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Hoshii T, Kikuchi S, Kujirai T, Masuda T, Ito T, Yasuda S, Matsumoto M, Rahmutulla B, Fukuyo M, Murata T, Kurumizaka H, Kaneda A. BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A. Nucleic Acids Res 2024; 52:9463-9480. [PMID: 38989615 PMCID: PMC11381347 DOI: 10.1093/nar/gkae605] [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: 03/18/2024] [Revised: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
The H3K4 methyltransferase SETD1A plays an essential role in both development and cancer. However, essential components involved in SETD1A chromatin binding remain unclear. Here, we discovered that BOD1L exhibits the highest correlated SETD1A co-dependency in human cancer cell lines. BOD1L knockout reduces leukemia cells in vitro and in vivo, and mimics the transcriptional profiles observed in SETD1A knockout cells. The loss of BOD1L immediately reduced SETD1A distribution at transcriptional start sites (TSS), induced transcriptional elongation defect, and increased the RNA polymerase II content at TSS; however, it did not reduce H3K4me3. The Shg1 domain of BOD1L has a DNA binding ability, and a tryptophan residue (W104) in the domain recruits SETD1A to chromatin through the association with SETD1A FLOS domain. In addition, the BOD1L-SETD1A complex associates with transcriptional regulators, including E2Fs. These results reveal that BOD1L mediates chromatin and SETD1A, and regulates the non-canonical function of SETD1A in transcription.
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Affiliation(s)
- Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Sota Kikuchi
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takeshi Masuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Tomoko Ito
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba-shi, Chiba 263-8522, Japan
| | - Makoto Matsumoto
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba-shi, Chiba 263-8522, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
- Health and Disease Omics Center, Chiba University, Chiba-shi, Chiba 260-8670, Japan
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Sinha P, Bhardwaj V, Muniyasamy A, Mohan KV, Jain K, Chaudhary K, Upadhyay P. Monocyte Transcriptome in Different Phases of Chronic Hepatitis B Virus Infection Uncovers Potential Functional Roles. Viral Immunol 2024; 37:287-297. [PMID: 39049796 DOI: 10.1089/vim.2024.0006] [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] [Indexed: 07/27/2024] Open
Abstract
The hepatitis B virus (HBV) chronic infection goes through different phases, i.e., immune tolerant (IT), immune clearance (IC), and inactive carrier (IN) resulting from the interplay of viral replication and immune response. Although the adaptive immune response is central to viral control, roles of the innate immune cells are less prominent. We explored monocyte transcriptome in these different phases of HBV infection to understand the nature of its involvement and identify unique differentially expressed genes (DEGs) in each phase. CD14+ peripheral blood monocytes were isolated from patients in the IT, IC, and IN phases and from healthy subjects and their RNA was sequenced. The significant DEGs were studied through gene annotation databases to understand differentially modulated pathways. The DEGs were further validated by qRT-PCR to identify genes that were uniquely expressed in each phase. It was found that TNFRSF12A was upregulated in all the HBV samples. The IN phase had six uniquely upregulated genes, i.e., PI3, EMP1, STX1A, RRAD, SPINK1, and SNORD3B-2. E2F7 was most consistently downregulated in the IT phase, and in the IC phase, IL23A and PI3 were specifically downregulated. Cut-off values were generated by ROC curve analysis to differentiate between the groups based on their expression levels. The monocyte functions are majorly suppressed in the IT and IC phases and are, however, somewhat metabolically active in the IN phase.
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Affiliation(s)
| | - Vaishali Bhardwaj
- Department of Gastroenterology, Dr. Ram Mahohar Lohia Hospital, New Delhi, India
| | | | | | - Kshama Jain
- National Institute of Immunology, New Delhi, India
| | - Kiran Chaudhary
- Department of Transfusion Medicine, Dr. Ram Mahohar Lohia Hospital, New Delhi, India
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Sánchez-Ramón S, Fuentes-Antrás J, Rider NL, Pérez-Segura P, de la Fuente-Muñoz E, Fernández-Arquero M, Neves E, Pérez de Diego R, Ocaña A, Guevara-Hoyer K. Exploring gastric cancer genetics: A turning point in common variable immunodeficiency. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100203. [PMID: 38283086 PMCID: PMC10818086 DOI: 10.1016/j.jacig.2023.100203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 01/30/2024]
Abstract
Background Gastric cancer (GC) stands as a prominent cause of cancer-related mortality and ranks second among the most frequently diagnosed malignancies in individuals with common variable immunodeficiency (CVID). Objective We sought to conduct a comprehensive, large-scale genetic analysis to explore the CVID-associated germline variant landscape within gastric adenocarcinoma samples and to seek to delineate the transcriptomic similarities between GC and CVID. Methods We investigated the presence of CVID-associated germline variants in 1591 GC samples and assessed their impact on tumor mutational load. The progression of GC was evaluated in patients with and without these variants. Transcriptomic similarities were explored by matching differentially expressed genes in GC to healthy gastric tissue with a CVID transcriptomic signature. Results CVID-associated germline variants were found in 60% of GC samples. Our analysis revealed a significant association between the presence of CVID-related genetic variants and higher tumor mutational load in GC (P < .0001); high GC mutational load seems to be linked to immunotherapy response and worse prognosis. Transcriptomic similarities unveiled key genes and pathways implicated in innate immune responses and tumorigenesis. We identified upregulated genes related to oncogene drivers, inflammation, tumor suppression, DNA repair, and downregulated immunomodulatory genes shared between GC and CVID. Conclusions Our findings contribute to a deeper understanding of potential molecular modulators of GC and shed light on the intricate interplay between immunodeficiency and cancer. This study underscores the clinical relevance of CVID-related variants in influencing GC progression and opens avenues for further exploration into novel therapeutic approaches.
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Affiliation(s)
- Silvia Sánchez-Ramón
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Jesús Fuentes-Antrás
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Department of Medical Oncology, IdSSC, San Carlos University Hospital, and CIBERONC, Madrid, Spain
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nicholas L. Rider
- Division of Clinical Informatics, Pediatrics, Allergy and Immunology, Liberty University College of Osteopathic Medicine and Collaborative Health Partners, Lynchburg, Va
| | - Pedro Pérez-Segura
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
| | - Eduardo de la Fuente-Muñoz
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Miguel Fernández-Arquero
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Esmeralda Neves
- Department of Immunology, Centro Hospitalar e Universitário de Santo António, Porto, Portugal
| | - Rebeca Pérez de Diego
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Alberto Ocaña
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Department of Medical Oncology, IdSSC, San Carlos University Hospital, and CIBERONC, Madrid, Spain
| | - Kissy Guevara-Hoyer
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
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Meng J, Qian W, Yang Z, Gong L, Xu D, Huang H, Jiang X, Pu Z, Yin Y, Zou J. p53/E2F7 axis promotes temozolomide chemoresistance in glioblastoma multiforme. BMC Cancer 2024; 24:317. [PMID: 38454344 PMCID: PMC10921682 DOI: 10.1186/s12885-024-12017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is the most aggressive form of brain cancer, and chemoresistance poses a significant challenge to the survival and prognosis of GBM. Although numerous regulatory mechanisms that contribute to chemoresistance have been identified, many questions remain unanswered. This study aims to identify the mechanism of temozolomide (TMZ) resistance in GBM. METHODS Bioinformatics and antibody-based protein detection were used to examine the expression of E2F7 in gliomas and its correlation with prognosis. Additionally, IC50, cell viability, colony formation, apoptosis, doxorubicin (Dox) uptake, and intracranial transplantation were used to confirm the role of E2F7 in TMZ resistance, using our established TMZ-resistance (TMZ-R) model. Western blot and ChIP experiments provided confirmation of p53-driven regulation of E2F7. RESULTS Elevated levels of E2F7 were detected in GBM tissue and were correlated with a poor prognosis for patients. E2F7 was found to be upregulated in TMZ-R tumors, and its high levels were linked to increased chemotherapy resistance by limiting drug uptake and decreasing DNA damage. The expression of E2F7 was also found to be regulated by the activation of p53. CONCLUSIONS The high expression of E2F7, regulated by activated p53, confers chemoresistance to GBM cells by inhibiting drug uptake and DNA damage. These findings highlight the significant connection between sustained p53 activation and GBM chemoresistance, offering the potential for new strategies to overcome this resistance.
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Affiliation(s)
- Jiao Meng
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Wei Qian
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Department of Clinical Laborator, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, 215300, Suzhou, Jiangsu, China
| | - Zhenkun Yang
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Lingli Gong
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Daxing Xu
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Hongbo Huang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, 214063, Wuxi, China
| | - Xinyi Jiang
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
| | - Ying Yin
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
| | - Jian Zou
- Department of Laboratory Medicine, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
- Center of Clinical Research, Wuxi People's Hospital, Wuxi Medical Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Nanjing Medical University, 214023, Wuxi, Jiangsu, China.
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Liu Z, Feng C, Li C, He T, Wu G, Fu C, Li H, Shen M, Liu H. IGF-I protects porcine granulosa cells from hypoxia-induced apoptosis by promoting homologous recombination repair through the PI3K/AKT/E2F8/RAD51 pathway. FASEB J 2024; 38:e23332. [PMID: 38095232 DOI: 10.1096/fj.202301464r] [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: 07/18/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Severe hypoxia induced by vascular compromise (ovarian torsion, surgery), obliteration of vessels (aging, chemotherapy, particularly platinum drugs) can cause massive follicle atresia. On the other hand, hypoxia increases the occurrence of DNA double-strand breaks (DSBs) and triggers cellular damage repair mechanisms; however, if the damage is not promptly repaired, it can also induce the apoptosis program. Insulin-like growth factor-I (IGF-I) is a polypeptide hormone that plays essential roles in stimulating mammalian follicular development. Here, we report a novel role for IGF-I in protecting hypoxic GCs from apoptosis by promoting DNA repair through the homologous recombination (HR) process. Indeed, the hypoxic environment within follicles significantly inhibited the efficiency of HR-directed DNA repair. The presence of IGF-I-induced HR pathway to alleviate hypoxia-induced DNA damage and apoptosis primarily through upregulating the expression of the RAD51 recombinase. Importantly, we identified a new transcriptional regulator of RAD51, namely E2F8, which mediates the protective effects of IGF-I on hypoxic GCs by facilitating the transcriptional activation of RAD51. Furthermore, we demonstrated that the PI3K/AKT pathway is crucial for IGF-I-induced E2F8 expression, resulting in increased RAD51 expression and enhanced HR activity, which mitigates hypoxia-induced DNA damage and thereby protects against GCs apoptosis. Together, these findings define a novel mechanism of IGF-I-mediated GCs protection by activating the HR repair through the PI3K/AKT/E2F8/RAD51 pathway under hypoxia.
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Affiliation(s)
- Zhaojun Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chengyu Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Tong He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Gang Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chen Fu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hongmin Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ming Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Ulaganathan K, Puranam K, Mukta S, Hanumanth SR. Expression profiling of luminal B breast tumor in Indian women. J Cancer Res Clin Oncol 2023; 149:13645-13664. [PMID: 37516983 DOI: 10.1007/s00432-023-05195-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
PURPOSE In this study, we aimed at profiling of luminal B breast cancer specific gene expression pattern in Indian women using mRNA-seq and validation based on TCGA expression data. METHODS RNA isolated from luminal B tumor and adjacent normal tissues was used for library construction and sequencing. Reference-based assemblies of these reads were used for differential gene expression analysis using DeSeq2. The DEGs were evaluated using TCGA expression data. Kaplan-Meier survival method was used to evaluate association between genes showing luminal B specific differential expression pattern and breast cancer prognosis and statistical significance was assessed using log-rank test. Alternate splicing analysis was done using rmats. RESULTS Differential expression analysis identified 2371 differentially expressed genes (DEGs) in luminal B breast tumors in comparison with adjacent normal tissues of Indian Women. Of them, 1692 DEGs were validated using TCGA luminal B paired samples. Integration of this data with the DEGs obtained by comparative analysis of unpaired luminal B with luminal A unpaired samples from TCGA resulted in 291 DEGs showing luminal B specific expression pattern. Further, 26 genes of prognostic value were identified. Differential splicing analysis between luminal B tumors and adjacent normal tissues in our cohort led to the identification of 687 genes showing significant differential alternate splicing events. CONCLUSION This study profiled gene expression pattern of luminal B tumors of Indian women and identified 26 key genes of prognostic value for luminal B breast cancer. This study also profiled differential alternate splicing and identified important alternate splicing events in luminal B breast cancer.
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Affiliation(s)
| | - Kaushik Puranam
- Department of Genetics, Osmania University, Hyderabad, Telangana, 500007, India
| | - Srinivasulu Mukta
- Department of Surgical Oncology, MNJ Institute of Oncology and RCC, Hyderabad, Telangana, India
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Liu N, Jing Z, Wen-Qi D, Ting-Ting L, Cong W, Li-Na H, Feng-Ying Y, Hong-Wei Y, Di G. Natural compound So-2 suppresses triple-negative breast cancer through inducing ferroptosis via downregulating transcription factor E2F7. Arch Biochem Biophys 2023; 744:109694. [PMID: 37481196 DOI: 10.1016/j.abb.2023.109694] [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: 04/11/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Triple-negative breast cancer (TNBC), accounting for about 15∼18% of all breast cancers, is notorious for its poor prognosis, high rate of relapse and short overall survival. Because of lacking effective therapeutic targets or drugs, treatment of TNBC in clinical encounters great obstacle. Siegesbeckiaorientalis L. have been used as a traditional Chinese medicine "Xi-Xian-Cao" for centuries with multiple medicinal benefits including cancerous treatment. We have reported the isolation of twenty-seven germacranolides including So-2 from the aerial parts of S. orientalis with potent cytotoxicity against breast cancer cells. The studyaims to verified the anti-TNBC function of the natural compound So-2 both in vitro and vivo and uncover the underlying mechanism. The results showed that So-2 caused cell cycle arrest and suppress TNBC cell proliferation and migration. Also, So-2 was first identified to be a bona fide ferroptosis inducer in TNBC cells. So-2 effectively suppressed tumor growth of TNBC by using an orthotopic transplantation tumor model. We also characterized the oncogenic role of the transcription factor E2F7 in TNBC. E2F7 was demonstrated to be involved in the ferroptosis-inducing and tumor suppression effect of So-2. Altogether, So-2 exhibits inhibitory effect on TNBC both in vitro and vivo by inducing TNBC ferroptosis via downregulating the expression of E2F7. These findings provide valuable insight into the pathogenesis of TNBC. The natural compound So-2, isolated from Chinese traditional medicine, might be a prospective drug candidate in TNBC therapy.
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Affiliation(s)
- Na Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250024, China
| | - Zhang Jing
- School of Biological Science and Technology, University of Jinan, Jinan, 250024, China
| | - Duan Wen-Qi
- School of Biological Science and Technology, University of Jinan, Jinan, 250024, China
| | - Luo Ting-Ting
- School of Biological Science and Technology, University of Jinan, Jinan, 250024, China
| | - Wu Cong
- School of Biological Science and Technology, University of Jinan, Jinan, 250024, China
| | - Han Li-Na
- School of Biological Science and Technology, University of Jinan, Jinan, 250024, China
| | - Yang Feng-Ying
- School of Biological Science and Technology, University of Jinan, Jinan, 250024, China
| | - Yue Hong-Wei
- Department of Emergency Medicine, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital, Shandong University, Jinan, China.
| | - Ge Di
- School of Biological Science and Technology, University of Jinan, Jinan, 250024, China.
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8
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Lin KH, Lee SC, Dacheux MA, Norman DD, Balogh A, Bavaria M, Lee H, Tigyi G. E2F7 drives autotaxin/Enpp2 transcription via chromosome looping: Repression by p53 in murine but not in human carcinomas. FASEB J 2023; 37:e23058. [PMID: 37358838 PMCID: PMC10364077 DOI: 10.1096/fj.202300838r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/31/2023] [Accepted: 06/13/2023] [Indexed: 06/27/2023]
Abstract
Dysregulation of the autotaxin (ATX, Enpp2)-lysophosphatidic acid (LPA) signaling in cancerous cells contributes to tumorigenesis and therapy resistance. We previously found that ATX activity was elevated in p53-KO mice compared to wild-type (WT) mice. Here, we report that ATX expression was upregulated in mouse embryonic fibroblasts from p53-KO and p53R172H mutant mice. ATX promoter analysis combined with yeast one-hybrid testing revealed that WT p53 directly inhibits ATX expression via E2F7. Knockdown of E2F7 reduced ATX expression and chromosome immunoprecipitation showed that E2F7 promotes Enpp2 transcription through cooperative binding to two E2F7 sites (promoter region -1393 bp and second intron 996 bp). Using chromosome conformation capture, we found that chromosome looping brings together the two E2F7 binding sites. We discovered a p53 binding site in the first intron of murine Enpp2, but not in human ENPP2. Binding of p53 disrupted the E2F7-mediated chromosomal looping and repressed Enpp2 transcription in murine cells. In contrast, we found no disruption of E2F7-mediated ENPP2 transcription via direct p53 binding in human carcinoma cells. In summary, E2F7 is a common transcription factor that upregulates ATX in human and mouse cells but is subject to steric interference by direct intronic p53 binding only in mice.
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Affiliation(s)
- Kuan-Hung Lin
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Sue Chin Lee
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Mélanie A Dacheux
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Derek D Norman
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Andrea Balogh
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Mitul Bavaria
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
| | - Hsinyu Lee
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Gabor Tigyi
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee, USA
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
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Gugnoni M, Lorenzini E, Faria do Valle I, Remondini D, Castellani G, Torricelli F, Sauta E, Donati B, Ragazzi M, Ghini F, Piana S, Ciarrocchi A, Manzotti G. Adding pieces to the puzzle of differentiated-to-anaplastic thyroid cancer evolution: the oncogene E2F7. Cell Death Dis 2023; 14:99. [PMID: 36765037 PMCID: PMC9918458 DOI: 10.1038/s41419-023-05603-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 02/12/2023]
Abstract
Anaplastic Thyroid Cancer (ATC) is the most aggressive and de-differentiated subtype of thyroid cancer. Many studies hypothesized that ATC derives from Differentiated Thyroid Carcinoma (DTC) through a de-differentiation process triggered by specific molecular events still largely unknown. E2F7 is an atypical member of the E2F family. Known as cell cycle inhibitor and keeper of genomic stability, in specific contexts its function is oncogenic, guiding cancer progression. We performed a meta-analysis on 279 gene expression profiles, from 8 Gene Expression Omnibus patient samples datasets, to explore the causal relationship between DTC and ATC. We defined 3 specific gene signatures describing the evolution from normal thyroid tissue to DTC and ATC and validated them in a cohort of human surgically resected ATCs collected in our Institution. We identified E2F7 as a key player in the DTC-ATC transition and showed in vitro that its down-regulation reduced ATC cells' aggressiveness features. RNA-seq and ChIP-seq profiling allowed the identification of the E2F7 specific gene program, which is mainly related to cell cycle progression and DNA repair ability. Overall, this study identified a signature describing DTC de-differentiation toward ATC subtype and unveiled an E2F7-dependent transcriptional program supporting this process.
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Affiliation(s)
- Mila Gugnoni
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Eugenia Lorenzini
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | | | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Elisabetta Sauta
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Moira Ragazzi
- Pathology Unit, Department of Oncology and Advanced Technologies, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesco Ghini
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Simonetta Piana
- Pathology Unit, Department of Oncology and Advanced Technologies, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy.
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL - IRCCS di Reggio Emilia, Reggio Emilia, Italy.
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10
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Hamidi AA, Taghehchian N, Basirat Z, Zangouei AS, Moghbeli M. MicroRNAs as the critical regulators of cell migration and invasion in thyroid cancer. Biomark Res 2022; 10:40. [PMID: 35659780 PMCID: PMC9167543 DOI: 10.1186/s40364-022-00382-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/07/2022] [Indexed: 12/14/2022] Open
Abstract
Thyroid cancer (TC) is one of the most frequent endocrine malignancies that is more common among females. Tumor recurrence is one of the most important clinical manifestations in differentiated TC which is associated with different factors including age, tumor size, and histological features. Various molecular processes such as genetic or epigenetic modifications and non-coding RNAs are also involved in TC progression and metastasis. The epithelial-to-mesenchymal transition (EMT) is an important biological process during tumor invasion and migration that affects the initiation and transformation of early-stage tumors into invasive malignancies. A combination of transcription factors, growth factors, signaling pathways, and epigenetic regulations affect the thyroid cell migration and EMT process. MicroRNAs (miRNAs) are important molecular factors involved in tumor metastasis by regulation of EMT-activating signaling pathways. Various miRNAs are involved in the signaling pathways associated with TC metastasis which can be used as diagnostic and therapeutic biomarkers. Since, the miRNAs are sensitive, specific, and non-invasive, they can be suggested as efficient and optimal biomarkers of tumor invasion and metastasis. In the present review, we have summarized all of the miRNAs which have been significantly involved in thyroid tumor cells migration and invasion. We also categorized all of the reported miRNAs based on their cellular processes to clarify the molecular role of miRNAs during thyroid tumor cell migration and invasion. This review paves the way of introducing a non-invasive diagnostic and prognostic panel of miRNAs in aggressive and metastatic TC patients.
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Affiliation(s)
- Amir Abbas Hamidi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Negin Taghehchian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Basirat
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Sadra Zangouei
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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11
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Glathar AR, Oyelakin A, Gluck C, Bard J, Sinha S. p63 Directs Subtype-Specific Gene Expression in HPV+ Head and Neck Squamous Cell Carcinoma. Front Oncol 2022; 12:879054. [PMID: 35712470 PMCID: PMC9192977 DOI: 10.3389/fonc.2022.879054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/19/2022] [Indexed: 11/22/2022] Open
Abstract
The complex heterogeneity of head and neck squamous cell carcinoma (HNSCC) reflects a diverse underlying etiology. This heterogeneity is also apparent within Human Papillomavirus-positive (HPV+) HNSCC subtypes, which have distinct gene expression profiles and patient outcomes. One aggressive HPV+ HNSCC subtype is characterized by elevated expression of genes involved in keratinization, a process regulated by the oncogenic transcription factor ΔNp63. Furthermore, the human TP63 gene locus is a frequent HPV integration site and HPV oncoproteins drive ΔNp63 expression, suggesting an unexplored functional link between ΔNp63 and HPV+ HNSCC. Here we show that HPV+ HNSCCs can be molecularly stratified according to ΔNp63 expression levels and derive a ΔNp63-associated gene signature profile for such tumors. We leveraged RNA-seq data from p63 knockdown cells and ChIP-seq data for p63 and histone marks from two ΔNp63high HPV+ HNSCC cell lines to identify an epigenetically refined ΔNp63 cistrome. Our integrated analyses reveal crucial ΔNp63-bound super-enhancers likely to mediate HPV+ HNSCC subtype-specific gene expression that is anchored, in part, by the PI3K-mTOR pathway. These findings implicate ΔNp63 as a key regulator of essential oncogenic pathways in a subtype of HPV+ HNSCC that can be exploited as a biomarker for patient stratification and treatment choices.
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12
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Al Hrout A, Cervantes-Gracia K, Chahwan R, Amin A. Modelling liver cancer microenvironment using a novel 3D culture system. Sci Rep 2022; 12:8003. [PMID: 35568708 PMCID: PMC9107483 DOI: 10.1038/s41598-022-11641-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/27/2022] [Indexed: 12/22/2022] Open
Abstract
The tumor microenvironment and its contribution to tumorigenesis has been a focal highlight in recent years. A two-way communication between the tumor and the surrounding microenvironment sustains and contributes to the growth and metastasis of tumors. Progression and metastasis of hepatocellular carcinoma (HCC) have been reported to be exceedingly influenced by diverse microenvironmental cues. In this study, we present a 3D-culture model of liver cancer to better mimic in vivo tumor settings. By creating novel 3D co-culture model that combines free-floating and scaffold-based 3D-culture techniques of liver cancer cells and fibroblasts, we aimed to establish a simple albeit reproducible ex vivo cancer microenvironment model that captures tumor-stroma interactions. The model presented herein exhibited unique gene expression and protein expression profiles when compared to 2D and 3D mono-cultures of liver cancer cells. Our results showed that in vivo like conditions cannot be mimicked by simply growing cancer cells as spheroids, but by co-culturing them with 3D fibroblast with which they were able to crosstalk. This was evident by the upregulation of several pathways involved in HCC, and the increase in secreted factors by co-cultured cancer cells, many of which are also involved in tumor-stroma interactions. Compared to the conventional 2D culture, the proposed model exhibits an increase in the expression of genes associated with development, progression, and poor prognosis of HCC. Our results correlated with an aggressive outcome that better mirrors in vivo HCC, and therefore, a more reliable platform for molecular understanding of HCC.
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Affiliation(s)
- Ala'a Al Hrout
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, United Arab Emirates
| | - Karla Cervantes-Gracia
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| | - Amr Amin
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, United Arab Emirates.
- The University of Chicago, Chicago, IL, 60637, USA.
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13
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Delgadillo DM, Céspedes-Cruz AI, Ríos-Castro E, Rodríguez Maldonado MG, López-Nogueda M, Márquez-Gutiérrez M, Villalobos-Manzo R, Ramírez-Reyes L, Domínguez-Fuentes M, Tapia-Ramírez J. Differential Expression of Proteins in an Atypical Presentation of Autoimmune Lymphoproliferative Syndrome. Int J Mol Sci 2022; 23:5366. [PMID: 35628184 PMCID: PMC9140392 DOI: 10.3390/ijms23105366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023] Open
Abstract
Autoimmune lymphoproliferative syndrome (ALPS) is a rare disease defined as a defect in the lymphocyte apoptotic pathway. Currently, the diagnosis of ALPS is based on clinical aspects, defective lymphocyte apoptosis and mutations in Fas, FasL and Casp 10 genes. Despite this, ALPS has been misdiagnosed. The aim of this work was to go one step further in the knowledge of the disease, through a molecular and proteomic analysis of peripheral blood mononuclear cells (PBMCs) from two children, a 13-year-old girl and a 6-year-old boy, called patient 1 and patient 2, respectively, with clinical data supporting the diagnosis of ALPS. Fas, FasL and Casp10 genes from both patients were sequenced, and a sample of the total proteins from patient 1 was analyzed by label-free proteomics. Pathway analysis of deregulated proteins from PBMCs was performed on the STRING and PANTHER bioinformatics databases. A mutation resulting in an in-frame premature stop codon and protein truncation was detected in the Fas gene from patient 2. From patient 1, the proteomic analysis showed differences in the level of expression of proteins involved in, among other processes, cell cycle, regulation of cell cycle arrest and immune response. Noticeably, the most down-regulated protein is an important regulator of the cell cycle process. This could be an explanation of the disease in patient 1.
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Affiliation(s)
- Dulce María Delgadillo
- Unidad de Genómica, Proteómica y Metabolómica, Laboratorio Nacional de Servicios Experimentales (LaNSE), Centro de Investigación y de Estudios Avanzados, Mexico City 07360, CP, Mexico
| | - Adriana Ivonne Céspedes-Cruz
- Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional La Raza Hospital General, Mexico City 02990, CP, Mexico
| | - Emmanuel Ríos-Castro
- Unidad de Genómica, Proteómica y Metabolómica, Laboratorio Nacional de Servicios Experimentales (LaNSE), Centro de Investigación y de Estudios Avanzados, Mexico City 07360, CP, Mexico
| | | | - Mariel López-Nogueda
- Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional La Raza Hospital General, Mexico City 02990, CP, Mexico
| | - Miguel Márquez-Gutiérrez
- Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional La Raza Hospital General, Mexico City 02990, CP, Mexico
| | - Rocío Villalobos-Manzo
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados, Mexico City 07360, CP, Mexico
| | - Lorena Ramírez-Reyes
- Unidad de Genómica, Proteómica y Metabolómica, Laboratorio Nacional de Servicios Experimentales (LaNSE), Centro de Investigación y de Estudios Avanzados, Mexico City 07360, CP, Mexico
| | - Misael Domínguez-Fuentes
- Unidad de Genómica, Proteómica y Metabolómica, Laboratorio Nacional de Servicios Experimentales (LaNSE), Centro de Investigación y de Estudios Avanzados, Mexico City 07360, CP, Mexico
| | - José Tapia-Ramírez
- Unidad de Genómica, Proteómica y Metabolómica, Laboratorio Nacional de Servicios Experimentales (LaNSE), Centro de Investigación y de Estudios Avanzados, Mexico City 07360, CP, Mexico
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados, Mexico City 07360, CP, Mexico
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14
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Zhang ZM, Cao HB, Li ZH, Zhuo R, Tao YF, Li XL, Li G, Liao XM, Fang F, Xie Y, Wu D, Wang HR, Wang JW, Chen YL, Yu JJ, Jia SQ, Yang RD, Guo XY, Yang Y, Feng CX, Xu YY, Qian GH, Pan J. SAPCD2 promotes neuroblastoma progression by altering the subcellular distribution of E2F7. Cell Death Dis 2022; 13:174. [PMID: 35197448 PMCID: PMC8866461 DOI: 10.1038/s41419-022-04624-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/23/2022] [Accepted: 02/07/2022] [Indexed: 11/16/2022]
Abstract
Recent studies uncovered the emerging roles of SAPCD2 (suppressor anaphase-promoting complex domain containing 2) in several types of human cancer. However, the functions and underlying mechanisms of SAPCD2 in the progression of neuroblastoma (NB) remain elusive. Herein, through integrative analysis of public datasets and regulatory network of GSK-J4, a small-molecule drug with anti-NB activity, we identified SAPCD2 as an appealing target with a high connection to poor prognosis in NB. SAPCD2 promoted NB progression in vitro and in vivo. Mechanistically, SAPCD2 could directly bind to cytoplasmic E2F7 but not E2F1, alter the subcellular distribution of E2F7 and regulate E2F activity. Among the E2F family members, the roles of E2F7 in NB are poorly understood. We found that an increasing level of nuclear E2F7 was induced by SAPCD2 knockdown, thereby affecting the expression of genes involved in the cell cycle and chromosome instability. In addition, Selinexor (KTP-330), a clinically available inhibitor of exportin 1 (XPO1), could induce nuclear accumulation of E2F7 and suppress the growth of NB. Overall, our studies suggested a previously unrecognized role of SAPCD2 in the E2F signaling pathway and a potential therapeutic approach for NB, as well as clues for understanding the differences in subcellular distribution of E2F1 and E2F7 during their nucleocytoplasmic shuttling.
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15
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Lang L, Pettkó-Szandtner A, Tunçay Elbaşı H, Takatsuka H, Nomoto Y, Zaki A, Dorokhov S, De Jaeger G, Eeckhout D, Ito M, Magyar Z, Bögre L, Heese M, Schnittger A. The DREAM complex represses growth in response to DNA damage in Arabidopsis. Life Sci Alliance 2021; 4:4/12/e202101141. [PMID: 34583930 PMCID: PMC8500230 DOI: 10.26508/lsa.202101141] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022] Open
Abstract
The DNA of all organisms is constantly damaged by physiological processes and environmental conditions. Upon persistent damage, plant growth and cell proliferation are reduced. Based on previous findings that RBR1, the only Arabidopsis homolog of the mammalian tumor suppressor gene retinoblastoma, plays a key role in the DNA damage response in plants, we unravel here the network of RBR1 interactors under DNA stress conditions. This led to the identification of homologs of every DREAM component in Arabidopsis, including previously not recognized homologs of LIN52. Interestingly, we also discovered NAC044, a mediator of DNA damage response in plants and close homolog of the major DNA damage regulator SOG1, to directly interact with RBR1 and the DREAM component LIN37B. Consistently, not only mutants in NAC044 but also the double mutant of the two LIN37 homologs and mutants for the DREAM component E2FB showed reduced sensitivities to DNA-damaging conditions. Our work indicates the existence of multiple DREAM complexes that work in conjunction with NAC044 to mediate growth arrest after DNA damage.
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Affiliation(s)
- Lucas Lang
- Department of Developmental Biology, University of Hamburg, Institute for Plant Sciences and Microbiology, Hamburg, Germany
| | - Aladár Pettkó-Szandtner
- Laboratory of Proteomic Research, Biological Research Centre, Szeged, Hungary.,Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Hasibe Tunçay Elbaşı
- Department of Developmental Biology, University of Hamburg, Institute for Plant Sciences and Microbiology, Hamburg, Germany
| | - Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Yuji Nomoto
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Ahmad Zaki
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, UK.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Stefan Dorokhov
- Department of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, UK
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Vlaams Instituut voor Biotechnologie (VIB) Center for Plant Systems Biology, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Vlaams Instituut voor Biotechnologie (VIB) Center for Plant Systems Biology, Ghent, Belgium
| | - Masaki Ito
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - László Bögre
- Vlaams Instituut voor Biotechnologie (VIB) Center for Plant Systems Biology, Ghent, Belgium
| | - Maren Heese
- Department of Developmental Biology, University of Hamburg, Institute for Plant Sciences and Microbiology, Hamburg, Germany
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Institute for Plant Sciences and Microbiology, Hamburg, Germany
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16
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Lu RJ, Taylor S, Contrepois K, Kim M, Bravo JI, Ellenberger M, Sampathkumar NK, Benayoun BA. Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex and age-related functional regulation. NATURE AGING 2021; 1:715-733. [PMID: 34514433 PMCID: PMC8425468 DOI: 10.1038/s43587-021-00086-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 06/10/2021] [Indexed: 12/18/2022]
Abstract
Neutrophils are the most abundant human white blood cell and constitute a first line of defense in the innate immune response. Neutrophils are short-lived cells, and thus the impact of organismal aging on neutrophil biology, especially as a function of biological sex, remains poorly understood. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male mice, at the transcriptomic, metabolomic and lipidomic levels. We identify widespread regulation of neutrophil 'omics' landscapes with organismal aging and biological sex. In addition, we leverage our resource to predict functional differences, including changes in neutrophil responses to activation signals. To date, this dataset represents the largest multi-omics resource for neutrophils across sex and ages. This resource identifies neutrophil characteristics which could be targeted to improve immune responses as a function of sex and/or age.
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Affiliation(s)
- Ryan J. Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Shalina Taylor
- Departments of Pediatrics and of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Nirmal K. Sampathkumar
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Present Address: UK-Dementia Research Institute, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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17
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Zhou B, Ge Y, Shao Q, Yang L, Chen X, Jiang G. Long noncoding RNA LINC00284 facilitates cell proliferation in papillary thyroid cancer via impairing miR-3127-5p targeted E2F7 suppression. Cell Death Discov 2021; 7:156. [PMID: 34226533 PMCID: PMC8257569 DOI: 10.1038/s41420-021-00551-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/05/2021] [Accepted: 05/26/2021] [Indexed: 12/21/2022] Open
Abstract
Accumulating evidence has suggested that long noncoding RNAs (lncRNAs) exert crucial modulation roles in the biological behaviors of multiple malignancies. Nonetheless, the specific function of lncRNA LINC00284 in papillary thyroid cancer (PTC) remains not fully understood. The objective of this research was to explore the influence of LINC00284 in PTC and elucidate its potential mechanism. The Cancer Genome Atlas (TCGA), gene expression omnibus (GEO) datasets were used to analyze LINC00284 expression differences in thyroid cancer and normal samples, followed by the verification of qRT-PCR in our own PTC and adjacent non-tumor tissues. The impacts of LINC00284 on PTC cell growth were detected in vitro via CCK-8, colony formation, EdU assays, and in vivo via a xenograft tumor model. Bioinformatics analyses and biological experiments were conducted to illuminate the molecular mechanism. We found that LINC00284 expression was remarkably increased in PTC tissues and its overexpression was closely correlated with larger tumor size. In addition, silencing LINC00284 could effectively attenuate PTC cell proliferation, induce apoptosis and G1 arrest in vitro, as well as suppress tumorigenesis in mouse xenografts. Mechanistic investigations showed that LINC00284 acted as a competing endogenous RNA (ceRNA) for miR-3127-5p, thus resulting in the disinhibition of its endogenous target E2F7. In short, our findings indicated that LINC00284–miR-3127-5p–E2F7 axis exerted oncogenic properties in PTC and may offer a new promising target for the diagnosis and therapy of PTC.
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Affiliation(s)
- Bin Zhou
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province, China.,Department of Thyroid and Breast Surgery, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, 214000, Jiangsu Province, China
| | - Yugang Ge
- Department of Thyroid and Breast Surgery, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, 214000, Jiangsu Province, China
| | - Qing Shao
- Department of Thyroid and Breast Surgery, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, 214000, Jiangsu Province, China
| | - Liyi Yang
- Department of Thyroid and Breast Surgery, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, 214000, Jiangsu Province, China
| | - Xin Chen
- Department of Thyroid and Breast Surgery, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, 214000, Jiangsu Province, China
| | - Guoqin Jiang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province, China.
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18
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Orhan E, Velazquez C, Tabet I, Sardet C, Theillet C. Regulation of RAD51 at the Transcriptional and Functional Levels: What Prospects for Cancer Therapy? Cancers (Basel) 2021; 13:2930. [PMID: 34208195 PMCID: PMC8230762 DOI: 10.3390/cancers13122930] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 01/07/2023] Open
Abstract
The RAD51 recombinase is a critical effector of Homologous Recombination (HR), which is an essential DNA repair mechanism for double-strand breaks. The RAD51 protein is recruited onto the DNA break by BRCA2 and forms homopolymeric filaments that invade the homologous chromatid and use it as a template for repair. RAD51 filaments are detectable by immunofluorescence as distinct foci in the cell nucleus, and their presence is a read out of HR proficiency. RAD51 is an essential gene, protecting cells from genetic instability. Its expression is low and tightly regulated in normal cells and, contrastingly, elevated in a large fraction of cancers, where its level of expression and activity have been linked with sensitivity to genotoxic treatment. In particular, BRCA-deficient tumors show reduced or obliterated RAD51 foci formation and increased sensitivity to platinum salt or PARP inhibitors. However, resistance to treatment sets in rapidly and is frequently based on a complete or partial restoration of RAD51 foci formation. Consequently, RAD51 could be a highly valuable therapeutic target. Here, we review the multiple levels of regulation that impact the transcription of the RAD51 gene, as well as the post-translational modifications that determine its expression level, recruitment on DNA damage sites and the efficient formation of homofilaments. Some of these regulation levels may be targeted and their impact on cancer cell survival discussed.
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Affiliation(s)
- Esin Orhan
- IRCM, Institut de Recherche en Cancérologie de Montpellier U1194 INSERM, Université de Montpellier, 34090 Montpellier, France; (E.O.); (I.T.); (C.S.)
| | | | - Imene Tabet
- IRCM, Institut de Recherche en Cancérologie de Montpellier U1194 INSERM, Université de Montpellier, 34090 Montpellier, France; (E.O.); (I.T.); (C.S.)
| | - Claude Sardet
- IRCM, Institut de Recherche en Cancérologie de Montpellier U1194 INSERM, Université de Montpellier, 34090 Montpellier, France; (E.O.); (I.T.); (C.S.)
| | - Charles Theillet
- IRCM, Institut de Recherche en Cancérologie de Montpellier U1194 INSERM, Université de Montpellier, 34090 Montpellier, France; (E.O.); (I.T.); (C.S.)
- ICM, Institut du Cancer de Montpellier, 34090 Montpellier, France;
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19
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Li L, Shi Q, Li Z, Gao J. Genome-wide identification and functional characterization of the PheE2F/DP gene family in Moso bamboo. BMC PLANT BIOLOGY 2021; 21:158. [PMID: 33781213 PMCID: PMC8008544 DOI: 10.1186/s12870-021-02924-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/11/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND E2F/DP proteins have been shown to regulate genes implicated in cell cycle control and DNA repair. However, to date, research into the potential role of the Moso bamboo E2F/DP family has been limited. RESULTS Here, we identified 23 E2F/DPs in the Moso bamboo genome, including nine E2F genes, six DP genes, eight DEL genes and one gene with a partial E2F domain. An estimation of the divergence time of the paralogous gene pairs suggested that the E2F/DP family expansion primarily occurred through a whole-genome duplication event. A regulatory element and coexpression network analysis indicated that E2F/DP regulated the expression of cell cycle-related genes. A yeast two-hybrid assay and expression analysis based on transcriptome data and in situ hybridization indicated that the PheE2F-PheDP complex played important roles in winter Moso bamboo shoot growth. The qRT-PCR results showed that the PheE2F/DPs exhibited diverse expression patterns in response to drought and salt treatment and diurnal cycles. CONCLUSION Our findings provide novel insights into the Moso bamboo E2F/DP family and partial experimental evidence for further functional verification of the PheE2F/DPs.
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Affiliation(s)
- Long Li
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhouqi Li
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, China.
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20
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Guo X, Liu L, Zhang Q, Yang W, Zhang Y. E2F7 Transcriptionally Inhibits MicroRNA-199b Expression to Promote USP47, Thereby Enhancing Colon Cancer Tumor Stem Cell Activity and Promoting the Occurrence of Colon Cancer. Front Oncol 2021; 10:565449. [PMID: 33489876 PMCID: PMC7819137 DOI: 10.3389/fonc.2020.565449] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022] Open
Abstract
microRNAs (miRNAs) can modulate the expression level of genes in a post-transcription manner, which are closely related to growth and metastasis of colon cancer. Herein, we aimed to explore how miR-199b influences colon cancer and to characterize its underlying molecular mechanism associating with E2F transcription factor 7 (E2F7). Assays of RT-qPCR, Western blot, and immunohistochemistry were utilized to detect the expression of E2F7 in the tissue samples collected from 30 patients diagnosed with colon cancer. Flow analysis was utilized to detect the ratio of ALDH1+ and CD133+ colon cancer stem cells. The interaction between E2F7, miR-199b, USP47, and MAPK was identified by ChIP-Seq analysis, luciferase reporter, RNA pull-down, co-immunoprecipitation, as well as glutathione-S-transferase (GST) pull-down experiments. Based on the gain- and loss-of-function approaches, the cellular functions of colon cancer cells by the E2F7-regulated miR-199b/USP47/MAPK axis were assessed. It was identified that E2F7 are expressed highly in the collected colon cancer tissues. E2F7 silencing reduced the production of ALDH1+ and CD133+ colon cancer stem cells and antagonized the effects of 5-fluorouracil (5-FU) treatment. Besides, the silencing of E2F7 was observed to suppress the oxidative stress, proliferation, migration, as well as invasion of ALDH1+ cells in vitro and tumorigenesis of colon cancer cells in vivo. Our findings reveal the pro-oncogenic effect of E2F7 on colon cancer development, highlighting E2F7 as a novel target for therapeutic strategy for colon cancer.
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Affiliation(s)
- Xiong Guo
- Department of Colorectal and Anal Surgery, Hepatobiliary and Enteric Surgery Center, Xiangya Hospital, Central South University, Changsha, China
| | - Ling Liu
- Hepatobiliary & Enteric Surgery Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Qi Zhang
- Hepatobiliary & Enteric Surgery Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Weiming Yang
- Hepatobiliary & Enteric Surgery Research Center, Xiangya Hospital of Central South University, Changsha, China
| | - Yang Zhang
- Department of Colorectal and Anal Surgery, Hepatobiliary and Enteric Surgery Center, Xiangya Hospital, Central South University, Changsha, China
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21
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Wang Y, Wo Y, Lu T, Sun X, Liu A, Dong Y, Du W, Su W, Huang Z, Jiao W. Circ-AASDH functions as the progression of early stage lung adenocarcinoma by targeting miR-140-3p to activate E2F7 expression. Transl Lung Cancer Res 2021; 10:57-70. [PMID: 33569293 PMCID: PMC7867743 DOI: 10.21037/tlcr-20-1062] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Lung adenocarcinoma (LUAD), which is the most common subtype of non-small cell lung cancer, is a leading course of cancer-related mortality worldwide. Recently, circular RNA (CircRNAs) has become a hot spot in cancer research because of its important role in tumorigenesis and development and its superior stability. This study aims to clarify the role of circ-AASDH in LUAD and explore its competitive endogenous RNA mechanism. Methods The circ-AASDH, miR-140-3p and E2F transcription factor 7 (E2F7) mRNA expression levels were detected via qRT-PCR. CCK-8 and colony formation assay were used to evaluate the ability of cell proliferation. Transwell assay and wound healing assay were performed to measure the invasion and migration ability. Flow cytometry was used to detect the apoptosis of cells. Moreover, Sanger sequencing, RNaseR treatment and divergent primers were used to verify the circular structure. Luciferase reporter and RNA pull-down experiment were performed to characterize the ceRNA mechanism of circ-AASDH. The xenograft model of mice was established to investigate the tumorigenicity of circ-AASDH to LUAD in vivo. Results By screening for differentially expressed circRNAs, we found that circ-AASDH was highly expressed in LUAD tissues and cells and correlated with tumor size, clinical stage and poor prognosis. Transfection of si-circ-AASDH can inhibit the proliferation and migration of LUAD cells and promote apoptosis in vitro. In mechanism, circ-AASDH could be used as a sponge of miR-140-3p to weaken its inhibition on the expression of E2F7. Additionally, the overexpression of circ-AASDH could deduce the suppression of miR-140-3p on the malignant progression of LUAD cells. Besides, silencing of circ-AASDH inhibited cell proliferation and migration by regulating the expression of E2F7. Furthermore, overexpression of circ-AASDH can promote the growth of LUAD in vivo. Conclusions Circ-AASDH/miR-140-3p/E2F7 regulating axis promoted the progression in LUAD. Our results provided ideas for understanding the biological mechanism of circ-AASDH and clarify potential therapeutic targets in LUAD.
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Affiliation(s)
- Yuanyong Wang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yang Wo
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiao Sun
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ao Liu
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yanting Dong
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenxing Du
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenhao Su
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhangfeng Huang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenjie Jiao
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
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22
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Moreno E, Toussaint MJ, van Essen SC, Bongiovanni L, van Liere EA, Koster MH, Yuan R, van Deursen JM, Westendorp B, de Bruin A. E2F7 Is a Potent Inhibitor of Liver Tumor Growth in Adult Mice. Hepatology 2021; 73:303-317. [PMID: 32259305 PMCID: PMC7898887 DOI: 10.1002/hep.31259] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 03/12/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Up-regulation of the E2F-dependent transcriptional network has been identified in nearly every human malignancy and is an important driver of tumorigenesis. Two members of the E2F family, E2F7 and E2F8, are potent repressors of E2F-dependent transcription. They are atypical in that they do not bind to dimerization partner proteins and are not controlled by retinoblastoma protein. The physiological relevance of E2F7 and E2F8 remains incompletely understood, largely because tools to manipulate their activity in vivo have been lacking. APPROACH AND RESULTS Here, we generated transgenic mice with doxycycline-controlled transcriptional activation of E2f7 and E2f8 and induced their expression during postnatal development, in adulthood, and in the context of cancer. Systemic induction of E2f7 and, to lesser extent, E2f8 transgenes in juvenile mice impaired cell proliferation, caused replication stress, DNA damage, and apoptosis, and inhibited animal growth. In adult mice, however, E2F7 and E2F8 induction was well tolerated, yet profoundly interfered with DNA replication, DNA integrity, and cell proliferation in diethylnitrosamine-induced liver tumors. CONCLUSION Collectively, our findings demonstrate that atypical E2Fs can override cell-cycle entry and progression governed by other E2F family members and suggest that this property can be exploited to inhibit proliferation of neoplastic hepatocytes when growth and development have subsided during adulthood.
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Affiliation(s)
- Eva Moreno
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Mathilda J.M. Toussaint
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Saskia C. van Essen
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Laura Bongiovanni
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Elsbeth A. van Liere
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Mirjam H. Koster
- Division Molecular GeneticsDepartment of PediatricsUniversity Medical Center GroningenUniversity of GroningenGroningenthe Netherlands
| | - Ruixue Yuan
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands,Department of PathologyAcademic Medical CenterAmsterdamthe Netherlands
| | - Jan M. van Deursen
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN,Department of Pediatric and Adolescent MedicineMayo ClinicRochesterMN
| | - Bart Westendorp
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Alain de Bruin
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands,Division Molecular GeneticsDepartment of PediatricsUniversity Medical Center GroningenUniversity of GroningenGroningenthe Netherlands
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Cheng C, Guo L, Ma Y, Wang Z, Fan X, Shan Z. Up-Regulation of miR-26a-5p Inhibits E2F7 to Regulate the Progression of Renal Carcinoma Cells. Cancer Manag Res 2020; 12:11723-11733. [PMID: 33235501 PMCID: PMC7680095 DOI: 10.2147/cmar.s271710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Background Metastasis is the main cause of renal cell carcinoma (RCC) tumor death, and effective inhibition of RCC metastasis is an essential means to meliorate the prognosis of RCC patients. MicroRNAs (miRs) have been proved to be stable and important biomarkers for several malignancies. This study is therefore set out to explore the metastasis-related miR and its mechanism in RCC. Methods The expression of miR- 26a -5p in RCC was analyzed using the expression profile in the Cancer Genome Atlas (TCGA). MiR-26a-5p and E2F transcription factor 7 (E2F7) in RCC patients were detected by qRT-PCR. Cell Counting Kit-8 (CCK-8) was adopted to assess cell proliferation, Transwell was utilized to evaluate migration and invasion, and flow cytometry (FC) was used to determine apoptosis. Mouse cell-derived and patient-derived xenotransplantation models were established to evaluate the effect of miR-26a-5p on tumor growth and metastasis in vivo. The molecular mechanism of miR-26a-5p was analyzed by dual-luciferase reporter (DLR) gene analysis, qRT-PCR, and Western blot (WB) both in vivo and in vitro. Results MiR-26a-5p was reduced in renal carcinoma cells and may serve as a biomarker for renal cancer metastasis and prognosis. MiR-26a-5p up-regulation inhibited migration and invasion in renal cell lines and tumor metastasis in vivo. Bioinformatics target prediction and RNA-seq results showed that E2F7 was among the targets of miR-26a-5p and was significantly inhibited by miR-26a-5p in vivo and in vitro. Conclusion MiR-26a-5p presents low expression in RCC and promotes RCC cell apoptosis and prevents cells from proliferating and invading by targeting E2F7, which is a promising therapeutic target for RCC.
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Affiliation(s)
- Chuanyu Cheng
- Department of Urology, People's Hospital of Zhengzhou, People's Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450014, People's Republic of China
| | - Liang Guo
- Department of Urology, People's Hospital of Zhengzhou, People's Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450014, People's Republic of China
| | - Yaohui Ma
- Department of Urology, People's Hospital of Zhengzhou, People's Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450014, People's Republic of China
| | - Zhe Wang
- Department of Urology, People's Hospital of Zhengzhou, People's Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450014, People's Republic of China
| | - Xinpeng Fan
- Department of Urology, People's Hospital of Zhengzhou, People's Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450014, People's Republic of China
| | - Zhongjie Shan
- Department of Urology, People's Hospital of Zhengzhou, People's Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan 450014, People's Republic of China
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24
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Teng F, Zhang JX, Chang QM, Wu XB, Tang WG, Wang JF, Feng JF, Zhang ZP, Hu ZQ. LncRNA MYLK-AS1 facilitates tumor progression and angiogenesis by targeting miR-424-5p/E2F7 axis and activating VEGFR-2 signaling pathway in hepatocellular carcinoma. J Exp Clin Cancer Res 2020; 39:235. [PMID: 33168027 PMCID: PMC7650167 DOI: 10.1186/s13046-020-01739-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are crucial in the invasion, angiogenesis, progression, and metastasis of hepatocellular carcinoma (HCC). The lncRNA MYLK-AS1 promotes the growth and invasion of HCC through the EGFR/HER2-ERK1/2 signaling pathway. However, the clinical significance of MYLK-AS1 in HCC still needs to be further determined. METHODS Bioinformatic analysis was performed to determine the potential relationship among MYLK-AS1, miRNAs and mRNAs. A total of 156 samples of normal liver and paired HCC tissues from HCC patients were used to evaluate MYLK-AS1 expression by qRT-PCR. Human HCC cell lines were used to evaluate the colony formation, cell proliferation, migration, invasion, cell cycle and apoptosis after transfection of lentiviral short-hairpin RNAs (shRNAs) targeting MYLK-AS1 or MYLK-AS1 vectors. The competitive endogenous RNA (ceRNA) mechanism was clarified using fluorescence in situ hybridization (FISH), Western blotting, qPCR, RNA binding protein immunoprecipitation (RIP), and dual luciferase reporter analysis. RESULTS MYLK-AS1 up-regulation was detected in the HCC tumor tissues and cell lines associated with the enhancement of the angiogenesis and tumor progression. The down-regulation of MYLK-AS1 reversed the effects on angiogenesis, proliferation, invasion and metastasis in the HCC cells and in vivo. MYLK-AS1 acted as ceRNA, capable of regulating the angiogenesis in HCC, while the microRNA miR-424-5p was the direct target of MYLK-AS1. Promoting the angiogenesis and the tumor proliferation, the complex MYLK-AS1/miR-424-5p activated the VEGFR-2 signaling through E2F7, whereas the specific targeting of E2F transcription factor 7 (E2F7) by miR-424-5p, was indicated by the mechanism studies. CONCLUSIONS MYLK-AS1 and E2F7 are closely related to some malignant clinicopathological features and prognosis of HCC, thus the MYLK-AS1/ miR-424-5p/E2F7 signaling pathway might represent a promising treatment strategy to combat HCC.
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MESH Headings
- Calcium-Binding Proteins/genetics
- Carcinoma, Hepatocellular/blood supply
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Disease Progression
- E2F7 Transcription Factor/metabolism
- Female
- Humans
- Liver Neoplasms/blood supply
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Male
- MicroRNAs/metabolism
- Middle Aged
- Myosin-Light-Chain Kinase/genetics
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/pathology
- Prognosis
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Long Noncoding/metabolism
- Signal Transduction
- Transfection
- Vascular Endothelial Growth Factor Receptor-2/metabolism
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Affiliation(s)
- Fei Teng
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
| | - Ju-Xiang Zhang
- Shanghai Med-X Engineering Center for Medical Equipment and Technology, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Qi-Meng Chang
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
| | - Xu-Bo Wu
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
| | - Wei-Guo Tang
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
| | - Jian-Fa Wang
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
| | - Jin-Feng Feng
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China
| | - Zi-Ping Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China.
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China.
| | - Zhi-Qiu Hu
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China.
- Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, 201199, People's Republic of China.
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25
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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease. Nat Genet 2020; 52:1024-1035. [PMID: 32989324 PMCID: PMC8098004 DOI: 10.1038/s41588-020-0696-0] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 08/20/2020] [Indexed: 12/19/2022]
Abstract
Protein aggregation is the hallmark of neurodegeneration but the molecular mechanisms underlying late-onset Alzheimer’s disease (AD) remain unclear. Here we integrated transcriptomic, proteomic and epigenomic analyses of post-mortem human brains to identify molecular pathways involved in AD. RNA-seq analysis revealed upregulation of transcription- and chromatin-related genes, including the histone acetyltransferases for H3K27ac and H3K9ac. An unbiased proteomic screening singled out H3K27ac and H3K9ac as main enrichments specific to AD. In turn, epigenomic profiling revealed gains of H3K27ac and H3K9ac linked to transcription, chromatin, and disease pathways in AD. Increasing genome-wide H3K27ac and H3K9ac in a fly model of AD exacerbated amyloid-β42-driven neurodegeneration. Together, these findings suggest that AD involves a reconfiguration of the epigenome, where H3K27ac and H3K9ac impact disease pathways by dysregulating transcription- and chromatin-gene feedback loops. The identification of this process highlights potential epigenetic strategies for early-stage disease treatment.
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Wang Y, Pei X, Xu P, Tan Z, Zhu Z, Zhang G, Jiang Z, Deng Z. E2F7, regulated by miR‑30c, inhibits apoptosis and promotes cell cycle of prostate cancer cells. Oncol Rep 2020; 44:849-862. [PMID: 32582990 PMCID: PMC7388350 DOI: 10.3892/or.2020.7659] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 03/10/2020] [Indexed: 01/01/2023] Open
Abstract
Prostate cancer (PCa) remains a leading cause of mortality among men in the United States and Western Europe. The molecular mechanism of PCa pathogenesis has not been fully elucidated. In the present study, the expression profile of E2F transcription factor 7 (E2F7) in PCa was examined using immunohistochemistry and reverse transcription‑quantitative PCR, whilst cell cycle progression and apoptosis were determined using fluorescent cell activated sorting techniques. Cell viability was measured using Cell Counting Kit‑8 in loss‑ and gain‑of‑function studies. Dual‑luciferase reporter assay was used to verify if E2F7 was one of the potential targets of miR‑30c. The staining score of E2F7 of PCa tissues was found to be notably higher compared with that of adjacent normal tissues. Suppression of E2F7 expression in PCa cell lines led to significantly reduced proliferation rates, increased proportion of cells in the G1 phase of the cell cycle and higher apoptotic rates compared with those in negative control groups. Dual‑luciferase reporter assay revealed E2F7 to be one of the binding targets of microRNA (miR)‑30c. In addition, transfection of miR‑30c mimics into PCa cells resulted in reduced cell viability, increased proportion of cells in the G1 phase and higher apoptotic rates. By contrast, transfection with the miR‑30c inhibitor led to lower apoptosis rates of PCa cells compared with negative control groups, whilst E2F7 siRNA co‑transfection reversed stimulatory effects of miR‑30c inhibitors on cell viability. In addition, the expression of cyclin‑dependent kinase inhibitor p21 were found to be upregulated by transfection with either E2F7 siRNA or miR‑30c mimics into PCa cells. In conclusion, the present study suggested that E2F7 may be positively associated with PCa cell proliferation by inhibiting p21, whereas E2F7 is in turn under regulation by miR‑30c. These observations suggest the miR‑30c/E2F7/p21 axis to be a viable therapeutic target for PCa.
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Affiliation(s)
- Ying Wang
- Oncology Department, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
- Oncology Department, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471000, P.R. China
| | - Xiaojuan Pei
- Pathology Department, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
| | - Po Xu
- Emergency Department, The First Affiliated Hospital, Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| | - Zhibo Tan
- Oncology Department, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
| | - Zhenwei Zhu
- Oncology Department, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
| | - Guangping Zhang
- Oncology Department, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471000, P.R. China
| | - Zeying Jiang
- Oncology Department, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
| | - Zhe Deng
- Emergency Department, The First Affiliated Hospital, Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
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27
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Hammouz RY, Kostanek JK, Dudzisz A, Witas P, Orzechowska M, Bednarek AK. Differential expression of lung adenocarcinoma transcriptome with signature of tobacco exposure. J Appl Genet 2020; 61:421-437. [PMID: 32564237 PMCID: PMC7413900 DOI: 10.1007/s13353-020-00569-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/12/2020] [Accepted: 06/09/2020] [Indexed: 12/17/2022]
Abstract
Smoking accounts for almost 80-90% of lung cancer cases, which is also the most frequent cause of cancer-related deaths in humans. With over 60 carcinogens in tobacco smoke, cells dividing at the time of carcinogen exposure are at particular risk of neoplasia. The present study aimed to investigate global gene expression differences in lung adenocarcinoma (LUAD) tumour samples of current smokers and non-smokers, in an attempt to elucidate biological mechanisms underlying divergent smoking effects. Current and non-smoker tumour samples were analysed using bioinformatics tools, examining differences in molecular drivers of cancer initiation and progression, as well as evaluating the effect of smoking and sex on epithelial mesenchymal transition (EMT). As a result, we identified 1150 differentially expressed genes showing visible differences in the expression profiles between the smoking subgroups. The genes were primarily involved in cell cycle, DNA replication, DNA repair, VEGF, GnRH, ErbB and T cell receptor signalling pathways. Our results show that smoking clearly affected E2F transcriptional activity and DNA repair pathways including mismatch repair, base excision repair and homologous recombination. We observed that sex could modify the effects of PLA2G2A and PRG4 in LUAD tumour samples, whereas sex and smoking status might possibly have a biological effect on the EMT-related genes: HEY2, OLFM1, SFRP1 and STRAP. We also identified potential epigenetic changes smoking solely might have on EMT-related genes, which may serve as potential diagnostic and prognostic biomarkers for LUAD patients.
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Affiliation(s)
- Raneem Y. Hammouz
- Department of Molecular Carcinogenesis, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
| | - Joanna K. Kostanek
- Department of Molecular Carcinogenesis, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
| | - Aleksandra Dudzisz
- Department of Molecular Carcinogenesis, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
| | - Piotr Witas
- Department of Molecular Carcinogenesis, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
| | - Magdalena Orzechowska
- Department of Molecular Carcinogenesis, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
| | - Andrzej K. Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland
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28
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Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
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Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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29
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Lu T, Wang R, Cai H, Cui Y. Long non-coding RNA DLEU2 promotes the progression of esophageal cancer through miR-30e-5p/E2F7 axis. Biomed Pharmacother 2020; 123:109650. [DOI: 10.1016/j.biopha.2019.109650] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/03/2019] [Accepted: 11/06/2019] [Indexed: 12/20/2022] Open
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30
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Yuan R, Liu Q, Segeren HA, Yuniati L, Guardavaccaro D, Lebbink RJ, Westendorp B, de Bruin A. Cyclin F-dependent degradation of E2F7 is critical for DNA repair and G2-phase progression. EMBO J 2019; 38:e101430. [PMID: 31475738 PMCID: PMC6792010 DOI: 10.15252/embj.2018101430] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 01/24/2023] Open
Abstract
E2F7 and E2F8 act as tumor suppressors via transcriptional repression of genes involved in S-phase entry and progression. Previously, we demonstrated that these atypical E2Fs are degraded by APC/CCdh1 during G1 phase of the cell cycle. However, the mechanism driving the downregulation of atypical E2Fs during G2 phase is unknown. Here, we show that E2F7 is targeted for degradation by the E3 ubiquitin ligase SCFcyclin F during G2. Cyclin F binds via its cyclin domain to a conserved C-terminal CY motif on E2F7. An E2F7 mutant unable to interact with SCFcyclin F remains stable during G2. Furthermore, SCFcyclin F can also interact and induce degradation of E2F8. However, this does not require the cyclin domain of SCFcyclin F nor the CY motifs in the C-terminus of E2F8, implying a different regulatory mechanism than for E2F7. Importantly, depletion of cyclin F causes an atypical-E2F-dependent delay of the G2/M transition, accompanied by reduced expression of E2F target genes involved in DNA repair. Live cell imaging of DNA damage revealed that cyclin F-dependent regulation of atypical E2Fs is critical for efficient DNA repair and cell cycle progression.
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Affiliation(s)
- Ruixue Yuan
- Department of PathobiologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Qingwu Liu
- Department of PathobiologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Hendrika A Segeren
- Department of PathobiologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Laurensia Yuniati
- Hubrecht Institute‐KNAW and University Medical Center UtrechtUtrechtThe Netherlands
| | - Daniele Guardavaccaro
- Hubrecht Institute‐KNAW and University Medical Center UtrechtUtrechtThe Netherlands
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | - Robert J Lebbink
- Medical MicrobiologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Bart Westendorp
- Department of PathobiologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Alain de Bruin
- Department of PathobiologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
- Division Molecular GeneticsDepartment PediatricsUniversity Medical Center GroningenGroningenThe Netherlands
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31
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Mohammadzadeh A, Mirza-Aghazadeh-Attari M, Hallaj S, Saei AA, Alivand MR, Valizadeh A, Yousefi B, Majidinia M. Crosstalk between P53 and DNA damage response in ageing. DNA Repair (Amst) 2019; 80:8-15. [DOI: 10.1016/j.dnarep.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/19/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023]
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32
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Silva E, Ideker T. Transcriptional responses to DNA damage. DNA Repair (Amst) 2019; 79:40-49. [PMID: 31102970 PMCID: PMC6570417 DOI: 10.1016/j.dnarep.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/20/2019] [Accepted: 05/04/2019] [Indexed: 12/31/2022]
Abstract
In response to the threat of DNA damage, cells exhibit a dramatic and multi-factorial response spanning from transcriptional changes to protein modifications, collectively known as the DNA damage response (DDR). Here, we review the literature surrounding the transcriptional response to DNA damage. We review differences in observed transcriptional responses as a function of cell cycle stage and emphasize the importance of experimental design in these transcriptional response studies. We additionally consider topics including structural challenges in the transcriptional response to DNA damage as well as the connection between transcription and protein abundance.
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Affiliation(s)
- Erica Silva
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA.
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA; Program in Bioinformatics, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.
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33
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A hypergraph-based method for large-scale dynamic correlation study at the transcriptomic scale. BMC Genomics 2019; 20:397. [PMID: 31117943 PMCID: PMC6530038 DOI: 10.1186/s12864-019-5787-x] [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: 10/30/2018] [Accepted: 05/09/2019] [Indexed: 12/22/2022] Open
Abstract
Background The biological regulatory system is highly dynamic. Correlations between functionally related genes change over different biological conditions, which are often unobserved in the data. At the gene level, the dynamic correlations result in three-way gene interactions involving a pair of genes that change correlation, and a third gene that reflects the underlying cellular conditions. This type of ternary relation can be quantified by the Liquid Association statistic. Studying these three-way interactions at the gene triplet level have revealed important regulatory mechanisms in the biological system. Currently, due to the extremely large amount of possible combinations of triplets within a high-throughput gene expression dataset, no method is available to examine the ternary relationship at the biological system level and formally address the false discovery issue. Results Here we propose a new method, Hypergraph for Dynamic Correlation (HDC), to construct module-level three-way interaction networks. The method is able to present integrative uniform hypergraphs to reflect the global dynamic correlation pattern in the biological system, providing guidance to down-stream gene triplet-level analyses. To validate the method’s ability, we conducted two real data experiments using a melanoma RNA-seq dataset from The Cancer Genome Atlas (TCGA) and a yeast cell cycle dataset. The resulting hypergraphs are clearly biologically plausible, and suggest novel relations relevant to the biological conditions in the data. Conclusions We believe the new approach provides a valuable alternative method to analyze omics data that can extract higher order structures. The software is at https://github.com/yunchuankong/HypergraphDynamicCorrelation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5787-x) contains supplementary material, which is available to authorized users.
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34
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Guo H, Zhang L. MicroRNA-30a suppresses papillary thyroid cancer cell proliferation, migration and invasion by directly targeting E2F7. Exp Ther Med 2019; 18:209-215. [PMID: 31258655 PMCID: PMC6566087 DOI: 10.3892/etm.2019.7532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 02/05/2019] [Indexed: 01/23/2023] Open
Abstract
microRNA (miRNA/miR)-30a, a tumor-associated miRNA, has been implicated in the tumorigenesis and progression of different types of human cancer. Thyroid cancer is a common endocrine malignancy, of which papillary thyroid cancer (PTC) accounts for ~80-90% of all TC. However, the effect of miR-30a in PTC is yet to be fully elucidated. The TPC-1 human PTC cell line, as well as the normal human thyroid cell line (HT-ori3), were utilized in the current study. The PTC cell line was transfected with a miR-30a mimic. Subsequently, reverse transcription-quantitative polymerase chain reaction was performed to detect the expression of miR-30a and E2F transcription factor 7 (E2F7). Cell proliferation was assessed via a MTT assay and transwell migration and invasion assays were performed to detect the migration and invasion of PTC cells. A dual-luciferase reporter assay was also utilized to clarify the association between miR-30a and E2F7. The results of the current study revealed that miR-30a was significantly downregulated in TPC-1 cells compared with HT-ori3 cells and that the expression of E2F7 was significantly upregulated in PTC cells. The upregulation of miR-30a also inhibited the proliferation, migration and invasion of PTC cells. Furthermore, the luciferase assay revealed that miR-30a binds to the 3'-UTR of E2F7. Additionally, the overexpression of miR-30a decreased E2F7 levels in TPC-1 cells. These results indicate that miR-30a functions as a tumor suppressor in PTC by direct targeting E2F7 and that miR-30a may be a novel therapeutic target for patients with PTC.
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Affiliation(s)
- Haiyan Guo
- Department of Clinical Medicine, Fenyang College, Shanxi Medical University, Fenyang, Shanxi 032200, P.R. China
| | - Linyun Zhang
- Shanxi Fenyang Prison Hospital, Fenyang, Shanxi 032200, P.R. China
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Peñalver-González B, Vallejo-Rodríguez J, Mentxaka G, Fullaondo A, Iglesias-Ara A, Field SJ, Zubiaga AM. Golgi Oncoprotein GOLPH3 Gene Expression Is Regulated by Functional E2F and CREB/ATF Promoter Elements. Genes (Basel) 2019; 10:genes10030247. [PMID: 30934642 PMCID: PMC6471639 DOI: 10.3390/genes10030247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/12/2019] [Accepted: 03/20/2019] [Indexed: 01/24/2023] Open
Abstract
The Golgi organelle duplicates its protein and lipid content to segregate evenly between two daughter cells after mitosis. However, how Golgi biogenesis is regulated during interphase remains largely unknown. Here we show that messenger RNA (mRNA) expression of GOLPH3 and GOLGA2, two genes encoding Golgi proteins, is induced specifically in G1 phase, suggesting a link between cell cycle regulation and Golgi growth. We have examined the role of E2F transcription factors, critical regulators of G1 to S progression of the cell cycle, in the expression of Golgi proteins during interphase. We show that promoter activity for GOLPH3, a Golgi protein that is also oncogenic, is induced by E2F1-3 and repressed by E2F7. Mutation of the E2F motifs present in the GOLPH3 promoter region abrogates E2F1-mediated induction of a GOLPH3 luciferase reporter construct. Furthermore, we identify a critical CREB/ATF element in the GOLPH3 promoter that is required for its steady state and ATF2-induced expression. Interestingly, depletion of GOLPH3 with small interfering RNA (siRNA) delays the G1 to S transition in synchronized U2OS cells. Taken together, our results reveal a link between cell cycle regulation and Golgi function, and suggest that E2F-mediated regulation of Golgi genes is required for the timely progression of the cell cycle.
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Affiliation(s)
- Beatriz Peñalver-González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain.
| | - Jon Vallejo-Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain.
| | - Gartze Mentxaka
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain.
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain.
| | - Ainhoa Iglesias-Ara
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain.
| | - Seth J Field
- Division of Endocrinology and Metabolism, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Ana M Zubiaga
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48080 Bilbao, Spain.
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36
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Zhou Q, Zhang F, He Z, Zuo MZ. E2F2/5/8 Serve as Potential Prognostic Biomarkers and Targets for Human Ovarian Cancer. Front Oncol 2019; 9:161. [PMID: 30967995 PMCID: PMC6439355 DOI: 10.3389/fonc.2019.00161] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/25/2019] [Indexed: 12/21/2022] Open
Abstract
E2Fs are a family of pivotal transcription factors. Accumulative evidence indicates that aberrant expression or activation of E2Fs is a common phenomenon in malignances, and significant associations have been noted between E2Fs and tumorigenesis or progression in a wide range of cancers. However, the expression patterns and exact roles of each E2F contributing to tumorigenesis and progression of ovarian cancer (OC) have not yet been elucidated. In this study, we investigated the distinct expression and prognostic value of E2Fs in patients with OC by analyzing a series of databases, including ONCOMINE, GEPIA, cBioPortal, Metascape, and Kaplan–Meier plotter. The mRNA expression levels of E2F1/3/5/8 were found to be significantly upregulated in patients with OC and were obviously associated with tumor stage for OC. Aberrant expression of E2F2/5/7/8 was found to be associated with the clinical outcomes of patients with OC. These results suggest that E2F2/5/8 might serve as potential prognostic biomarkers and targets for OC. However, future studies are required to validate our findings and promote the clinical utility of E2Fs in OC.
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Affiliation(s)
- Quan Zhou
- Department of Gynecology and Obstetrics, The People's Hospital of China Three Gorges University/The First People's Hospital of Yichang, Yichang, China
| | - Fan Zhang
- Department of Gynecology and Obstetrics, The People's Hospital of China Three Gorges University/The First People's Hospital of Yichang, Yichang, China
| | - Ze He
- Department of Gynecology and Obstetrics, The People's Hospital of China Three Gorges University/The First People's Hospital of Yichang, Yichang, China
| | - Man-Zhen Zuo
- Department of Gynecology and Obstetrics, The People's Hospital of China Three Gorges University/The First People's Hospital of Yichang, Yichang, China
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