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Yao B, Xing M, Zeng X, Zhang M, Zheng Q, Wang Z, Peng B, Qu S, Li L, Jin Y, Li H, Yuan H, Zhao Q, Ma C. KMT2D-mediated H3K4me1 recruits YBX1 to facilitate triple-negative breast cancer progression through epigenetic activation of c-Myc. Clin Transl Med 2024; 14:e1753. [PMID: 38967349 PMCID: PMC11225074 DOI: 10.1002/ctm2.1753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/28/2024] [Accepted: 06/16/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Lysine methyltransferase 2D (KMT2D) mediates mono-methylation of histone H3 lysine 4 (H3K4me1) in mammals. H3K4me1 mark is involved in establishing an active chromatin structure to promote gene transcription. However, the precise molecular mechanism underlying the KMT2D-mediated H3K4me1 mark modulates gene expression in triple-negative breast cancer (TNBC) progression is unresolved. METHODS AND RESULTS We recognized Y-box-binding protein 1 (YBX1) as a "reader" of the H3K4me1 mark, and a point mutation of YBX1 (E121A) disrupted this interaction. We found that KMT2D and YBX1 cooperatively promoted cell growth and metastasis of TNBC cells in vitro and in vivo. The expression levels of KMT2D and YBX1 were both upregulated in tumour tissues and correlated with poor prognosis for breast cancer patients. Combined analyses of ChIP-seq and RNA-seq data indicated that YBX1 was co-localized with KMT2D-mediated H3K4me1 in the promoter regions of c-Myc and SENP1, thereby activating their expressions in TNBC cells. Moreover, we demonstrated that YBX1 activated the expressions of c-Myc and SENP1 in a KMT2D-dependent manner. CONCLUSION Our results suggest that KMT2D-mediated H3K4me1 recruits YBX1 to facilitate TNBC progression through epigenetic activation of c-Myc and SENP1. These results together unveil a crucial interplay between histone mark and gene regulation in TNBC progression, thus providing novel insights into targeting the KMT2D-H3K4me1-YBX1 axis for TNBC treatment. HIGHLIGHTS YBX1 is a KMT2D-mediated H3K4me1-binding effector protein and mutation of YBX1 (E121A) disrupts its binding to H3K4me1. KMT2D and YBX1 cooperatively promote TNBC proliferation and metastasis by activating c-Myc and SENP1 expression in vitro and in vivo. YBX1 is colocalized with H3K4me1 in the c-Myc and SENP1 promoter regions in TNBC cells and increased YBX1 expression predicts a poor prognosis in breast cancer patients.
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Affiliation(s)
- Bing Yao
- Department of Medical GeneticsNanjing Medical UniversityNanjingChina
- Department of General Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical MedicineNanjing Medical UniversityTaizhouChina
- Jiangsu Key Laboratory of XenotransplantationNanjing Medical UniversityNanjingChina
| | - Mengying Xing
- Department of Medical GeneticsNanjing Medical UniversityNanjingChina
| | - Xiangwei Zeng
- The State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingChina
| | - Ming Zhang
- Department of Medical GeneticsNanjing Medical UniversityNanjingChina
| | - Que Zheng
- Department of Medical GeneticsNanjing Medical UniversityNanjingChina
| | - Zhi Wang
- The State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingChina
| | - Bo Peng
- MOE Key Laboratory of Protein SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center for Biological StructureTsinghua‐Peking Joint Center for Life SciencesDepartment of Basic Medical SciencesSchool of MedicineTsinghua UniversityBeijingChina
| | - Shuang Qu
- School of Life Science and TechnologyChina Pharmaceutical UniversityNanjingJiangsuChina
| | - Lingyun Li
- Department of Medical GeneticsNanjing Medical UniversityNanjingChina
| | - Yucui Jin
- Department of Medical GeneticsNanjing Medical UniversityNanjingChina
| | - Haitao Li
- MOE Key Laboratory of Protein SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center for Biological StructureTsinghua‐Peking Joint Center for Life SciencesDepartment of Basic Medical SciencesSchool of MedicineTsinghua UniversityBeijingChina
| | - Hongyan Yuan
- Department of Oncology and Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashingtonDistrict of ColumbiaUSA
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingChina
| | - Changyan Ma
- Department of Medical GeneticsNanjing Medical UniversityNanjingChina
- Jiangsu Key Laboratory of XenotransplantationNanjing Medical UniversityNanjingChina
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Dheeraj A, Garcia Marques FJ, Tailor D, Bermudez A, Resendez A, Pandrala M, Grau B, Kumar P, Haley CB, Honkala A, Kujur P, Jeffrey SS, Pitteri S, Malhotra SV. Inhibition of protein translational machinery in triple-negative breast cancer as a promising therapeutic strategy. Cell Rep Med 2024; 5:101552. [PMID: 38729158 PMCID: PMC11148772 DOI: 10.1016/j.xcrm.2024.101552] [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: 08/18/2022] [Revised: 07/11/2023] [Accepted: 04/11/2024] [Indexed: 05/12/2024]
Abstract
Y-box binding protein-1 (YB-1) is a proto-oncogenic protein associated with protein translation regulation. It plays a crucial role in the development and progression of triple-negative breast cancer (TNBC). In this study, we describe a promising approach to inhibit YB-1 using SU056, a small-molecule inhibitor. SU056 physically interacts with YB-1 and reduces its expression, which helps to restrain the progression of TNBC. Proteome profiling analysis indicates that the inhibition of YB-1 by SU056 can alter the proteins that regulate protein translation, an essential process for cancer cell growth. Preclinical studies on human cells, mice, and patient-derived xenograft tumor models show the effectiveness of SU056. Moreover, toxicological studies have shown that SU056 treatment and dosing are well tolerated without any adverse effects. Overall, our study provides a strong foundation for the further development of SU056 as a potential treatment option for patients with TNBC by targeting YB-1.
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Affiliation(s)
- Arpit Dheeraj
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Fernando Jose Garcia Marques
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Dhanir Tailor
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Abel Bermudez
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Angel Resendez
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Mallesh Pandrala
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Benedikt Grau
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Praveen Kumar
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Carrsyn B Haley
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alexander Honkala
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Praveen Kujur
- Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Stefanie S Jeffrey
- Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sharon Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sanjay V Malhotra
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA.
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Ichikawa K, Ito S, Kato E, Abe N, Machida T, Iwasaki J, Tanaka G, Araki H, Wakayama K, Jona H, Sugimoto T, Miyadera K, Ohkubo S. TAS0612, a Novel RSK, AKT, and S6K Inhibitor, Exhibits Antitumor Effects in Preclinical Tumor Models. Mol Cancer Ther 2024; 23:174-186. [PMID: 37906695 DOI: 10.1158/1535-7163.mct-21-1037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 11/18/2022] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
The MAPK and PI3K pathways are involved in cancer growth and survival; however, the clinical efficacy of single inhibitors of each pathway is limited or transient owing to resistance mechanisms, such as feedback signaling and/or reexpression of receptor-type tyrosine kinases (RTK). This study identified a potent and novel kinase inhibitor, TAS0612, and characterized its properties. We found that TAS0612 is a potent, orally available compound that can inhibit p90RSK (RSK), AKT, and p70S6K (S6K) as a single agent and showed a strong correlation with the growth inhibition of cancer cells with PTEN loss or mutations, regardless of the presence of KRAS and BRAF mutations. Additional RSK inhibitory activity may differentiate the sensitivity profile of TAS0612 from that of signaling inhibitors that target only the PI3K pathway. Moreover, TAS0612 demonstrated broad-spectrum activity against tumor models wherein inhibition of MAPK or PI3K pathways was insufficient to exert antitumor effects. TAS0612 exhibited a stronger growth-inhibitory activity against the cancer cell lines and tumor models with dysregulated signaling with the genetic abnormalities described above than treatment with inhibitors against AKT, PI3K, MEK, BRAF, and EGFR/HER2. In addition, TAS0612 demonstrated the persistence of blockade of downstream growth and antiapoptotic signals, despite activation of upstream effectors in the signaling pathway and FoxO-dependent reexpression of HER3. In conclusion, TAS0612 with RSK/AKT/S6K inhibitory activity may provide a novel therapeutic strategy for patients with cancer to improve clinical responses and overcome resistance mechanisms.
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Affiliation(s)
- Koji Ichikawa
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Satoshi Ito
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Emi Kato
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Naomi Abe
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Takumitsu Machida
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Junya Iwasaki
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Gotaro Tanaka
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Hikari Araki
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Kentaro Wakayama
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Hideki Jona
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Tetsuya Sugimoto
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Kazutaka Miyadera
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Shuichi Ohkubo
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
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Rosell R, Jain A, Codony-Servat J, Jantus-Lewintre E, Morrison B, Ginesta JB, González-Cao M. Biological insights in non-small cell lung cancer. Cancer Biol Med 2023; 20:j.issn.2095-3941.2023.0108. [PMID: 37381723 PMCID: PMC10466437 DOI: 10.20892/j.issn.2095-3941.2023.0108] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023] Open
Abstract
Lung oncogenesis relies on intracellular cysteine to overcome oxidative stress. Several tumor types, including non-small cell lung cancer (NSCLC), upregulate the system xc- cystine/glutamate antiporter (xCT) through overexpression of the cystine transporter SLC7A11, thus sustaining intracellular cysteine levels to support glutathione synthesis. Nuclear factor erythroid 2-related factor 2 (NRF2) serves as a master regulator of oxidative stress resistance by regulating SLC7A11, whereas Kelch-like ECH-associated protein (KEAP1) acts as a cytoplasmic repressor of the oxidative responsive transcription factor NRF2. Mutations in KEAP1/NRF2 and p53 induce SLC7A11 activation in NSCLC. Extracellular cystine is crucial in supplying the intracellular cysteine levels necessary to combat oxidative stress. Disruptions in cystine availability lead to iron-dependent lipid peroxidation, thus resulting in a type of cell death called ferroptosis. Pharmacologic inhibitors of xCT (either SLC7A11 or GPX4) induce ferroptosis of NSCLC cells and other tumor types. When cystine uptake is impaired, the intracellular cysteine pool can be sustained by the transsulfuration pathway, which is catalyzed by cystathionine-B-synthase (CBS) and cystathionine g-lyase (CSE). The involvement of exogenous cysteine/cystine and the transsulfuration pathway in the cysteine pool and downstream metabolites results in compromised CD8+ T cell function and evasion of immunotherapy, diminishing immune response and potentially reducing the effectiveness of immunotherapeutic interventions. Pyroptosis is a previously unrecognized form of regulated cell death. In NSCLCs driven by EGFR, ALK, or KRAS, selective inhibitors induce pyroptotic cell death as well as apoptosis. After targeted therapy, the mitochondrial intrinsic apoptotic pathway is activated, thus leading to the cleavage and activation of caspase-3. Consequently, gasdermin E is activated, thus leading to permeabilization of the cytoplasmic membrane and cell-lytic pyroptosis (indicated by characteristic cell membrane ballooning). Breakthroughs in KRAS G12C allele-specific inhibitors and potential mechanisms of resistance are also discussed herein.
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Affiliation(s)
- Rafael Rosell
- Germans Trias i Pujol Research Institute, Badalona 08028, Spain
- IOR, Hospital Quiron-Dexeus, Barcelona 08028, Spain
| | - Anisha Jain
- Department of Microbiology, JSS Academy of Higher Education & Research, Mysuru 570015, India
| | | | - Eloisa Jantus-Lewintre
- Department of Biotechnology, Universitat Politècnica de Valencia; Mixed Unit TRIAL (General University Hospital of Valencia Research Foundation and Príncipe Felipe Research Center), CIBERONC, Valencia 46014, Spain
| | - Blake Morrison
- Sumitomo Pharma Oncology, Inc., Cambridge, MA and Lehi, UT 84043, USA
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Hamidi AA, Taghehchian N, Zangouei AS, Akhlaghipour I, Maharati A, Basirat Z, Moghbeli M. Molecular mechanisms of microRNA-216a during tumor progression. Cancer Cell Int 2023; 23:19. [PMID: 36740668 PMCID: PMC9899407 DOI: 10.1186/s12935-023-02865-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) as the members of non-coding RNAs family are involved in post-transcriptional regulation by translational inhibiting or mRNA degradation. They have a critical role in regulation of cell proliferation and migration. MiRNAs aberrations have been reported in various cancers. Considering the importance of these factors in regulation of cellular processes and their high stability in body fluids, these factors can be suggested as suitable non-invasive markers for the cancer diagnosis. MiR-216a deregulation has been frequently reported in different cancers. Therefore, in the present review we discussed the molecular mechanisms of the miR-216a during tumor progression. It has been reported that miR-216a mainly functioned as a tumor suppressor through the regulation of signaling pathways and transcription factors. This review paves the way to suggest the miR-216a as a probable therapeutic and diagnostic target in cancer patients.
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Affiliation(s)
- Amir Abbas Hamidi
- grid.411583.a0000 0001 2198 6209Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Negin Taghehchian
- grid.411583.a0000 0001 2198 6209Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Sadra Zangouei
- grid.411583.a0000 0001 2198 6209Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Iman Akhlaghipour
- grid.411583.a0000 0001 2198 6209Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhosein Maharati
- grid.411583.a0000 0001 2198 6209Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Basirat
- grid.411583.a0000 0001 2198 6209Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- grid.411583.a0000 0001 2198 6209Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Dorai S, Alex Anand D. Differentially Expressed Cell Cycle Genes and STAT1/3-Driven Multiple Cancer Entanglement in Psoriasis, Coupled with Other Comorbidities. Cells 2022; 11:cells11233867. [PMID: 36497125 PMCID: PMC9740537 DOI: 10.3390/cells11233867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Psoriasis is a persistent T-cell-supported inflammatory cutaneous disorder, which is defined by a significant expansion of basal cells in the epidermis. Cell cycle and STAT genes that control cell cycle progression and viral infection have been revealed to be comorbid with the development of certain cancers and other disorders, due to their abnormal or scanty expression. The purpose of this study is to evaluate the expression of certain cell cycle and STAT1/3 genes in psoriasis patients and to determine the types of comorbidities associated with these genes. To do so, we opted to adopt the in silico methodology, since it is a quick and easy way to discover any potential comorbidity risks that may exist in psoriasis patients. With the genes collected from early research groups, protein networks were created in this work using the NetworkAnalyst program. The crucial hub genes were identified by setting the degree parameter, and they were then used in gene ontology and pathway assessments. The transcription factors that control the hub genes were detected by exploring TRRUST, and DGIdb was probed for remedies that target transcription factors and hubs. Using the degree filter, the first protein subnetwork produced seven hub genes, including STAT3, CCNB1, STAT1, CCND1, CDC20, HSPA4, and MAD2L1. The hub genes were shown to be implicated in cell cycle pathways by the gene ontology and Reactome annotations. The former four hubs were found in signaling pathways, including prolactin, FoxO, JAK/STAT, and p53, according to the KEGG annotation. Furthermore, they enhanced several malignancies, including pancreatic cancer, Kaposi's sarcoma, non-small cell lung cancer, and acute myeloid leukemia. Viral infections, including measles, hepatitis C, Epstein-Barr virus, and HTLV-1 and viral carcinogenesis were among the other susceptible diseases. Diabetes and inflammatory bowel disease were conjointly annotated. In total, 129 medicines were discovered in DGIdb to be effective against the transcription factors BRCA1, RELA, TP53, and MYC, as opposed to 10 medications against the hubs, STAT3 and CCND1, in tandem with 8 common medicines. The study suggests that the annotated medications should be tested in suitable psoriatic cell lines and animal models to optimize the drugs used based on the kind, severity, and related comorbidities of psoriasis. Furthermore, a personalized medicine protocol must be designed for each psoriasis patient that displays different comorbidities.
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Liu C, Kuang J, Wang Y, Duan T, Min L, Lu C, Zhang T, Chen R, Wu Y, Zhu L. A functional reference map of the RNF8 interactome in cancer. Biol Direct 2022; 17:17. [PMID: 35831895 PMCID: PMC9277853 DOI: 10.1186/s13062-022-00331-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Background RNF8 is an E3 ligase identified as a critical DNA damage-responsive protein. Recently, multiple reports have shown that RNF8 could be used as an important therapeutic target for cancer chemo/radiotherapy. However, the understanding of RNF8 remains limited due to the lack of its interactome reference map and comprehensive analysis of RNF8 in diverse cancers, which underscores the need to map the interactome of RNF8 via high-throughput methods. Results A two-way identification method based on LC–MS was designed for the identification of the RNF8 interactome with high-specificity. By in silico analysis and in vitro validation, we identified a new reference map of the RNF8 interactome network containing many new targets, such as YBX1, DNMT1, and HDCA1, new biological functions and the gene-disease associations of RNF8. Our results revealed a close relationship between RNF8 and neurodegenerative diseases or tumor-infiltrating immune cells using bulk RNA-seq and scRNA-seq datasets. As a proof of concept of our interactome map, we validated the direct binding between RNF8 and YBX1 and showed that RNF8 catalyzed the ubiquitination of YBX1. These results demonstrated that RNF8 might be a crucial regulator of YBX1. Conclusions Our work provides a unique framework for researchers and clinicians who seek to better explore or understand RNF8-regulated biological functions in cancers. This study will hopefully facilitate the rational design and further development of anti-RNF8 therapy in cancers. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13062-022-00331-z.
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Affiliation(s)
- Chuanyang Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Jingyu Kuang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China.
| | - Yuxuan Wang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Ting Duan
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Lu Min
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Chenyu Lu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Tianyi Zhang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Ruifen Chen
- Joint Logistic Support Force 921th Hospital, Changsha, 410073, Hunan, China
| | - Ying Wu
- Department of Critical Care Medicine, Second Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China.
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Gupta T, Malkin MG, Huang S. tRNA Function and Dysregulation in Cancer. Front Cell Dev Biol 2022; 10:886642. [PMID: 35721477 PMCID: PMC9198291 DOI: 10.3389/fcell.2022.886642] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/05/2022] [Indexed: 11/24/2022] Open
Abstract
Transfer RNA (tRNA) is a central component of protein synthesis and plays important roles in epigenetic regulation of gene expression in tumors. tRNAs are also involved in many cell processes including cell proliferation, cell signaling pathways and stress response, implicating a role in tumorigenesis and cancer progression. The complex role of tRNA in cell regulation implies that an understanding of tRNA function and dysregulation can be used to develop treatments for many cancers including breast cancer, colon cancer, and glioblastoma. Moreover, tRNA modifications including methylation are necessary for tRNA folding, stability, and function. In response to certain stress conditions, tRNAs can be cleaved in half to form tiRNAs, or even shorter tRNA fragments (tRF). tRNA structure and modifications, tiRNA induction of stress granule formation, and tRF regulation of gene expression through the repression of translation can all impact a cell’s fate. This review focuses on how these functions of tRNAs, tiRNA, and tRFs can lead to tumor development and progression. Further studies focusing on the specific pathways of tRNA regulation could help identify tRNA biomarkers and therapeutic targets, which might prevent and treat cancers.
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Affiliation(s)
- Tania Gupta
- Virginia Commonwealth University, Richmond, VA, United States
| | - Mark G. Malkin
- Department of Neurology, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Suyun Huang
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- *Correspondence: Suyun Huang,
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Lin Y, Zhang J, Li Y, Guo W, Chen L, Chen M, Chen X, Zhang W, Jin X, Jiang M, Xiao H, Wang C, Song C, Fu F. CTPS1 promotes malignant progression of triple-negative breast cancer with transcriptional activation by YBX1. J Transl Med 2022; 20:17. [PMID: 34991621 PMCID: PMC8734240 DOI: 10.1186/s12967-021-03206-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/17/2021] [Indexed: 01/18/2023] Open
Abstract
Background Cytidine nucleotide triphosphate synthase 1 (CTPS1) is a CTP synthase which play critical roles in DNA synthesis. However, its biological regulation and mechanism in triple-negative breast cancer (TNBC) has not been reported yet. Methods The expression of CTPS1 in TNBC tissues was determined by GEO, TCGA databases and immunohistochemistry (IHC). The effect of CTPS1 on TNBC cell proliferation, migration, invasion, apoptosis and tumorigenesis were explored in vivo and in vitro. In addition, the transcription factor Y-box binding protein 1 (YBX1) was identified by bioinformatics methods, dual luciferase reporter and chromatin immunoprecipitation (CHIP) assays. Pearson correlation analysis was utilized to assess the association between YBX1 and CTPS1 expression. Results CTPS1 expression was significantly upregulated in TNBC tissues and cell lines. Higher CTPS1 expression was correlated with a poorer disease-free survival (DFS) and overall survival (OS) in TNBC patients. Silencing of CTPS1 dramatically inhibited the proliferation, migration, invasion ability and induced apoptosis of MDA-MB-231 and HCC1937 cells. Xenograft tumor model also indicated that CTPS1 knockdown remarkably reduced tumor growth in mice. Mechanically, YBX1 could bind to the promoter of CTPS1 to promote its transcription. Furthermore, the expression of YBX1 was positively correlated with CTPS1 in TNBC tissues. Rescue experiments confirmed that the enhanced cell proliferation and invasion ability induced by YBX1 overexpression could be reversed by CTPS1 knockdown. Conclusion Our data demonstrate that YBX1/CTPS1 axis plays an important role in the progression of TNBC. CTPS1 might be a promising prognosis biomarker and potential therapeutic target for patients with triple-negative breast cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03206-5.
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Affiliation(s)
- Yuxiang Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Jie Zhang
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Yan Li
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenhui Guo
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Lili Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Minyan Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaobin Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenzhe Zhang
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Xuan Jin
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Meichen Jiang
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Han Xiao
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Chuan Wang
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China. .,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China. .,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China.
| | - Chuangui Song
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China. .,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China. .,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China.
| | - Fangmeng Fu
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China. .,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China. .,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China.
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10
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Dittmer J. Nuclear Mechanisms Involved in Endocrine Resistance. Front Oncol 2021; 11:736597. [PMID: 34604071 PMCID: PMC8480308 DOI: 10.3389/fonc.2021.736597] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022] Open
Abstract
Endocrine therapy is a standard treatment offered to patients with ERα (estrogen receptor α)-positive breast cancer. In endocrine therapy, ERα is either directly targeted by anti-estrogens or indirectly by aromatase inhibitors which cause estrogen deficiency. Resistance to these drugs (endocrine resistance) compromises the efficiency of this treatment and requires additional measures. Endocrine resistance is often caused by deregulation of the PI3K/AKT/mTOR pathway and/or cyclin-dependent kinase 4 and 6 activities allowing inhibitors of these factors to be used clinically to counteract endocrine resistance. The nuclear mechanisms involved in endocrine resistance are beginning to emerge. Exploring these mechanisms may reveal additional druggable targets, which could help to further improve patients' outcome in an endocrine resistance setting. This review intends to summarize our current knowledge on the nuclear mechanisms linked to endocrine resistance.
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Affiliation(s)
- Jürgen Dittmer
- Clinic for Gynecology, Martin Luther University Halle-Wittenberg, Halle, Germany
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11
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Long non-coding RNA MIR200CHG promotes breast cancer proliferation, invasion, and drug resistance by interacting with and stabilizing YB-1. NPJ Breast Cancer 2021; 7:94. [PMID: 34272387 PMCID: PMC8285504 DOI: 10.1038/s41523-021-00293-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNA) have been identified as key regulators of tumorigenesis and development. We aim to explore the biological functions and molecular mechanisms of lncRNA MIR200CHG in breast cancer. We found that MIR200CHG is highly expressed in breast cancer tissues and is related to the tumor size and histopathological grade. In vitro and in vivo experiments confirmed that MIR200CHG can promote breast cancer proliferation, invasion, and drug resistance. MIR200CHG directly binds to the transcription factor Y-box binding protein-1 (YB-1), and inhibits its ubiquitination and degradation. MIR200CHG regulates YB-1 phosphorylation at serine 102, thereby affecting the expression of genes related to tumor cell proliferation, apoptosis, invasion, and drug resistance. Additionally, MIR200CHG partially affects the expression of miR-200c/141-3p encoded by its intron region. Therefore, MIR200CHG can promote the proliferation, invasion, and drug resistance of breast cancer by interacting with and stabilizing YB-1, and has the potential to become a target for breast cancer treatment.
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12
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Lettau K, Khozooei S, Kosnopfel C, Zips D, Schittek B, Toulany M. Targeting the Y-box Binding Protein-1 Axis to Overcome Radiochemotherapy Resistance in Solid Tumors. Int J Radiat Oncol Biol Phys 2021; 111:1072-1087. [PMID: 34166770 DOI: 10.1016/j.ijrobp.2021.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/18/2022]
Abstract
Multifunctional Y-box binding protein-1 (YB-1) is highly expressed in different human solid tumors and is involved in various cellular processes. DNA damage is the major mechanism by which radiochemotherapy (RCT) induces cell death. On induction of DNA damage, a multicomponent signal transduction network, known as the DNA damage response, is activated to induce cell cycle arrest and initiate DNA repair, which protects cells against damage. YB-1 regulates nearly all cancer hallmarks described to date by participating in DNA damage response, gene transcription, mRNA splicing, translation, and tumor stemness. YB-1 lacks kinase activity, and p90 ribosomal S6 kinase and AKT are the key kinases within the RAS/mitogen-activated protein kinase and phosphoinositide 3-kinase pathways that directly activate YB-1. Thus, the molecular targeting of ribosomal S6 kinase and AKT is thought to be the most effective strategy for blocking the cellular function of YB-1 in human solid tumors. In this review, after describing the prosurvival effect of YB-1 with a focus on DNA damage repair and cancer cell stemness, clinical evidence will be provided indicating an inverse correlation between YB-1 expression and the treatment outcome of solid tumors after RCT. In the interest of being concise, YB-1 signaling cascades will be briefly discussed and the current literature on YB-1 posttranslational modifications will be summarized. Finally, the current status of targeting the YB-1 axis, especially in combination with RCT, will be highlighted.
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Affiliation(s)
- Konstanze Lettau
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tübingen, Tübingen Germany; German Cancer Consortium (DKTK), partner site Tübingen, and German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Shayan Khozooei
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tübingen, Tübingen Germany; German Cancer Consortium (DKTK), partner site Tübingen, and German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Corinna Kosnopfel
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Daniel Zips
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tübingen, Tübingen Germany; German Cancer Consortium (DKTK), partner site Tübingen, and German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Birgit Schittek
- Department of Dermatology, Division of Dermatooncology, Eberhard-Karls-Universität, Tübingen, Tübingen, Germany
| | - Mahmoud Toulany
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tübingen, Tübingen Germany; German Cancer Consortium (DKTK), partner site Tübingen, and German Cancer Research Center (DKFZ) Heidelberg, Germany.
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13
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Mei Y, Bi WL, Agolia J, Hu C, Giantini Larsen AM, Meredith DM, Al Abdulmohsen S, Bale T, Dunn GP, Abedalthagafi M, Dunn IF. Immune profiling of pituitary tumors reveals variations in immune infiltration and checkpoint molecule expression. Pituitary 2021; 24:359-373. [PMID: 33492612 DOI: 10.1007/s11102-020-01114-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE Pituitary tumors are the second most common primary brain tumors. Functional tumors demonstrate increased PD-L1 expression, but expression of other checkpoint regulators has not been characterized. We sought to characterize the immune microenvironment of human pituitary tumors to identify new treatment opportunities. METHODS 72 pituitary tumors were evaluated for expression of the immune regulatory markers programmed death ligand 1 (PD-L1), programmed death ligand 2 (PD-L2), V-domain Ig suppressor of T cell activation (VISTA), lymphocyte activation gene 3 (LAG3) and tumor necrosis factor receptor superfamily member 4 (OX40) by immunohistochemistry (IHC). Lymphocyte infiltration, macrophage infiltration, and angiogenesis were analyzed using IHC. Expression of pituitary tumor initiating cell marker CD15 and mismatch repair proteins MutS protein homolog 2 (MSH2) and MutS protein homolog 6 (MSH6) was also assessed. RESULTS Pituitary tumors were infiltrated by macrophages and T cells, and they expressed varying levels of PD-L1, PD-L2, VISTA, LAG3, and OX40. Functional tumors and tumors with high expression of tumor stem cell markers had higher immune cell infiltration and greater expression of immunosuppressive checkpoint regulators. Increased PD-L1 and LAG3 and reduced VISTA were observed in primary tumors compared to recurrent tumors. CONCLUSION Immune cell infiltration and checkpoint regulator expression vary depending on functional status and presence of pituitary tumor initiating cells. Functional tumors may have a particularly immunosuppressive microenvironment. Further studies of immune checkpoint blockade of pituitary tumors, particularly functional tumors, are warranted, though combination therapy may be required.
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Affiliation(s)
- Yu Mei
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Wenya Linda Bi
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA.
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - James Agolia
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Changchen Hu
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
- Department of Neurosurgery, Shanxi Provincial People's Hospital, Shanxi Medical University, Taiyuan, China
| | | | - David M Meredith
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Sally Al Abdulmohsen
- Center for Skull Base and Pituitary Surgery, Department of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA
- King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Tejus Bale
- Department of Neuropathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gavin P Dunn
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Malak Abedalthagafi
- King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ian F Dunn
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, HHDC Suite 4000, 1000 N. Lincoln Blvd, Oklahoma City, OK, 73104, USA.
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14
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Epigenetic mechanisms in breast cancer therapy and resistance. Nat Commun 2021; 12:1786. [PMID: 33741974 PMCID: PMC7979820 DOI: 10.1038/s41467-021-22024-3] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of breast cancers express the estrogen receptor (ERα) and agents targeting this pathway represent the main treatment modality. Endocrine therapy has proven successful in the treatment of hormone-responsive breast cancer since its early adoption in the 1940s as an ablative therapy. Unfortunately, therapeutic resistance arises, leading to disease recurrence and relapse. Recent studies increased our understanding in how changes to the chromatin landscape and deregulation of epigenetic factors orchestrate the resistant phenotype. Here, we will discuss how the epigenome is an integral determinant in hormone therapy response and why epigenetic factors are promising targets for overcoming clinical resistance. Endocrine therapy has been the mainstay for hormone responsive breast cancer treatment. Here, Garcia-Martinez and colleagues discuss epigenetic mechanisms regulating ER + breast cancer and endocrine therapy resistance, and highlight approaches to rewire the cancer epigenome to improve targeted therapies for this cancer.
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15
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Chang KC, Diermeier SD, Yu AT, Brine LD, Russo S, Bhatia S, Alsudani H, Kostroff K, Bhuiya T, Brogi E, Pappin DJ, Bennett CF, Rigo F, Spector DL. MaTAR25 lncRNA regulates the Tensin1 gene to impact breast cancer progression. Nat Commun 2020; 11:6438. [PMID: 33353933 PMCID: PMC7755919 DOI: 10.1038/s41467-020-20207-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 11/20/2020] [Indexed: 12/31/2022] Open
Abstract
Misregulation of long non-coding RNA (lncRNA) genes has been linked to a wide variety of cancer types. Here we report on Mammary Tumor Associated RNA 25 (MaTAR25), a nuclear enriched and chromatin associated lncRNA that plays a role in mammary tumor cell proliferation, migration, and invasion, both in vitro and in vivo. MaTAR25 functions by interacting with purine rich element binding protein B (PURB), and associating with a major downstream target gene Tensin1 (Tns1) to regulate its expression in trans. The Tns1 protein product is a critical component of focal adhesions linking signaling between the extracellular matrix and the actin cytoskeleton. Knockout of MaTAR25 results in down-regulation of Tns1 leading to a reorganization of the actin cytoskeleton, and a reduction of focal adhesions and microvilli. We identify LINC01271 as the human ortholog of MaTAR25, and importantly, increased expression of LINC01271 is associated with poor patient prognosis and metastasis. Our findings demonstrate that LINC01271 represents a potential therapeutic target to alter breast cancer progression.
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Affiliation(s)
- Kung-Chi Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA
- Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Sarah D Diermeier
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Allen T Yu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA
- Genetics Program, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Lily D Brine
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA
| | - Suzanne Russo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA
| | - Sonam Bhatia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA
| | - Habeeb Alsudani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA
| | - Karen Kostroff
- Department of Surgical Oncology, Northwell Health, Lake Success, NY, 11042, USA
| | - Tawfiqul Bhuiya
- Department of Pathology, Northwell Health, Lake Success, NY, 11042, USA
| | - Edi Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Darryl J Pappin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, 92010, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, New York, USA.
- Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, 11794, USA.
- Genetics Program, Stony Brook University, Stony Brook, NY, 11794, USA.
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16
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Hisey CL, Tomek P, Nursalim YNS, Chamley LW, Leung E. Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer. F1000Res 2020; 9:1362. [PMID: 33447385 PMCID: PMC7780337 DOI: 10.12688/f1000research.27393.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs
BIRC5 (Survivin) and
YBX1,
as well as long-noncoding RNAs
HOTAIR,
ZFAS1, and
AGAP2-AS1 were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that
BIRC5 and
HOTAIR RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.
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Affiliation(s)
- Colin L Hisey
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand.,Hub for Extracellular Vesicle Investigations, University of Auckland, Auckland, New Zealand
| | - Petr Tomek
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Yohanes N S Nursalim
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
| | - Lawrence W Chamley
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand.,Hub for Extracellular Vesicle Investigations, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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17
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Zhang Y, Huang YX, Wang DL, Yang B, Yan HY, Lin LH, Li Y, Chen J, Xie LM, Huang YS, Liao JY, Hu KS, He JH, Saw PE, Xu X, Yin D. LncRNA DSCAM-AS1 interacts with YBX1 to promote cancer progression by forming a positive feedback loop that activates FOXA1 transcription network. Theranostics 2020; 10:10823-10837. [PMID: 32929382 PMCID: PMC7482804 DOI: 10.7150/thno.47830] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/15/2020] [Indexed: 12/21/2022] Open
Abstract
Rationale: The forkhead box A1 (FOXA1) is a crucial transcription factor in initiation and development of breast, lung and prostate cancer. Previous studies about the FOXA1 transcriptional network were mainly focused on protein-coding genes. Its regulatory network of long non-coding RNAs (lncRNAs) and their role in FOXA1 oncogenic activity remains unknown. Methods: The Cancer Genome Atlas (TCGA) data, RNA-seq and ChIP-seq data were used to analyze FOXA1 regulated lncRNAs. RT-qPCR was used to detect the expression of DSCAM-AS1, RT-qPCR and Western blotting were used to determine the expression of FOXA1, estrogen receptor α (ERα) and Y box binding protein 1 (YBX1). RNA pull-down and RIP-qPCR were employed to investigate the interaction between DSCAM-AS1 and YBX1. The effect of DSCAM-AS1 on malignant phenotypes was examined through in vitro and in vivo assays. Results: In this study, we conducted a global analysis of FOXA1 regulated lncRNAs. For detailed analysis, we chose lncRNA DSCAM-AS1, which is specifically expressed in lung adenocarcinoma, breast and prostate cancer. The expression level of DSCAM-AS1 is regulated by two super-enhancers (SEs) driven by FOXA1. High expression levels of DSCAM-AS1 was associated with poor prognosis. Knockout experiments showed DSCAM-AS1 was essential for the growth of xenograft tumors. Moreover, we demonstrated DSCAM-AS1 can regulate the expression of the master transcriptional factor FOXA1. In breast cancer, DSCAM-AS1 was also found to regulate ERα. Mechanistically, DSCAM-AS1 interacts with YBX1 and influences the recruitment of YBX1 in the promoter regions of FOXA1 and ERα. Conclusion: Our study demonstrated that lncRNA DSCAM-AS1 was transcriptionally activated by super-enhancers driven by FOXA1 and exhibited lineage-specific expression pattern. DSCAM-AS1 can promote cancer progression by interacting with YBX1 and regulating expression of FOXA1 and ERα.
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18
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Gandhi M, Groß M, Holler JM, Coggins SA, Patil N, Leupold JH, Munschauer M, Schenone M, Hartigan CR, Allgayer H, Kim B, Diederichs S. The lncRNA lincNMR regulates nucleotide metabolism via a YBX1 - RRM2 axis in cancer. Nat Commun 2020; 11:3214. [PMID: 32587247 PMCID: PMC7316977 DOI: 10.1038/s41467-020-17007-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
Long intergenic non-coding RNA-Nucleotide Metabolism Regulator (lincNMR) is a long non-coding RNA (lncRNA) which is induced in hepatocellular carcinoma. Its depletion invokes a proliferation defect, triggers senescence and inhibits colony formation in liver, but also breast and lung cancer cells. Triple-label SILAC proteomics profiles reveal a deregulation of key cell cycle regulators in lincNMR-depleted cells like the key dNTP synthesizing enzymes RRM2, TYMS and TK1, implicating lincNMR in regulating nucleotide metabolism. LincNMR silencing decreases dNTP levels, while exogenous dNTPs rescues the proliferation defect induced by lincNMR depletion. In vivo RNA Antisense Purification (RAP-MS) identifies YBX1 as a direct interaction partner of lincNMR which regulates RRM2, TYMS and TK1 expression and binds to their promoter regions. In a Chick Chorioallantoic Membrane (CAM) in vivo model, lincNMR-depleted tumors are significantly smaller. In summary, we discover a lincRNA, lincNMR, which regulates tumor cell proliferation through a YBX1-RRM2-TYMS-TK1 axis governing nucleotide metabolism.
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Affiliation(s)
- Minakshi Gandhi
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Academic Exchange Service (DAAD), Bonn, Germany; Helmholtz International Graduate School for Cancer Research (HIGS), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Matthias Groß
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica M Holler
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Si'Ana A Coggins
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Nitin Patil
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Mannheim, Germany
| | - Joerg H Leupold
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Mannheim, Germany
| | | | | | | | - Heike Allgayer
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Mannheim, Germany
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center, Faculty of Medicine, University of Freiburg, German Cancer Consortium (DKTK)-Partner Site Freiburg, Freiburg, Germany.
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19
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Roy S, Kumar R, Mittal V, Gupta D. Classification models for Invasive Ductal Carcinoma Progression, based on gene expression data-trained supervised machine learning. Sci Rep 2020; 10:4113. [PMID: 32139710 PMCID: PMC7057992 DOI: 10.1038/s41598-020-60740-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/12/2020] [Indexed: 12/20/2022] Open
Abstract
Early detection of breast cancer and its correct stage determination are important for prognosis and rendering appropriate personalized clinical treatment to breast cancer patients. However, despite considerable efforts and progress, there is a need to identify the specific genomic factors responsible for, or accompanying Invasive Ductal Carcinoma (IDC) progression stages, which can aid the determination of the correct cancer stages. We have developed two-class machine-learning classification models to differentiate the early and late stages of IDC. The prediction models are trained with RNA-seq gene expression profiles representing different IDC stages of 610 patients, obtained from The Cancer Genome Atlas (TCGA). Different supervised learning algorithms were trained and evaluated with an enriched model learning, facilitated by different feature selection methods. We also developed a machine-learning classifier trained on the same datasets with training sets reduced data corresponding to IDC driver genes. Based on these two classifiers, we have developed a web-server Duct-BRCA-CSP to predict early stage from late stages of IDC based on input RNA-seq gene expression profiles. The analysis conducted by us also enables deeper insights into the stage-dependent molecular events accompanying IDC progression. The server is publicly available at http://bioinfo.icgeb.res.in/duct-BRCA-CSP.
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Affiliation(s)
- Shikha Roy
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rakesh Kumar
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vaibhav Mittal
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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20
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Splicing Players Are Differently Expressed in Sporadic Amyotrophic Lateral Sclerosis Molecular Clusters and Brain Regions. Cells 2020; 9:cells9010159. [PMID: 31936368 PMCID: PMC7017305 DOI: 10.3390/cells9010159] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/23/2019] [Accepted: 01/04/2020] [Indexed: 12/12/2022] Open
Abstract
Splicing is a tightly orchestrated process by which the brain produces protein diversity over time and space. While this process specializes and diversifies neurons, its deregulation may be responsible for their selective degeneration. In amyotrophic lateral sclerosis (ALS), splicing defects have been investigated at the singular gene level without considering the higher-order level, involving the entire splicing machinery. In this study, we analyzed the complete spectrum (396) of genes encoding splicing factors in the motor cortex (41) and spinal cord (40) samples from control and sporadic ALS (SALS) patients. A substantial number of genes (184) displayed significant expression changes in tissue types or disease states, were implicated in distinct splicing complexes and showed different topological hierarchical roles based on protein–protein interactions. The deregulation of one of these splicing factors has a central topological role, i.e., the transcription factor YBX1, which might also have an impact on stress granule formation, a pathological marker associated with ALS.
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21
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Shibata T, Watari K, Kawahara A, Sudo T, Hattori S, Murakami Y, Izumi H, Itou J, Toi M, Akiba J, Akagi Y, Tanaka M, Kuwano M, Ono M. Targeting Phosphorylation of Y-Box-Binding Protein YBX1 by TAS0612 and Everolimus in Overcoming Antiestrogen Resistance. Mol Cancer Ther 2019; 19:882-894. [PMID: 31879363 DOI: 10.1158/1535-7163.mct-19-0690] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/16/2019] [Accepted: 12/18/2019] [Indexed: 11/16/2022]
Abstract
Nuclear expression of Y-box-binding protein (YBX1) is closely correlated with clinical poor outcomes and drug resistance in breast cancer. Nuclear translocation of YBX1 is facilitated by YBX1 phosphorylation at serine 102 by AKT, p70S6K, and p90RSK, and the phosphorylated YBX1 (pYBX1) promotes expression of genes related to drug resistance and cell growth. A forthcoming problem to be addressed is whether targeting the phosphorylation of YBX1 overcomes antiestrogen resistance by progressive breast cancer. Here, we found that increased expression of pYBX1 was accompanied by acquired resistance to antiestrogens, fulvestrant and tamoxifen. Forced expression of YBX1/S102E, a constitutive phosphorylated form, resulted in acquired resistance to fulvestrant. Inversely, YBX1 silencing specifically overcame antiestrogen resistance. Furthermore, treatment with everolimus, an mTORC1 inhibitor, or TAS0612, a novel multikinase inhibitor of AKT, p70S6K, and p90RSK, suppressed YBX1 phosphorylation and overcame antiestrogen resistance in vitro and in vivo IHC analysis revealed that expression of pYBX1 and YBX1 was augmented in patients who experienced recurrence during treatment with adjuvant endocrine therapies. Furthermore, pYBX1 was highly expressed in patients with triple-negative breast cancer compared with other subtypes. TAS0612 also demonstrated antitumor effect against triple-negative breast cancer in vivo Taken together, our findings suggest that pYBX1 represents a potential therapeutic target for treatment of antiestrogen-resistant and progressive breast cancer.
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Affiliation(s)
- Tomohiro Shibata
- Department of Pharmaceutical Oncology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kosuke Watari
- Department of Pharmaceutical Oncology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akihiko Kawahara
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Tomoya Sudo
- Department of Surgery, Kurume University School of Medicine, Kurume, Japan
| | - Satoshi Hattori
- Department of Integrated Medicine, Biomedical Statistics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yuichi Murakami
- Department of Pharmaceutical Oncology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.,Cancer Translational Research Center, St. Mary's Institute of Health Sciences, Kurume, Japan
| | - Hiroto Izumi
- Department of Occupational Pneumology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Junji Itou
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masakazu Toi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jun Akiba
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Yoshito Akagi
- Department of Surgery, Kurume University School of Medicine, Kurume, Japan
| | - Maki Tanaka
- Kurume General Hospital, Japan Community Health Care Organization (JCHO), Kurume, Japan
| | - Michihiko Kuwano
- Cancer Translational Research Center, St. Mary's Institute of Health Sciences, Kurume, Japan
| | - Mayumi Ono
- Department of Pharmaceutical Oncology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
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22
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Kuwano M, Shibata T, Watari K, Ono M. Oncogenic Y-box binding protein-1 as an effective therapeutic target in drug-resistant cancer. Cancer Sci 2019; 110:1536-1543. [PMID: 30903644 PMCID: PMC6500994 DOI: 10.1111/cas.14006] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/13/2019] [Accepted: 03/18/2019] [Indexed: 12/30/2022] Open
Abstract
Y-box binding protein-1 (YBX1), a multifunctional oncoprotein containing an evolutionarily conserved cold shock domain, dysregulates a wide range of genes involved in cell proliferation and survival, drug resistance, and chromatin destabilization by cancer. Expression of a multidrug resistance-associated ATP binding cassette transporter gene, ABCB1, as well as growth factor receptor genes, EGFR and HER2/ErbB2, was initially discovered to be transcriptionally activated by YBX1 in cancer cells. Expression of other drug resistance-related genes, MVP/LRP, TOP2A, CD44, CD49f, BCL2, MYC, and androgen receptor (AR), is also transcriptionally activated by YBX1, consistently indicating that YBX1 is involved in tumor drug resistance. Furthermore, there is strong evidence to support that nuclear localization and/or overexpression of YBX1 can predict poor outcomes in patients with more than 20 different tumor types. YBX1 is phosphorylated by kinases, including AKT, p70S6K, and p90RSK, and translocated into the nucleus to promote the transcription of resistance- and malignancy-related genes. Phosphorylated YBX1, therefore, plays a crucial role as a potent transcription factor in cancer. Herein, a novel anticancer therapeutic strategy is presented by targeting activated YBX1 to overcome drug resistance and malignant progression.
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Affiliation(s)
- Michihiko Kuwano
- Cancer Translational Research Center, St. Mary's Institute of Health Sciences, Kurume, Japan
| | - Tomohiro Shibata
- Department of Pharmaceutical Oncology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kosuke Watari
- Department of Pharmaceutical Oncology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Mayumi Ono
- Department of Pharmaceutical Oncology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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