogenesis, and drug development.
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Affiliation(s)
- Eric A Levenson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Craig Martens
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Kishore Kanakabandi
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Charles V Turner
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Kimmo Virtaneva
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Monica Paneru
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Stacy Ricklefs
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Stanislav V Sosnovtsev
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Jordan A Johnson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Stephen F Porcella
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Kim Y Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
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Kim M, Tang JP, Moon NS. An alternatively spliced form affecting the Marked Box domain of Drosophila E2F1 is required for proper cell cycle regulation. PLoS Genet 2018; 14:e1007204. [PMID: 29420631 PMCID: PMC5821395 DOI: 10.1371/journal.pgen.1007204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/21/2018] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
Across metazoans, cell cycle progression is regulated by E2F family transcription factors that can function as either transcriptional activators or repressors. For decades, the Drosophila E2F family has been viewed as a streamlined RB/E2F network, consisting of one activator (dE2F1) and one repressor (dE2F2). Here, we report that an uncharacterized isoform of dE2F1, hereon called dE2F1b, plays an important function during development and is functionally distinct from the widely-studied dE2F1 isoform, dE2F1a. dE2F1b contains an additional exon that inserts 16 amino acids to the evolutionarily conserved Marked Box domain. Analysis of de2f1b-specific mutants generated via CRISPR/Cas9 indicates that dE2F1b is a critical regulator of the cell cycle during development. This is particularly evident in endocycling salivary glands in which a tight control of dE2F1 activity is required. Interestingly, close examination of mitotic tissues such as eye and wing imaginal discs suggests that dE2F1b plays a repressive function as cells exit from the cell cycle. We also provide evidence demonstrating that dE2F1b differentially interacts with RBF1 and alters the recruitment of RBF1 and dE2F1 to promoters. Collectively, our data suggest that dE2F1b is a novel member of the E2F family, revealing a previously unappreciated complexity in the Drosophila RB/E2F network.
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Affiliation(s)
- Minhee Kim
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
| | - Jack P. Tang
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
| | - Nam-Sung Moon
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec, Canada
- * E-mail:
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Ye L, Guo L, He Z, Wang X, Lin C, Zhang X, Wu S, Bao Y, Yang Q, Song L, Lin H. Upregulation of E2F8 promotes cell proliferation and tumorigenicity in breast cancer by modulating G1/S phase transition. Oncotarget 2018; 7:23757-71. [PMID: 26992224 PMCID: PMC5029661 DOI: 10.18632/oncotarget.8121] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/25/2016] [Indexed: 01/04/2023] Open
Abstract
E2F transcription factors are involved in cell cycle regulation and synthesis of DNA in mammalian cells, and simultaneously play important roles in the development and progression of cancer when dysregulated. E2F8, a novel identified E2F family member, was found to be associated with the progression of several human cancers; however, the biological role and clinical significance of E2F8 in breast cancer remain to be further elucidated. Herein, we report that E2F8 is robustly elevated in breast cancer cell lines and clinical breast cancer tissue samples, respectively. The high expression level of E2F8 significantly correlates with clinical progression (P = 0.001), poor patient survival (P < 0.001) and a high Ki67 staining index (P = 0.008) in 187 human breast cancer specimens. Furthermore, we find that overexpressing E2F8 promotes, whereas silencing E2F8 suppresses, the proliferation and tumorigenicity of breast cancer cells both in vitro and in vivo. We further demonstrate that E2F8 transcriptionally upregulates CCNE1 and CCNE2 via directly interacting with their respective gene promoter, which accelerates the transition of G1 to S phase of breast cancer cells. Taken together, these findings uncover a novel biologic role and regulatory mechanism of E2F8 responsible for the progression of breast cancer, indicating E2F8 may represent a novel prognostic biomarker and therapeutic target against breast cancer.
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Affiliation(s)
- Liping Ye
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Ling Guo
- Department of Nasopharyngeal Carcinoma, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Zhenyu He
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Xi Wang
- Department of Breast Surgery, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Chuyong Lin
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Xin Zhang
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Shu Wu
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Yong Bao
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Qi Yang
- Department of Nasopharyngeal Carcinoma, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Libing Song
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
| | - Huanxin Lin
- Department of Radiation Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, People's Republic of China
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Metformin induces cell cycle arrest at the G1 phase through E2F8 suppression in lung cancer cells. Oncotarget 2017; 8:101509-101519. [PMID: 29254182 PMCID: PMC5731892 DOI: 10.18632/oncotarget.21552] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/21/2017] [Indexed: 01/08/2023] Open
Abstract
A target molecule responsible for cell cycle arrest by metformin was discovered using a gene chip array in lung cancer cells and the effect of metformin on E2F8 was assessed. The siRNA-mediated knockdown of E2F8 significantly suppressed G1-S progression while ectopic expression of E2F8 relieved metformin-induced G1 arrest. The mRNA levels of p21 were found to be inversely related to those of E2F8 in lung cancer cells while siRNA-mediated knockdown of p21 partly rescued siE2F8-induced arrest of the cell cycle. Metformin had no effect on degradation of E2F8 mRNA. Activation and inhibition of AMPK by AICAR and Dorsomorphin, respectively, did not affect E2F8 suppression by metformin. The clinical significance of E2F8 was analyzed in The Cancer Genome Atlas (TCGA) data. One hundred six (13%) of 848 TCGA lung cancers overexpressed E2F8 mRNA. The overexpression of E2F8 was associated with poor overall survival (adjusted hazard ratio = 1.58, 95% confidence interval = 1.13-2.22; P = 0.008). The present study suggests that metformin may induce cell cycle arrest at the G1 phase by suppressing E2F8 expression in lung cancer cells. In addition, E2F8 may be associated with poor overall survival in lung cancer patients irrespective of histology.
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Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics 2017; 18:723. [PMID: 28899340 PMCID: PMC5596945 DOI: 10.1186/s12864-017-4111-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and those of its tissue of origin has not been conducted. The RNA-Seq data generated by the GTEx project is the first available data resource in which it is possible to perform a large-scale transcriptional and regulatory network analysis comparing cell lines with their tissues of origin. RESULTS We compared 127 paired Epstein-Barr virus transformed lymphoblastoid cell lines (LCLs) and whole blood samples, and 244 paired primary fibroblast cell lines and skin samples. While gene expression analysis confirms that these cell lines carry the expression signatures of their primary tissues, albeit at reduced levels, network analysis indicates that expression changes are the cumulative result of many previously unreported alterations in transcription factor (TF) regulation. More specifically, cell cycle genes are over-expressed in cell lines compared to primary tissues, and this alteration in expression is a result of less repressive TF targeting. We confirmed these regulatory changes for four TFs, including SMAD5, using independent ChIP-seq data from ENCODE. CONCLUSIONS Our results provide novel insights into the regulatory mechanisms controlling the expression differences between cell lines and tissues. The strong changes in TF regulation that we observe suggest that network changes, in addition to transcriptional levels, should be considered when using cell lines as models for tissues.
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Affiliation(s)
- Camila M. Lopes-Ramos
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Joseph N. Paulson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Cho-Yi Chen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Marieke L. Kuijjer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Maud Fagny
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - John Platig
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Abhijeet R. Sonawane
- Channing Division of Network Medicine, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Kimberly Glass
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA USA
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Fischer M, Müller GA. Cell cycle transcription control: DREAM/MuvB and RB-E2F complexes. Crit Rev Biochem Mol Biol 2017; 52:638-662. [PMID: 28799433 DOI: 10.1080/10409238.2017.1360836] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The precise timing of cell cycle gene expression is critical for the control of cell proliferation; de-regulation of this timing promotes the formation of cancer and leads to defects during differentiation and development. Entry into and progression through S phase requires expression of genes coding for proteins that function in DNA replication. Expression of a distinct set of genes is essential to pass through mitosis and cytokinesis. Expression of these groups of cell cycle-dependent genes is regulated by the RB pocket protein family, the E2F transcription factor family, and MuvB complexes together with B-MYB and FOXM1. Distinct combinations of these transcription factors promote the transcription of the two major groups of cell cycle genes that are maximally expressed either in S phase (G1/S) or in mitosis (G2/M). In this review, we discuss recent work that has started to uncover the molecular mechanisms controlling the precisely timed expression of these genes at specific cell cycle phases, as well as the repression of the genes when a cell exits the cell cycle.
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Affiliation(s)
- Martin Fischer
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany.,b Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA.,c Department of Medicine, Brigham and Women's Hospital , Harvard Medical School , Boston , MA , USA
| | - Gerd A Müller
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany
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Fortes MRS, Nguyen LT, Weller MMDCA, Cánovas A, Islas-Trejo A, Porto-Neto LR, Reverter A, Lehnert SA, Boe-Hansen GB, Thomas MG, Medrano JF, Moore SS. Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers. J Anim Sci 2017; 94:3693-3702. [PMID: 27898892 DOI: 10.2527/jas.2016-0471] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Puberty onset is a developmental process influenced by genetic determinants, environment, and nutrition. Mutations and regulatory gene networks constitute the molecular basis for the genetic determinants of puberty onset. The emerging knowledge of these genetic determinants presents opportunities for innovation in the breeding of early pubertal cattle. This paper presents new data on hypothalamic gene expression related to puberty in (Brahman) in age- and weight-matched heifers. Six postpubertal heifers were compared with 6 prepubertal heifers using whole-genome RNA sequencing methodology for quantification of global gene expression in the hypothalamus. Five transcription factors (TF) with potential regulatory roles in the hypothalamus were identified in this experiment: , , , , and . These TF genes were significantly differentially expressed in the hypothalamus of postpubertal versus prepubertal heifers and were also identified as significant according to the applied regulatory impact factor metric ( < 0.05). Two of these 5 TF, and , were zinc fingers, belonging to a gene family previously reported to have a central regulatory role in mammalian puberty. The gene belongs to the family of homologues of Drosophila sine oculis () genes implicated in transcriptional regulation of gonadotrope gene expression. Tumor-related genes such as and are known to affect basic cellular processes that are relevant in both cancer and developmental processes. Mutations in were associated with puberty in humans. Mutations in these TF, together with other genetic determinants previously discovered, could be used in genomic selection to predict the genetic merit of cattle (i.e., the likelihood of the offspring presenting earlier than average puberty for Brahman). Knowledge of key mutations involved in genetic traits is an advantage for genomic prediction because it can increase its accuracy.
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