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Shi X, Sheng Y, Fei H, Wei B, Zhang Z, Xia X, Mao C, Si X. Combined transcriptome and proteome analysis reveals MSN and ARFIP2 as biomarkers for trastuzumab resistance of breast cancer. Breast Cancer Res Treat 2024; 207:187-201. [PMID: 38750271 DOI: 10.1007/s10549-024-07355-1] [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: 12/11/2023] [Accepted: 04/24/2024] [Indexed: 07/09/2024]
Abstract
PURPOSE HER2-positive breast cancer (BC) accounts for 20-30% of all BC subtypes and is linked to poor prognosis. Trastuzumab (Tz), a humanized anti-HER2 monoclonal antibody, is a first-line treatment for HER2-positive breast cancer which faces resistance challenges. This study aimed to identify the biomarkers driving trastuzumab resistance. METHODS Differential expression analysis of genes and proteins between trastuzumab-sensitive (TS) and trastuzumab-resistant (TR) cells was conducted using RNA-seq and iTRAQ. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were used to study their functions. The prognostic significance and protein levels of ARFIP2 and MSN were evaluated using online tools and immunohistochemistry. Sensitivity of MSN and ARFIP2 to other therapies was assessed using public pharmacogenomics databases and the R language. RESULTS Five genes were up-regulated, and nine genes were down-regulated in TR cells at both transcriptional and protein levels. Low ARFIP2 and high MSN expression linked to poor BC prognosis. MSN increased and ARFIP2 decreased in TR patients, correlating with shorter OS. MSN negatively impacted fulvestrant and immunotherapy sensitivity, while ARFIP2 had a positive impact. CONCLUSION Our findings suggest that MSN and ARFIP2 could serve as promising biomarkers for predicting response to Tz, offering valuable insights for future research in the identification of diagnostic and therapeutic targets for BC patients with Tz resistance.
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Affiliation(s)
- Xiao Shi
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biotechnology, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Yuan Sheng
- Department of Pharmacy, Sir Run Run Hospital, Nanjing Medical University, Nanjing, 211116, China
| | - Haoran Fei
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biotechnology, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Bangbang Wei
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biotechnology, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhenyu Zhang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biotechnology, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Xinyu Xia
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biotechnology, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Changfei Mao
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China.
| | - Xinxin Si
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biotechnology, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China.
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Wang S, Song Y, Wang Z, Chang X, Wu H, Yan Z, Wu J, He Z, Kang L, Hu W, Xia T, Li Z, Ren X, Bai Y. Neutrophil-derived PAD4 induces citrullination of CKMT1 exacerbates mucosal inflammation in inflammatory bowel disease. Cell Mol Immunol 2024; 21:620-633. [PMID: 38720063 PMCID: PMC11143373 DOI: 10.1038/s41423-024-01158-6] [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: 09/22/2023] [Accepted: 03/21/2024] [Indexed: 06/02/2024] Open
Abstract
Peptidyl arginine deiminase 4 (PAD4) plays a pivotal role in infection and inflammatory diseases by facilitating the formation of neutrophil extracellular traps (NETs). However, the substrates of PAD4 and its exact role in inflammatory bowel disease (IBD) remain unclear. In this study, we employed single-cell RNA sequencing (scRNA-seq) and substrate citrullination mapping to decipher the role of PAD4 in intestinal inflammation associated with IBD. Our results demonstrated that PAD4 deficiency alleviated colonic inflammation and restored intestinal barrier function in a dextran sulfate sodium (DSS)-induced colitis mouse model. scRNA-seq analysis revealed significant alterations in intestinal cell populations, with reduced neutrophil numbers and changes in epithelial subsets upon PAD4 deletion. Gene expression analysis highlighted pathways related to inflammation and epithelial cell function. Furthermore, we found that neutrophil-derived extracellular vesicles (EVs) carrying PAD4 were secreted into intestinal epithelial cells (IECs). Within IECs, PAD4 citrullinates mitochondrial creatine kinase 1 (CKMT1) at the R242 site, leading to reduced CKMT1 protein stability via the autophagy pathway. This action compromises mitochondrial homeostasis, impairs intestinal barrier integrity, and induces IECs apoptosis. IEC-specific depletion of CKMT1 exacerbated intestinal inflammation and apoptosis in mice with colitis. Clinical analysis of IBD patients revealed elevated levels of PAD4, increased CKMT1 citrullination, and decreased CKMT1 expression. In summary, our findings highlight the crucial role of PAD4 in IBD, where it modulates IECs plasticity via CKMT1 citrullination, suggesting that PAD4 may be a potential therapeutic target for IBD.
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Affiliation(s)
- Shuling Wang
- National Clinical Research Center for Digestive Diseases, Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China
- Changhai Clinical Research Unit, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Yihang Song
- National Clinical Research Center for Digestive Diseases, Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Zhijie Wang
- National Clinical Research Center for Digestive Diseases, Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Xin Chang
- National Clinical Research Center for Digestive Diseases, Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Haicong Wu
- National Clinical Research Center for Digestive Diseases, Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Ziwei Yan
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Jiayi Wu
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China
| | - Zixuan He
- Changhai Clinical Research Unit, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Le Kang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Wenjun Hu
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Tian Xia
- National Clinical Research Center for Digestive Diseases, Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- Changhai Clinical Research Unit, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Zhaoshen Li
- National Clinical Research Center for Digestive Diseases, Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China.
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China.
- Changhai Clinical Research Unit, Changhai Hospital, Naval Medical University, Shanghai, 200433, China.
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China.
| | - Xingxing Ren
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Yu Bai
- National Clinical Research Center for Digestive Diseases, Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China.
- National Key Laboratory of Immunology and Inflammation, Naval Medical University, Shanghai, 200433, China.
- Changhai Clinical Research Unit, Changhai Hospital, Naval Medical University, Shanghai, 200433, China.
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China.
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Liu J, Zhao S, Yang C, Ma L, Wu Q, Meng X, Zheng B, Guo C, Feng K, Shang Q, Liu J, Wang J, Zhang J, Shan G, Xu B, Liu Y, Ying J, Wang X, Wang X. Establishment and validation of a multigene model to predict the risk of relapse in hormone receptor-positive early-stage Chinese breast cancer patients. Chin Med J (Engl) 2023; 136:184-193. [PMID: 36921106 PMCID: PMC10106185 DOI: 10.1097/cm9.0000000000002411] [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: 06/26/2022] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND Breast cancer patients who are positive for hormone receptor typically exhibit a favorable prognosis. It is controversial whether chemotherapy is necessary for them after surgery. Our study aimed to establish a multigene model to predict the relapse of hormone receptor-positive early-stage Chinese breast cancer after surgery and direct individualized application of chemotherapy in breast cancer patients after surgery. METHODS In this study, differentially expressed genes (DEGs) were identified between relapse and nonrelapse breast cancer groups based on RNA sequencing. Gene set enrichment analysis (GSEA) was performed to identify potential relapse-relevant pathways. CIBERSORT and Microenvironment Cell Populations-counter algorithms were used to analyze immune infiltration. The least absolute shrinkage and selection operator (LASSO) regression, log-rank tests, and multiple Cox regression were performed to identify prognostic signatures. A predictive model was developed and validated based on Kaplan-Meier analysis, receiver operating characteristic curve (ROC). RESULTS A total of 234 out of 487 patients were enrolled in this study, and 1588 DEGs were identified between the relapse and nonrelapse groups. GSEA results showed that immune-related pathways were enriched in the nonrelapse group, whereas cell cycle- and metabolism-relevant pathways were enriched in the relapse group. A predictive model was developed using three genes ( CKMT1B , SMR3B , and OR11M1P ) generated from the LASSO regression. The model stratified breast cancer patients into high- and low-risk subgroups with significantly different prognostic statuses, and our model was independent of other clinical factors. Time-dependent ROC showed high predictive performance of the model. CONCLUSIONS A multigene model was established from RNA-sequencing data to direct risk classification and predict relapse of hormone receptor-positive breast cancer in Chinese patients. Utilization of the model could provide individualized evaluation of chemotherapy after surgery for breast cancer patients.
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Affiliation(s)
- Jiaxiang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shuangtao Zhao
- Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Chenxuan Yang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Li Ma
- Breast Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050035, China
| | - Qixi Wu
- Research and Development Department, Beijing USCI Medical Laboratory, Beijing 100195, China
| | - Xiangzhi Meng
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Bo Zheng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Changyuan Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Kexin Feng
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qingyao Shang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jiaqi Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jie Wang
- Department of Ultrasound, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jingbo Zhang
- Research and Development Department, Beijing USCI Medical Laboratory, Beijing 100195, China
| | - Guangyu Shan
- Research and Development Department, Beijing USCI Medical Laboratory, Beijing 100195, China
| | - Bing Xu
- Research and Development Department, Beijing USCI Medical Laboratory, Beijing 100195, China
| | - Yueping Liu
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiang Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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Mi Y, Li Q, Liu B, Wang D, Liu Z, Wang T, Wang Y, Zang Y, Zhou Y, Wen Y, Ding Y. Ubiquitous mitochondrial creatine kinase promotes the progression of gastric cancer through a JNK-MAPK/JUN/HK2 axis regulated glycolysis. Gastric Cancer 2023; 26:69-81. [PMID: 36114400 PMCID: PMC9813075 DOI: 10.1007/s10120-022-01340-7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/02/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Ubiquitous mitochondrial creatine kinase (uMtCK) transfers high-energy phosphates from mitochondrially generated ATP to creatine to generate phosphocreatine. uMtCK overexpression has been reported in several malignant tumors, however, the clinical significance and impact of uMtCK in gastric cancer (GC) has not been comprehensively studied. METHODS We first examined uMtCK expression in GC by quantitative real-time PCR and western blot assays. Then the clinicopathological significance of aberrant uMtCK expression was determined by immunohistochemical staining in a GC tissue microarray. Kaplan-Meier analysis was used for survival analysis. The biological functions of uMtCK in GC cells were explored by wound-healing, transwell assays and glucose metabolism assays in vitro as well as a liver metastasis model by spleen injection in nude mice in vivo. RESULTS We verified that the expression of uMtCK was substantially elevated in GC tissues, significantly associating with a poorer prognosis in GC patients, especially for those with advanced stage. In univariate and multivariate analyses, uMtCK expression emerged as an independent prognostic factor for both disease-free survival and overall survival. Functionally, we demonstrated that uMtCK promoted glycolysis in GC cells and facilitated their migration, invasion and liver metastasis in vitro and in vivo. Mechanistically, uMtCK enhanced GC progression in a HK2-dependent glycolysis via acting the JNK-MAPK/JUN signaling pathway. CONCLUSIONS uMtCK could serve as a novel independent prognostic biomarker as well as potential therapeutic target for GC patients, particularly for GC patients with an advanced UICC stage and tumor recurrence.
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Affiliation(s)
- Yushuai Mi
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Quanhui Li
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Bingtian Liu
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Dehai Wang
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Ziping Liu
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Tianshi Wang
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Yuan Wang
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Yifeng Zang
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Yan Zhou
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Yugang Wen
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 85 Wujin Road, Shanghai, 200080, China
| | - Yinlu Ding
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China.
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Interactions between 14-3-3 Proteins and Actin Cytoskeleton and Its Regulation by microRNAs and Long Non-Coding RNAs in Cancer. ENDOCRINES 2022. [DOI: 10.3390/endocrines3040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
14-3-3s are a family of structurally similar proteins that bind to phosphoserine or phosphothreonine residues, forming the central signaling hub that coordinates or integrates various cellular functions, thereby controlling many pathways important in cancer, cell motility, cell death, cytoskeletal remodeling, neuro-degenerative disorders and many more. Their targets are present in all cellular compartments, and when they bind to proteins they alter their subcellular localization, stability, and molecular interactions with other proteins. Changes in environmental conditions that result in altered homeostasis trigger the interaction between 14-3-3 and other proteins to retrieve or rescue homeostasis. In circumstances where these regulatory proteins are dysregulated, it leads to pathological conditions. Therefore, deeper understanding is needed on how 14-3-3 proteins bind, and how these proteins are regulated or modified. This will help to detect disease in early stages or design inhibitors to block certain pathways. Recently, more research has been devoted to identifying the role of MicroRNAs, and long non-coding RNAs, which play an important role in regulating gene expression. Although there are many reviews on the role of 14-3-3 proteins in cancer, they do not provide a holistic view of the changes in the cell, which is the focus of this review. The unique feature of the review is that it not only focuses on how the 14-3-3 subunits associate and dissociate with their binding and regulatory proteins, but also includes the role of micro-RNAs and long non-coding RNAs and how they regulate 14-3-3 isoforms. The highlight of the review is that it focuses on the role of 14-3-3, actin, actin binding proteins and Rho GTPases in cancer, and how this complex is important for cell migration and invasion. Finally, the reader is provided with super-resolution high-clarity images of each subunit of the 14-3-3 protein family, further depicting their distribution in HeLa cells to illustrate their interactions in a cancer cell.
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Zhou J, Guo H, Zhang Y, Liu H, Dou Q. The role of PTP1B (PTPN1) in the prognosis of solid tumors: A meta-analysis. Medicine (Baltimore) 2022; 101:e30826. [PMID: 36221386 PMCID: PMC9543024 DOI: 10.1097/md.0000000000030826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Protein tyrosine phosphatase 1B (PTP1B) played different role in different solid tumors, and was associated with the prognosis of solid tumors. However, the roles existed controversy. This meta-analysis was performed to determine whether PTP1B was relevant to the prognosis of solid tumors. MATERIALS AND METHODS A literature search in Web of Science, Embase and PubMed databases were performed up to November 1, 2021. A meta-analysis dealed with PTP1B assessment in solid tumors, providing clinical stages and survival comparisons according to the PTP1B status. RESULTS High PTP1B expression was significantly associated with later clinical stage of solid tumors (Odds ratio [OR] 2.25, 95% confidence interval [CI]: 1.71-2.98, P < .001). For solid tumors, the hazard ratio (HR) for disease free survival (DFS) detrimental with high PTP1B expression compared with low PTP1B expression was 1.07 (95%CI: 0.67-1.73, P = .77) with the obvious heterogeneity (P = .03, I2 = 66%). The HR of overall survival (OS) for solid tumors with high PTP1B expression versus low PTP1B expression was 1.26 (95%CI: 1.03-1.55, P = .03) with significant publication bias (t = 3.28, P = .005). Subgroup analysis indicated that the high expression of PTP1B was remarkably correlated with poor OS in colorectal carcinoma, only (HR = 1.43; 95%CI: 1.18-1.74; P = .003). CONCLUSIONS High PTP1B expression is significantly associated with later clinical stage of solid tumors. The high expression of PTP1B is remarkably correlated with poor OS in colorectal carcinoma, only. There is no definite conclusion that PTP1B was, or not associated with DFS and OS of solid tumors because of heterogeneity and publication bias. Whether PTP1B can be used as a biomarker for predicting the prognosis of solid tumors needs further study.
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Affiliation(s)
- Jiupeng Zhou
- Xi’an Chest Hospital, Xi’an, Shaanxi Province, China
- *Correspondence: Jiupeng Zhou, Xian Chest Hospital, Xi’an 710000, Shaanxi Province, China (e-mail: )
| | - Hui Guo
- The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | | | - Heng Liu
- Xi’an Chest Hospital, Xi’an, Shaanxi Province, China
| | - Quanli Dou
- Xi’an Chest Hospital, Xi’an, Shaanxi Province, China
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Yousefi H, Delavar MR, Piroozian F, Baghi M, Nguyen K, Cheng T, Vittori C, Worthylake D, Alahari SK. Hippo signaling pathway: A comprehensive gene expression profile analysis in breast cancer. Biomed Pharmacother 2022; 151:113144. [PMID: 35623167 DOI: 10.1016/j.biopha.2022.113144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/10/2022] [Accepted: 05/15/2022] [Indexed: 11/30/2022] Open
Abstract
Breast cancer (BC) is the most frequently diagnosed malignancy in women and a major public health concern. The Hippo pathway is an evolutionarily conserved signaling pathway that serves as a key regulator for a wide variety of biological processes. Hippo signaling has been shown to have both oncogenic and tumor-suppressive functions in various cancers. Core components of the Hippo pathway consist of various kinases and downstream effectors such as YAP/TAZ. In the current report, differential expression of Hippo pathway elements as well as the correlation of Hippo pathway mRNAs with various clinicopathologic characteristics, including molecular subtypes, receptor status, and methylation status, has been investigated in BC using METABRIC and TCGA datasets. In this review, we note deregulation of several Hippo signaling elements in BC patients. Moreover, we see examples of negative correlations between methylation of Hippo genes and mRNA expression. The expression of Hippo genes significantly varies between different receptor subgroups. Because of the clear associations between mRNA expression and methylation status, DNA methylation may be one of the mechanisms that regulate the Hippo pathway in BC cells. Differential expression of Hippo genes among various BC molecular subtypes suggests that Hippo signaling may function differently in different subtypes of BC. Our data also highlights an interesting link between Hippo components' transcription and ER negativity in BC. In conclusion, substantial deregulation of Hippo signaling components suggests an important role of these genes in breast cancer.
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Affiliation(s)
- Hassan Yousefi
- Louisiana State University Health Science Center (LSUHSC), Biochemistry & Molecular Biology, New Orleans, LA, USA
| | - Mahsa Rostamian Delavar
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Masoud Baghi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Khoa Nguyen
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Thomas Cheng
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Cecilia Vittori
- Louisiana State University Health Sciences Center and Stanley S. Scott Cancer Center, New Orleans, LA, USA
| | - David Worthylake
- Louisiana State University Health Science Center (LSUHSC), Biochemistry & Molecular Biology, New Orleans, LA, USA
| | - Suresh K Alahari
- Louisiana State University Health Science Center (LSUHSC), Biochemistry & Molecular Biology, New Orleans, LA, USA.
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Novel Diagnostic Biomarkers in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23020852. [PMID: 35055034 PMCID: PMC8776048 DOI: 10.3390/ijms23020852] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/27/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is still a leading cause of cancer death worldwide. Less than half of cases are diagnosed when the cancer is locally advanced. CRC is a heterogenous disease associated with a number of genetic or somatic mutations. Diagnostic markers are used for risk stratification and early detection, which might prolong overall survival. Nowadays, the widespread use of semi-invasive endoscopic methods and feacal blood tests characterised by suboptimal accuracy of diagnostic results has led to the detection of cases at later stages. New molecular noninvasive tests based on the detection of CRC alterations seem to be more sensitive and specific then the current methods. Therefore, research aiming at identifying molecular markers, such as DNA, RNA and proteins, would improve survival rates and contribute to the development of personalized medicine. The identification of “ideal” diagnostic biomarkers, having high sensitivity and specificity, being safe, cheap and easy to measure, remains a challenge. The purpose of this review is to discuss recent advances in novel diagnostic biomarkers for tumor tissue, blood and stool samples in CRC patients.
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Zhang L, Bu P. The two sides of creatine in cancer. Trends Cell Biol 2021; 32:380-390. [PMID: 34895811 DOI: 10.1016/j.tcb.2021.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022]
Abstract
Creatine is a nitrogen-containing organic acid naturally existing in mammals. It can be converted into phosphocreatine to provide energy for muscle and nerve tissues. Creatine and its analog, cyclocreatine, have been considered cancer suppressive metabolites due to their effects on suppression of subcutaneous cancer growth. Recently, emerging studies have demonstrated the promoting effect of creatine on cancer metastasis. Orthotopic mouse models revealed that creatine promoted invasion and metastasis of pancreatic cancer, colorectal cancer, and breast cancer. Thus, creatine possesses considerably complicated roles in cancer progression. In this review, we systematically summarized the role of creatine in tumor progression, which will call to caution when considering creatine supplementation to clinically treat cancer patients.
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Affiliation(s)
- Liwen Zhang
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengcheng Bu
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China.
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10
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Iskandar A, Zulkifli NW, Ahmad MK, Theva Das K, Zulkifle N. OTUB1 expression and interaction network analyses in MCF-7 breast cancer cells. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Sanchez-Lopez JM, Mandujano-Tinoco EA, Garcia-Venzor A, Lozada-Rodriguez LF, Zampedri C, Uribe-Carvajal S, Melendez-Zajgla J, Maldonado V, Lizarraga F. Integrative analysis of transcriptional profile reveals LINC00052 as a suppressor of breast cancer cell migration. Cancer Biomark 2021; 30:365-379. [PMID: 33361583 DOI: 10.3233/cbm-200337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Long-non-coding RNAs, a class of transcripts with lengths > 200 nt, play key roles in tumour progression. Previous reports revealed that LINC00052 (long intergenic non-coding RNA 00052) was strongly downregulated during breast cancer multicellular spheroids formation and suggested a role in cell migration and oxidative metabolism. OBJECTIVE To examine the function of LINC00052 in MCF-7 breast cancer cells. METHODS Loss-of-function studies were performed to evaluate LINC00052 role on MCF-7 breast cancer cells. Microarray expression assays were performed to determine genes and cellular functions modified after LINC00052 knockdown. Next, the impact of LINC00052 depletion on MCF-7 cell respiration and migration was evaluated. RESULTS 1,081 genes were differentially expressed upon LINC00052 inhibition. Gene set enrichment analysis, Gene Ontology and Key Pathway Advisor analysis showed that signalling networks related to cell migration and oxidative phosphorylation were enriched. However, whereas LINC00052 knockdown in MCF-7 cells revealed marginal difference in oxygen consumption rates when compared with control cells, LINC00052 inhibition enhanced cell migration in vitro and in vivo, as observed using a Zebrafish embryo xenotransplant model. CONCLUSION Our data show that LINC00052 modulates MCF-7 cell migration. Genome-wide microarray experiments suggest that cancer cell migration is affected by LINC00052 through cytoskeleton modulation and Notch/β-catenin/NF-κB signalling pathways.
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Affiliation(s)
- Jose Manuel Sanchez-Lopez
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Postgraduate Program in Biological Sciences, Faculty of Medicine, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Edna Ayerim Mandujano-Tinoco
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Laboratory of Connective Tissue, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación Luís Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Alfredo Garcia-Venzor
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - Cecilia Zampedri
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Salvador Uribe-Carvajal
- Department of Molecular Genetics, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge Melendez-Zajgla
- Functional Genomics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Vilma Maldonado
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Floria Lizarraga
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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12
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Transcript levels of keratin 1/5/6/14/15/16/17 as potential prognostic indicators in melanoma patients. Sci Rep 2021; 11:1023. [PMID: 33441834 PMCID: PMC7806772 DOI: 10.1038/s41598-020-80336-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Keratins (KRTs), the intermediate filament-forming proteins of epithelial cells, are extensively used as diagnostic biomarkers in cancers and associated with tumorigenesis and metastasis in multiple cancers. However, the diverse expression patterns and prognostic values of KRTs in melanoma have yet to be elucidated. In the current study, we examined the transcriptional and clinical data of KRTs in patients with melanoma from GEO, TCGA, ONCOMINE, GEPIA, cBioPortal, TIMER and TISIDB databases. We found that the mRNA levels of KRT1/2/5/6/8/10/14/15/16/17 were significantly differential expressed between primary melanoma and metastatic melanoma. The expression levels of KRT1/2/5/6/10/14/15/16/17 were correlated with advanced tumor stage. Survival analysis revealed that the high transcription levels of KRT1/5/6/14/15/16/17 were associated with low overall survival in melanoma patients. GSEA analysis indicated that the most involved hallmarks pathways were P53 pathway, KRAS signaling, estrogen response early and estrogen response late. Furthermore, we found some correlations among the expression of KRTs and the infiltration of immune cells. Our study may provide novel insights for the selection of prognostic biomarkers for melanoma.
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13
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Liu W, Zou J, Ren R, Liu J, Zhang G, Wang M. A Novel 10-Gene Signature Predicts Poor Prognosis in Low Grade Glioma. Technol Cancer Res Treat 2021; 20:1533033821992084. [PMID: 33550903 PMCID: PMC7876581 DOI: 10.1177/1533033821992084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/23/2020] [Accepted: 01/13/2021] [Indexed: 11/29/2022] Open
Abstract
AIM Low grade glioma (LGG) is a lethal brain cancer with relatively poor prognosis in young adults. Thus, this study was performed to develop novel molecular biomarkers to effectively predict the prognosis of LGG patients and finally guide treatment decisions. METHODS survival-related genes were determined by Kaplan-Meier survival analysis and multivariate Cox regression analysis using the expression and clinical data of 506 LGG patients from The Cancer Genome Atlas (TCGA) database and independently validated in a Chinese Glioma Genome Atlas (CGGA) dataset. A prognostic risk score was established based on a linear combination of 10 gene expression levels using the regression coefficients of the multivariate Cox regression models. GSEA was performed to analyze the altered signaling pathways between the high and low risk groups stratified by median risk score. RESULTS We identified a total of 1489 genes significantly correlated with patients' prognosis in LGG. The top 5 protective genes were DISP2, CKMT1B, AQP7, GPR162 and CHGB, the top 5 risk genes were SP1, EYA3, ZSCAN20, ITPRIPL1 and ZNF217 in LGG. The risk score was predictive of poor overall survival and relapse-free survival in LGG patients. Pathways of small cell lung cancer, pathways in cancer, chronic myeloid leukemia, colorectal cancer were the top 4 most enriched pathways in the high risk group. SP1, EYA3, ZSCAN20, ITPRIPL1, ZNF217 and GPR162 were significantly up-regulated, while DISP2, CKMT1B, AQP7 were down-regulated in 523 LGG tissues as compared to 1141 normal brain controls. CONCLUSIONS The 10-gene signature may become novel prognostic and diagnostic biomarkers to considerably improve the prognostic prediction in LGG.
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Affiliation(s)
- Wentao Liu
- Department of Neurosurgery, Qingdao Jiaozhou Central Hospital, Qingdao, Shandong Province, China
| | - Jiaxuan Zou
- Fuzhou Medical College of Nanchang University, Nanchang, Jiangxi Province, China
| | - Rijun Ren
- Department of Neurosurgery, Qingdao Jiaozhou Central Hospital, Qingdao, Shandong Province, China
| | - Jingping Liu
- Department of Neurosurgery, Qingdao Jiaozhou Central Hospital, Qingdao, Shandong Province, China
| | - Gentang Zhang
- Department of Neurosurgery, Qingdao Jiaozhou Central Hospital, Qingdao, Shandong Province, China
| | - Maokai Wang
- Department of Neurosurgery, Qingdao Jiaozhou Central Hospital, Qingdao, Shandong Province, China
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14
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DEAD-box RNA helicase protein DDX21 as a prognosis marker for early stage colorectal cancer with microsatellite instability. Sci Rep 2020; 10:22085. [PMID: 33328538 PMCID: PMC7745018 DOI: 10.1038/s41598-020-79049-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/30/2020] [Indexed: 12/29/2022] Open
Abstract
DEAD-box RNA helicase DDX21 (also named nucleolar RNA helicase 2) is a nuclear autoantigen with undefined roles in cancer. To explore possible roles of autoimmune recognition in cancer immunity, we examined DDX21 protein expression in colorectal cancer tissue and its association with patient clinical outcomes. Unbiased deep proteomic profiling of two independent colorectal cancer cohorts using mass spectrometry showed that DDX21 protein was significantly upregulated in cancer relative to benign mucosa. We then examined DDX21 protein expression in a validation group of 710 patients, 619 of whom with early stage and 91 with late stage colorectal cancers. DDX21 was detected mostly in the tumor cell nuclei, with high expression in some mitotic cells. High levels of DDX21 protein were found in 28% of stage I, 21% of stage II, 30% of stage III, and 32% of stage IV colorectal cancer cases. DDX21 expression levels correlated with non-mucinous histology in early stage cancers but not with other clinicopathological features such as patient gender, age, tumor location, tumor grade, or mismatch repair status in any cancer stage. Kaplan-Meier analyses revealed that high DDX21 protein levels was associated with longer survival in patients with early stage colorectal cancer, especially longer disease-free survival in patients with microsatellite instability (MSI) cancers, but no such correlations were found for the microsatellite stable subtype or late stage colorectal cancer. Univariate and multivariate analyses also identified high DDX21 protein expression as an independent favorable prognostic marker for early stage MSI colorectal cancer.
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15
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Parajón E, Surcel A, Robinson DN. The mechanobiome: a goldmine for cancer therapeutics. Am J Physiol Cell Physiol 2020; 320:C306-C323. [PMID: 33175572 DOI: 10.1152/ajpcell.00409.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer progression is dependent on heightened mechanical adaptation, both for the cells' ability to change shape and to interact with varying mechanical environments. This type of adaptation is dependent on mechanoresponsive proteins that sense and respond to mechanical stress, as well as their regulators. Mechanoresponsive proteins are part of the mechanobiome, which is the larger network that constitutes the cell's mechanical systems that are also highly integrated with many other cellular systems, such as gene expression, metabolism, and signaling. Despite the altered expression patterns of key mechanobiome proteins across many different cancer types, pharmaceutical targeting of these proteins has been overlooked. Here, we review the biochemistry of key mechanoresponsive proteins, specifically nonmuscle myosin II, α-actinins, and filamins, as well as the partnering proteins 14-3-3 and CLP36. We also examined a wide range of data sets to assess how gene and protein expression levels of these proteins are altered across many different cancer types. Finally, we determined the potential of targeting these proteins to mitigate invasion or metastasis and suggest that the mechanobiome is a goldmine of opportunity for anticancer drug discovery and development.
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Affiliation(s)
- Eleana Parajón
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexandra Surcel
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Douglas N Robinson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
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16
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Engbrecht M, Mangerich A. The Nucleolus and PARP1 in Cancer Biology. Cancers (Basel) 2020; 12:cancers12071813. [PMID: 32640701 PMCID: PMC7408768 DOI: 10.3390/cancers12071813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
The nucleolus has been known for a long time to fulfill crucial functions in ribosome biogenesis, of which cancer cells can become addicted to in order to produce sufficient amounts of proteins for cell proliferation. Recently, the nucleolus has emerged as a central regulatory hub in many other cancer-relevant processes, including stress sensing, DNA damage response, cell cycle control, and proteostasis. This fostered the idea that nucleolar processes can be exploited in cancer therapy. Interestingly, a significant proportion of poly(ADP-ribose) polymerase 1 (PARP1) molecules are localized in the nucleolus and PARP1 also plays crucial roles in many processes that are important in cancer biology, including genome maintenance, replication, transcription, and chromatin remodeling. Furthermore, during the last years, PARP1 came into focus in oncology since it represents a promising target of pharmacological PARP inhibitors in various types of cancers. Here, we provide an overview of our current understanding on the role of PARP1 in nucleolar functions and discuss potential implications in cancer biology and therapy.
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17
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A novel signature based on microvascular invasion predicts the recurrence of HCC. J Transl Med 2020; 18:272. [PMID: 32631357 PMCID: PMC7336478 DOI: 10.1186/s12967-020-02432-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/20/2020] [Indexed: 12/31/2022] Open
Abstract
Background and objectives In hepatocellular carcinoma (HCC) patients, microvascular invasion (MVI) is associated with worse outcomes regardless of treatment. No single reliable preoperative factor exists to predict MVI. The aim of the work described here was to develop a new MVI− based mRNA biomarker to differentiate between high and low risk patients. Methods Using The Cancer Genome Atlas (TCGA) database, we collected data from 315 HCC patients, including mRNA expression and complete clinical data. We generated a seven-mRNA signature to predict patient outcomes. The mRNA signature was validated using the GSE36376 cohort. Finally, we tested the formula in our own 53 HCC patients using qPCR for the seven mRNAs and analyzing the computed tomography (CT) features. Results This seven‐mRNA signature significantly correlated with length of recurrence-free survival (RFS) and overall survival (OS) for both the training and validation groups. RFS and OS were briefer in high risk versus low risk patients. A Kaplan–Meier analysis also indicated that survival time was significantly shortened in the high risk group versus the low risk group. Time-dependent receiver operating characteristic analysis demonstrated good predictive performance for the seven-mRNA signature. The mRNA signature also acts as an independent factor according to a Multivariate analysis. Our results are consistent with the seven-mRNA formula risk score. Conclusion Our research showed a novel seven-mRNA biomarker based on MVI predicting RFS and OS in HCC patients. This mRNA signature can stratify patients into subgroups based on their risk of recurrence to help guide individualized treatment and precision management in HCC.
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18
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Lin JB, Feng Z, Qiu ML, Luo RG, Li X, Liu B. KRT 15 as a prognostic biomarker is highly expressed in esophageal carcinoma. Future Oncol 2020; 16:1903-1909. [PMID: 32449621 DOI: 10.2217/fon-2019-0603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Aim: To investigate the expression and prognostic value of KRT 15 in esophageal carcinoma. Materials & methods: The expression levels of KRT 15 were measured in 128 cases of esophageal carcinoma and matched adjacent normal tissues by immunohistochemistry and Western blot assays. Results & conclusion: Western blot analysis shown the expression levels of KRT 15 in esophageal carcinoma were significantly higher compared with those in matched adjacent normal tissues (p < 0.001). immunohistochemistry result shown the high-expression rate of KRT 15 in esophageal carcinoma were 56.3%, which was significantly higher than those in normal tissues (35.9%; p = 0.002). KRT 15 high-expression correlated with T stage, lymph node metastasis, tumor node metastasis stage and prognosis (p < 0.05). These data indicate KRT 15 as a prognostic biomarker is highly expressed in esophageal carcinoma.
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Affiliation(s)
- Jian-Bo Lin
- Thoracic Surgery Department, First Affiliated Hospital, Fujian Medical University, Chazhong Road 20#, Fuzhou City, 350005, PR China
| | - Zhi Feng
- Thoracic Surgery Department, First Affiliated Hospital, Fujian Medical University, Chazhong Road 20#, Fuzhou City, 350005, PR China
| | - Ming-Lian Qiu
- Thoracic Surgery Department, First Affiliated Hospital, Fujian Medical University, Chazhong Road 20#, Fuzhou City, 350005, PR China
| | - Rong-Gang Luo
- Thoracic Surgery Department, First Affiliated Hospital, Fujian Medical University, Chazhong Road 20#, Fuzhou City, 350005, PR China
| | - Xu Li
- Thoracic Surgery Department, First Affiliated Hospital, Fujian Medical University, Chazhong Road 20#, Fuzhou City, 350005, PR China
| | - Bo Liu
- Thoracic Surgery Department, First Affiliated Hospital, Fujian Medical University, Chazhong Road 20#, Fuzhou City, 350005, PR China
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19
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McRae EKS, Dupas SJ, Booy EP, Piragasam RS, Fahlman RP, McKenna SA. An RNA guanine quadruplex regulated pathway to TRAIL-sensitization by DDX21. RNA (NEW YORK, N.Y.) 2020; 26:44-57. [PMID: 31653714 PMCID: PMC6913123 DOI: 10.1261/rna.072199.119] [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] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
DDX21 is a newly discovered RNA G-quadruplex (rG4) binding protein with no known biological rG4 targets. In this study we used label-free proteomic MS/MS to identify 26 proteins that are expressed at significantly different levels in cells expressing an rG4-binding deficient DDX21 (M4). MS data are available via ProteomeXchange with identifier PXD013501. From this list we validate MAGED2 as a protein that is regulated by DDX21 through rG4 in its 5'-UTR. MAGED2 protein levels, but not mRNA levels, are reduced by half in cells expressing DDX21 M4. MAGED2 has a repressive effect on TRAIL-R2 expression that is relieved under these conditions, resulting in elevated TRAIL-R2 mRNA and protein in MCF-7 cells, rendering them sensitive to TRAIL-mediated apoptosis. Our work identifies the role of DDX21 in regulation at the translational level through biologically relevant rG4 and shows that MAGED2 protein levels are regulated, at least in part, by the potential to form rG4 in their 5'-UTRs.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Steven J Dupas
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | | | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada T6G 2R7
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
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20
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Xie W, Zhang H, Qin S, Zhang J, Fan X, Yin Y, Liang R, Long H, Yi W, Fu D, Ma C, Lv M, Yu F. The expression and clinical significance of secretory leukocyte proteinase inhibitor (SLPI) in mammary carcinoma using bioinformatics analysis. Gene 2019; 720:144088. [DOI: 10.1016/j.gene.2019.144088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022]
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21
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Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21. Mol Cell 2019; 75:1270-1285.e14. [PMID: 31351877 DOI: 10.1016/j.molcel.2019.06.020] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 04/16/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
Abstract
PARP inhibitors (PARPi) prevent cancer cell growth by inducing synthetic lethality with DNA repair defects (e.g., in BRCA1/2 mutant cells). We have identified an alternative pathway for PARPi-mediated growth control in BRCA1/2-intact breast cancer cells involving rDNA transcription and ribosome biogenesis. PARP-1 binds to snoRNAs, which stimulate PARP-1 catalytic activity in the nucleolus independent of DNA damage. Activated PARP-1 ADP-ribosylates DDX21, an RNA helicase that localizes to nucleoli and promotes rDNA transcription when ADP-ribosylated. Treatment with PARPi or mutation of the ADP-ribosylation sites reduces DDX21 nucleolar localization, rDNA transcription, ribosome biogenesis, protein translation, and cell growth. The salient features of this pathway are evident in xenografts in mice and human breast cancer patient samples. Elevated levels of PARP-1 and nucleolar DDX21 are associated with cancer-related outcomes. Our studies provide a mechanistic rationale for efficacy of PARPi in cancer cells lacking defects in DNA repair whose growth is inhibited by PARPi.
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22
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Yang YF, Lee YC, Wang YY, Wang CH, Hou MF, Yuan SSF. YWHAE promotes proliferation, metastasis, and chemoresistance in breast cancer cells. Kaohsiung J Med Sci 2019; 35:408-416. [PMID: 31001932 DOI: 10.1002/kjm2.12075] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/01/2019] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is the most common female-specific malignancy in Taiwan and developed countries worldwide, and its incidence continues to grow. 14-3-3ε (YWHAE), which belong to 14-3-3 family, it has been reported up-regulated in breast cancer tissues. However, the clinical implication and function of YWHAE in breast cancer remains unclear. In this study, we investigated the prognostic value of the YWHAE in human breast cancer. Immunohistochemistry was used to analyze YWHAE expression in breast cancer tissues. Cell model was applied to examine the functions of YWHAE. The chemotherapeutic agents were used to evaluate the effect of YWHAE in breast cancer cell lines. YWHAE expression was associated with tumor size, lymph node metastasis, and poor patient survival in patients with breast cancer. YWHAE overexpression significantly increased the proliferation, migration, and invasion abilities of breast cancer cells. Knockdown of YWHAE expression reduced the expression of Snail and Twist in breast cancer cells. We also found that YWHAE was responsible for the resistance of breast cancer cells to chemotherapeutic agents, and knockdown of YWHAE enhanced sensitivity to multiple chemotherapeutic agents in breast cancer cells. Taken together, our findings indicated that YWHAE promoted cancer progression and chemoresistance in breast cancer cells and can be a potential therapeutic target for breast cancer.
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Affiliation(s)
- Yi-Fang Yang
- Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yi-Chen Lee
- Department of Anatomy, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Yun Wang
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chie-Hong Wang
- Graduate Institute of Biomedical Science, China Medical University, Taichung, Taiwan
| | - Ming-Feng Hou
- Division of Breast Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,National Sun Yat-Sen University-Kaohsiung Medical University Joint Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shyng-Shiou F Yuan
- Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Medical Research and Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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23
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Kurmi K, Hitosugi S, Yu J, Boakye-Agyeman F, Wiese EK, Larson TR, Dai Q, Machida YJ, Lou Z, Wang L, Boughey JC, Kaufmann SH, Goetz MP, Karnitz LM, Hitosugi T. Tyrosine Phosphorylation of Mitochondrial Creatine Kinase 1 Enhances a Druggable Tumor Energy Shuttle Pathway. Cell Metab 2018; 28:833-847.e8. [PMID: 30174304 PMCID: PMC6281770 DOI: 10.1016/j.cmet.2018.08.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 05/14/2018] [Accepted: 08/03/2018] [Indexed: 11/15/2022]
Abstract
How mitochondrial metabolism is altered by oncogenic tyrosine kinases to promote tumor growth is incompletely understood. Here, we show that oncogenic HER2 tyrosine kinase signaling induces phosphorylation of mitochondrial creatine kinase 1 (MtCK1) on tyrosine 153 (Y153) in an ABL-dependent manner in breast cancer cells. Y153 phosphorylation, which is commonly upregulated in HER2+ breast cancers, stabilizes MtCK1 to increase the phosphocreatine energy shuttle and promote proliferation. Inhibition of the phosphocreatine energy shuttle by MtCK1 knockdown or with the creatine analog cyclocreatine decreases proliferation of trastuzumab-sensitive and -resistant HER2+ cell lines in culture and in xenografts. Finally, we show that cyclocreatine in combination with the HER2 kinase inhibitor lapatinib reduces the growth of a trastuzumab-resistant HER2+ patient-derived xenograft. These findings suggest that activation of the phosphocreatine energy shuttle by MtCK1 Y153 phosphorylation creates a druggable metabolic vulnerability in cancer.
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Affiliation(s)
- Kiran Kurmi
- Molecular Pharmacology and Experimental Therapeutics Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Sadae Hitosugi
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jia Yu
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Elizabeth K Wiese
- Molecular Pharmacology and Experimental Therapeutics Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Thomas R Larson
- Molecular Pharmacology and Experimental Therapeutics Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Yuichi J Machida
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Scott H Kaufmann
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Larry M Karnitz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Taro Hitosugi
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA.
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Zhang H, Zhang Y, Chen C, Zhu X, Zhang C, Xia Y, Zhao Y, Andrisani OM, Kong L. A double-negative feedback loop between DEAD-box protein DDX21 and Snail regulates epithelial-mesenchymal transition and metastasis in breast cancer. Cancer Lett 2018; 437:67-78. [DOI: 10.1016/j.canlet.2018.08.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 01/19/2023]
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25
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Cao J, Wu N, Han Y, Hou Q, Zhao Y, Pan Y, Xie X, Chen F. DDX21 promotes gastric cancer proliferation by regulating cell cycle. Biochem Biophys Res Commun 2018; 505:1189-1194. [PMID: 30322617 DOI: 10.1016/j.bbrc.2018.10.060] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 01/12/2023]
Abstract
DEAD (Asp-Glu-Ala-Asp) cassette helicase 21 (DDX21) is an ATP-dependent RNA helicase that is overexpressed in various malignancies. There is increasing evidence that DDX21 is involved in carcinogenesis and cancer progression by promoting cell proliferation. However, the functional role of DDX21 in gastric cancer is largely unknown. In this study, we observed that DDX21 was significantly up-regulated in gastric cancer tissues compared to paired adjacent normal tissues. The expression of DDX21 was closely related to the pathological stage of gastric cancer. In vitro and in vivo studies had shown that knockdown of DDX21 inhibited gastric cancer cell proliferation, colony formation, G1/S cell cycle transition and xenograft growth, while ectopic expression of DDX21 promoted these cell functions. Mechanically, DDX21 induced gastric cancer cell growth by up-regulating levels of Cyclin D1 and CDK2. Taken together, these results revealed a novel role for DDX21 in the proliferation of gastric cancer cells via the Cyclin D1 and CDK2 pathways. Therefore, DDX21 can be used as a therapeutic target for gastric cancer.
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Affiliation(s)
- Jiayi Cao
- Lab of Tissue Engineering, Faculty of Life Science, Northwest University, 229 Taibai North Road, Xi'an, Shaanxi Province, 710069, People's Republic of China.
| | - Nan Wu
- Lab of Tissue Engineering, Faculty of Life Science, Northwest University, 229 Taibai North Road, Xi'an, Shaanxi Province, 710069, People's Republic of China.
| | - Yuying Han
- Lab of Tissue Engineering, Faculty of Life Science, Northwest University, 229 Taibai North Road, Xi'an, Shaanxi Province, 710069, People's Republic of China.
| | - Qiuqiu Hou
- Lab of Tissue Engineering, Faculty of Life Science, Northwest University, 229 Taibai North Road, Xi'an, Shaanxi Province, 710069, People's Republic of China.
| | - Yu Zhao
- Lab of Tissue Engineering, Faculty of Life Science, Northwest University, 229 Taibai North Road, Xi'an, Shaanxi Province, 710069, People's Republic of China.
| | - Yanan Pan
- Lab of Tissue Engineering, Faculty of Life Science, Northwest University, 229 Taibai North Road, Xi'an, Shaanxi Province, 710069, People's Republic of China.
| | - Xin Xie
- Lab of Tissue Engineering, Faculty of Life Science, Northwest University, 229 Taibai North Road, Xi'an, Shaanxi Province, 710069, People's Republic of China.
| | - Fulin Chen
- Lab of Tissue Engineering, Faculty of Life Science, Northwest University, 229 Taibai North Road, Xi'an, Shaanxi Province, 710069, People's Republic of China.
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26
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Abstract
Isoforms of creatine kinase (CK) generate and use phosphocreatine, a concentrated and highly diffusible cellular "high energy" intermediate, for the main purpose of energy buffering and transfer in order to maintain cellular energy homeostasis. The mitochondrial CK isoform (mtCK) localizes to the mitochondrial intermembrane and cristae space, where it assembles into peripherally membrane-bound, large cuboidal homooctamers. These are part of proteolipid complexes wherein mtCK directly interacts with cardiolipin and other anionic phospholipids, as well as with the VDAC channel in the outer membrane. This leads to a stabilization and cross-linking of inner and outer mitochondrial membrane, forming so-called contact sites. Also the adenine nucleotide translocator of the inner membrane can be recruited into these proteolipid complexes, probably mediated by cardiolipin. The complexes have functions mainly in energy transfer to the cytosol and stimulation of oxidative phosphorylation, but also in restraining formation of reactive oxygen species and apoptosis. In vitro evidence indicates a putative role of mtCK in mitochondrial phospholipid distribution, and most recently a role in thermogenesis has been proposed. This review summarizes the essential structural and functional data of these mtCK complexes and describes in more detail the more recent advances in phospholipid interaction, thermogenesis, cancer and evolution of mtCK.
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27
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Wang J, Zhang X, Ling J, Wang Y, Xu X, Liu Y, Jin C, Ju J, Yuan Y, He F, Zhao C, Wang J, Tian C. KRAB-containing zinc finger protein ZNF496 inhibits breast cancer cell proliferation by selectively repressing ERα activity. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30048-8. [PMID: 30012466 DOI: 10.1016/j.bbagrm.2018.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/25/2018] [Accepted: 07/10/2018] [Indexed: 12/20/2022]
Abstract
KRAB-containing zinc finger proteins (KZNF) constitute the largest family of transcriptional regulators in humans and play critical roles in normal development and tumorigenesis. However, the function and mechanism of most KZNFs remain unclear. Here, we report that ZNF496, a KZNF family member, interacts with the DNA binding domain (DBD) of estrogen receptor alpha (ERα) via its C2H2 domain. This interaction decreases ERα binding to chromatin DNA and results in the repression of ERα transactivation, the selective suppression of ERα target genes, and ultimately in a reduction of ERα-positive cell growth in the presence of E2. An analysis of clinical data revealed that the downregulation of ZNF496 expression is observed only in ERα-positive and not in ERα-negative breast cancer tissues when compared with that in matched adjacent tissues. Lastly, we also observed that the downregulation of ZNF496 is associated with poor recurrence-free survival among patients with breast cancer. Collectively, our findings demonstrate that ZNF496 is a novel ERα-binding protein that acts as a target gene-specific ERα corepressor and inhibits the growth of ERα-positive breast cancer cells.
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Affiliation(s)
- Jinlong Wang
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Department of Pathology, The 422th Hospital of PLA, Zhanjiang, Guangdong Province 524000, China
| | - Xiuyuan Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jiming Ling
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yun Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; College of Animal Science, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Xiaolin Xu
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuchen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chaozhi Jin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jiyu Ju
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China
| | - Yanzhi Yuan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chunling Zhao
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China.
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
| | - Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
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28
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McRae EKS, Davidson DE, Dupas SJ, McKenna SA. Insights into the RNA quadruplex binding specificity of DDX21. Biochim Biophys Acta Gen Subj 2018; 1862:1973-1979. [PMID: 29906500 DOI: 10.1016/j.bbagen.2018.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/28/2018] [Accepted: 06/11/2018] [Indexed: 11/20/2022]
Abstract
Guanine quadruplexes can form in both DNA and RNA and influence many biological processes through various protein interactions. The DEAD-box RNA helicase protein DDX21 has been shown to bind and remodel RNA quadruplexes but little is known about its specificity for different quadruplex species. Previous reports have suggested DDX21 may interact with telomeric repeat containing RNA quadruplex (TERRA), an integral component of the telomere that contributes to telomeric heterochromatin formation and telomere length regulation. Here we report that the C-terminus of DDX21 directly interacts with TERRA. We use, for the first time, 2D saturation transfer difference NMR to map the protein binding site on a ribonucleic acid species and show that the quadruplex binding domain of DDX21 interacts primarily with the phosphoribose backbone of quadruplexes. Furthermore, by mutating the 2'OH of loop nucleotides we can drastically reduce DDX21's affinity for quadruplex, indicating that the recognition of quadruplex and specificity for TERRA is mediated by interactions with the 2'OH of loop nucleotides.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David E Davidson
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Steven J Dupas
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada; Manitoba Institute for Materials, University of Manitoba, Winnipeg, Manitoba, Canada.
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29
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Fan H, Lv P, Mu T, Zhao X, Liu Y, Feng Y, Lv J, Liu M, Tang H. LncRNA n335586/miR-924/CKMT1A axis contributes to cell migration and invasion in hepatocellular carcinoma cells. Cancer Lett 2018; 429:89-99. [PMID: 29753758 DOI: 10.1016/j.canlet.2018.05.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 04/19/2018] [Accepted: 05/07/2018] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide and chronic hepatitis B virus (HBV) infection is a major risk factor for HCC. Emerging evidences indicate that long noncoding RNAs (lncRNAs) play a pivotal role in HCC development, but its contribution to HBV-related HCC remains largely unclear. Differentially expressed lncRNAs in HBV-related HCC tissues were identified by deep sequencing in our previous study. The function of lncRNA n335586, one of most up-regulated lncRNAs in HBV-related HCC, was characterized in the present study. We found that the expression of n335586 was significantly increased in HBV positive HCC tissues and cells and was induced by HBV in vitro. Function study indicated that lncRNA n335586 remarkably promoted HCC cells migration, invasion and epithelial-mesenchymal transition (EMT) in vitro and metastasis in vivo. Further mechanistic studies showed lncRNA n335586 promoted HCC cells migration and invasion through facilitating the expression of its host gene CKMT1A by competitively binding miR-924. In conclusion, we demonstrated that the n335586/miR-924/CKMT1A axis contributes to HCC cell migration and invasion, which may be helpful for understanding of pathogenesis of HBV-related HCC.
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Affiliation(s)
- Hongxia Fan
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ping Lv
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ting Mu
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaopei Zhao
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yankun Liu
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; The Cancer Institute, Tangshan People's Hospital, Tangshan, China
| | - Yujie Feng
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jing Lv
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Min Liu
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hua Tang
- Tianjin Life Science Research Center and Department of Pathogen Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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30
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Lin WF, Lin XL, Fu SW, Yang L, Tang CT, Gao YJ, Chen HY, Ge ZZ. Pseudopod-associated protein KIF20B promotes Gli1-induced epithelial-mesenchymal transition modulated by pseudopodial actin dynamic in human colorectal cancer. Mol Carcinog 2018; 57:911-925. [PMID: 29573464 DOI: 10.1002/mc.22812] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/27/2018] [Accepted: 03/20/2018] [Indexed: 12/30/2022]
Abstract
Kinesin family member 20B (KIF20B) has been reported to have an oncogenic role in bladder and hepatocellular cancer cells, but its role in colorectal cancer (CRC) progression remains unclear. In this study, we assessed the mRNA and protein levels of KIF20B in CRC tissues using qRT-PCR and immunohistochemistry, respectively. KIF20B was overexpressed in CRC tissues and was associated with cancer invasion and metastasis. Mechanistically, KIF20B overexpression promoted the epithelial-mesenchymal transition (EMT) process mediated by glioma-associated oncogene 1 (Gli1) as well as CRC cell migration and invasion. Interestingly, KIF20B was localized in pseudopod protrusions of CRC cells and influenced the formation of cell protrusions, especially the EMT-related invadopodia. Moreover, intracellular actin dynamic participated in the modulation of the Gli1-mediated EMT and EMT-related cell pseudopod protrusion formation induced by KIF20B. We identified a role for KIF20B in CRC progression and revealed a correlation between KIF20B expression in CRC tissues and patient prognosis. The underlying mechanism was associated with the Gli1-mediated EMT and EMT-related cell protrusion formation modulated by intracellular actin dynamic. Thus, KIF20B may be a potential biomarker and promising treatment target for CRC.
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Affiliation(s)
- Wen-Feng Lin
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China.,Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang Province, China
| | - Xiao-Lu Lin
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China.,Department of Digestive Endoscopy, Fujian Provincial Hospital, Provincial Clinic Medical College, Fujian Medical University, Fuzhou, China
| | - Seng-Wang Fu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Li Yang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Chao-Tao Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yun-Jie Gao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Hao-Yan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhi-Zheng Ge
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
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31
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Misiewicz-Krzeminska I, Corchete LA, Rojas EA, Martínez-López J, García-Sanz R, Oriol A, Bladé J, Lahuerta JJ, Miguel JS, Mateos MV, Gutiérrez NC. A novel nano-immunoassay method for quantification of proteins from CD138-purified myeloma cells: biological and clinical utility. Haematologica 2018; 103:880-889. [PMID: 29545347 PMCID: PMC5927993 DOI: 10.3324/haematol.2017.181628] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/31/2018] [Indexed: 12/30/2022] Open
Abstract
Protein analysis in bone marrow samples from patients with multiple myeloma has been limited by the low concentration of proteins obtained after CD138+ cell selection. A novel approach based on capillary nano-immunoassay could make it possible to quantify dozens of proteins from each myeloma sample in an automated manner. Here we present a method for the accurate and robust quantification of the expression of multiple proteins extracted from CD138-purified multiple myeloma samples frozen in RLT Plus buffer, which is commonly used for nucleic acid preservation and isolation. Additionally, the biological and clinical value of this analysis for a panel of 12 proteins essential to the pathogenesis of multiple myeloma was evaluated in 63 patients with newly diagnosed multiple myeloma. The analysis of the prognostic impact of CRBN/Cereblon and IKZF1/Ikaros mRNA/protein showed that only the protein levels were able to predict progression-free survival of patients; mRNA levels were not associated with prognosis. Interestingly, high levels of Cereblon and Ikaros proteins were associated with longer progression-free survival only in patients who received immunomodulatory drugs and not in those treated with other drugs. In conclusion, the capillary nano-immunoassay platform provides a novel opportunity for automated quantification of the expression of more than 20 proteins in CD138+ primary multiple myeloma samples.
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Affiliation(s)
- Irena Misiewicz-Krzeminska
- Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Spain.,National Medicines Institute, Warsaw, Poland
| | - Luis Antonio Corchete
- Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Spain
| | - Elizabeta A Rojas
- Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital 12 de Octubre, CNIO, Complutense University, CIBERONC, Madrid, Spain
| | - Ramón García-Sanz
- Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Spain.,Hospital Universitario de Salamanca, CIBERONC, Spain
| | - Albert Oriol
- Hospital Germans Trias i Pujol, Barcelona, Spain
| | | | | | - Jesús San Miguel
- Clínica Universidad de Navarra, CIMA, IDISNA, CIBERONC, Pamplona, Spain
| | - María-Victoria Mateos
- Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain.,Institute of Biomedical Research of Salamanca (IBSAL), Spain.,Hospital Universitario de Salamanca, CIBERONC, Spain
| | - Norma C Gutiérrez
- Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain .,Institute of Biomedical Research of Salamanca (IBSAL), Spain.,Hospital Universitario de Salamanca, CIBERONC, Spain
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32
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Kozin SV, Maimon N, Wang R, Gupta N, Munn L, Jain RK, Garkavtsev I. Secretory leukocyte protease inhibitor (SLPI) as a potential target for inhibiting metastasis of triple-negative breast cancers. Oncotarget 2017; 8:108292-108302. [PMID: 29312532 PMCID: PMC5752445 DOI: 10.18632/oncotarget.22660] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/30/2017] [Indexed: 01/29/2023] Open
Abstract
SLPI has been implicated in the progression and metastasis of certain cancers. However, the effects of SLPI seem to be tumor-specific and the mechanisms remain poorly defined. Here, we demonstrate that highly metastatic, triple-negative breast cancer (TNBC) 4T1 cells secreted more SLPI compared to their non-metastatic counterparts. Furthermore, SLPI secretion directly correlated with spontaneous lung metastasis from 4T1 tumors orthotopically implanted in mice. Consistent with our experimental results, we also found that higher SLPI expression levels correlate with worse clinical outcome in basal/TNBC patients. Using high-throughput screening we identified a novel compound, C74, which significantly inhibits SLPI secretion. C74 administration in our mouse model slows the growth of primary 4T1 tumors and inhibits their dissemination to the lung. We also discovered that SLPI physically interacts with the retinoblastoma tumor suppressor protein (Rb) and releases FoxM1 from the Rb-FoxM1 complex, which may activate FoxM1 target genes involved in breast cancer metastasis.
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Affiliation(s)
- Sergey V Kozin
- Department of Radiation Oncology, Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Nir Maimon
- Department of Radiation Oncology, Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Rong Wang
- Department of Radiation Oncology, Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Nisha Gupta
- Department of Radiation Oncology, Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Lance Munn
- Department of Radiation Oncology, Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Rakesh K Jain
- Department of Radiation Oncology, Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Igor Garkavtsev
- Department of Radiation Oncology, Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Boston, MA, USA
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33
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McRae EKS, Booy EP, Moya-Torres A, Ezzati P, Stetefeld J, McKenna SA. Human DDX21 binds and unwinds RNA guanine quadruplexes. Nucleic Acids Res 2017; 45:6656-6668. [PMID: 28472472 PMCID: PMC5499804 DOI: 10.1093/nar/gkx380] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/24/2017] [Indexed: 12/24/2022] Open
Abstract
Guanine quadruplexes (G4s) are an important structure of nucleic acids (DNA and RNA) with roles in several cellular processes. RNA G4s require specialized unwinding enzymes, of which only two have been previously identified. We describe the results of a simple and specific mass spectrometry guided method used to screen HEK293T cell lysate for G4 binding proteins. From these results, we validated the RNA helicase protein DDX21. DDX21 is an established RNA helicase, but has not yet been validated as a G4 binding protein. Through biochemical techniques, we confirm that DDX21-quadruplex RNA interactions are direct and mediated via a site of interaction at the C-terminus of the protein. Furthermore, through monitoring changes in nuclease sensitivity we show that DDX21 can unwind RNA G4. Finally, as proof of principle, we demonstrate the ability of DDX21 to suppress the expression of a protein with G4s in the 3΄ UTR of its mRNA.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aniel Moya-Torres
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, Section of Biomedical Proteomics, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba and Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Manitoba Institute for Materials, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Manitoba Institute for Materials, University of Manitoba, Winnipeg, Manitoba, Canada
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34
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Lu K, Rui G, Liu F, Yang L, Deng X, Shi S, Li Q. 14-3-3ε is a nuclear matrix protein, and its altered expression and localization are associated with curcumin-induced apoptosis of MG-63 cells. Oncol Lett 2017; 15:338-346. [PMID: 29285195 PMCID: PMC5738701 DOI: 10.3892/ol.2017.7283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/13/2017] [Indexed: 12/18/2022] Open
Abstract
The 14-3-3 protein family may regulates protein interaction, transportation and cellular localization. The regulatory role of 14-3-3ε is influenced by its altered localization. In the present study, human osteosarcoma MG-63 cells were treated with curcumin to induce apoptosis. Subsequently, the altered expression and localization of 14-3-3ε and its co-localization with other apoptosis-associated proteins during apoptosis was investigated. Analysis of nuclear matrix proteins (NMPs), using two-dimensional gel electrophoresis with matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry, revealed that 14-3-3ε existed on the nuclear matrix of MG-63 cells, and its expression was decreased compared with that in control cells following curcumin treatment. In addition, western blot analysis validated that the expression level of 14-3-3ε was downregulated during curcumin-induced apoptosis of MG-63 cells compared with that in control cells. Using immunofluorescence labeling, it was observed that 14-3-3ε was located on the nuclear matrix of MG-63 cells and the distribution of 14-3-3ε on the nuclear matrix was decreased following treatment with curcumin, compared with that in control cells. Double immunofluorescence staining and laser-scanning confocal microscopy demonstrated that 14-3-3ε was co-localized with B-cell lymphoma-2 (Bcl-2), Bcl-2-associated-X protein, p53 and c-FOS transcription factor in MG-63 cells. Furthermore, following treatment with curcumin, these co-localization regions were decreased. The results of the present study revealed that 14-3-3ε is an NMP in MG-63 cells, and its altered expression and co-localization with apoptosis-associated proteins indicated an important function of 14-3-3ε in apoptosis of MG-63 cells. Additional studies are required to investigate the results of the present study.
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Affiliation(s)
- Kun Lu
- Department of Basic Medicine, Medical College of Xiamen University, Xiamen, Fujian 361102, P.R. China.,Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Gang Rui
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - Fan Liu
- Department of Basic Medicine, Medical College of Xiamen University, Xiamen, Fujian 361102, P.R. China.,Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Ling Yang
- Department of Basic Medicine, Medical College of Xiamen University, Xiamen, Fujian 361102, P.R. China.,Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Xiaoling Deng
- Department of Basic Medicine, Medical College of Xiamen University, Xiamen, Fujian 361102, P.R. China.,Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Songlin Shi
- Department of Basic Medicine, Medical College of Xiamen University, Xiamen, Fujian 361102, P.R. China.,Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Qifu Li
- Department of Basic Medicine, Medical College of Xiamen University, Xiamen, Fujian 361102, P.R. China.,Cancer Research Center of Xiamen University, Xiamen, Fujian 361102, P.R. China
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Kanhaiya K, Czeizler E, Gratie C, Petre I. Controlling Directed Protein Interaction Networks in Cancer. Sci Rep 2017; 7:10327. [PMID: 28871116 PMCID: PMC5583175 DOI: 10.1038/s41598-017-10491-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023] Open
Abstract
Control theory is a well-established approach in network science, with applications in bio-medicine and cancer research. We build on recent results for structural controllability of directed networks, which identifies a set of driver nodes able to control an a-priori defined part of the network. We develop a novel and efficient approach for the (targeted) structural controllability of cancer networks and demonstrate it for the analysis of breast, pancreatic, and ovarian cancer. We build in each case a protein-protein interaction network and focus on the survivability-essential proteins specific to each cancer type. We show that these essential proteins are efficiently controllable from a relatively small computable set of driver nodes. Moreover, we adjust the method to find the driver nodes among FDA-approved drug-target nodes. We find that, while many of the drugs acting on the driver nodes are part of known cancer therapies, some of them are not used for the cancer types analyzed here; some drug-target driver nodes identified by our algorithms are not known to be used in any cancer therapy. Overall we show that a better understanding of the control dynamics of cancer through computational modelling can pave the way for new efficient therapeutic approaches and personalized medicine.
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Affiliation(s)
- Krishna Kanhaiya
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
| | - Eugen Czeizler
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
- National Institute for Research and Development for Biological Sciences, Bucharest, Romania
| | - Cristian Gratie
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
| | - Ion Petre
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland.
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Duan F, Xu Y. Applying Multivariate Adaptive Splines to Identify Genes With Expressions Varying After Diagnosis in Microarray Experiments. Cancer Inform 2017; 16:1176935117705381. [PMID: 28579740 PMCID: PMC5422340 DOI: 10.1177/1176935117705381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 02/20/2017] [Indexed: 12/17/2022] Open
Abstract
PURPOSE To analyze a microarray experiment to identify the genes with expressions varying after the diagnosis of breast cancer. METHODS A total of 44 928 probe sets in an Affymetrix microarray data publicly available on Gene Expression Omnibus from 249 patients with breast cancer were analyzed by the nonparametric multivariate adaptive splines. Then, the identified genes with turning points were grouped by K-means clustering, and their network relationship was subsequently analyzed by the Ingenuity Pathway Analysis. RESULTS In total, 1640 probe sets (genes) were reliably identified to have turning points along with the age at diagnosis in their expression profiling, of which 927 expressed lower after turning points and 713 expressed higher after the turning points. K-means clustered them into 3 groups with turning points centering at 54, 62.5, and 72, respectively. The pathway analysis showed that the identified genes were actively involved in various cancer-related functions or networks. CONCLUSIONS In this article, we applied the nonparametric multivariate adaptive splines method to a publicly available gene expression data and successfully identified genes with expressions varying before and after breast cancer diagnosis.
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Affiliation(s)
- Fenghai Duan
- Department of Biostatistics and Center for Statistical Sciences, School of Public Health, Brown University, Providence, RI, USA
| | - Ye Xu
- StubHub, San Francisco, CA, USA
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The creatine kinase pathway is a metabolic vulnerability in EVI1-positive acute myeloid leukemia. Nat Med 2017; 23:301-313. [PMID: 28191887 DOI: 10.1038/nm.4283] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/12/2017] [Indexed: 12/16/2022]
Abstract
Expression of the MECOM (also known as EVI1) proto-oncogene is deregulated by chromosomal translocations in some cases of acute myeloid leukemia (AML) and is associated with poor clinical outcome. Here, through transcriptomic and metabolomic profiling of hematopoietic cells, we reveal that EVI1 overexpression alters cellular metabolism. A screen using pooled short hairpin RNAs (shRNAs) identified the ATP-buffering, mitochondrial creatine kinase CKMT1 as necessary for survival of EVI1-expressing cells in subjects with EVI1-positive AML. EVI1 promotes CKMT1 expression by repressing the myeloid differentiation regulator RUNX1. Suppression of arginine-creatine metabolism by CKMT1-directed shRNAs or by the small molecule cyclocreatine selectively decreased the viability, promoted the cell cycle arrest and apoptosis of human EVI1-positive cell lines, and prolonged survival in both orthotopic xenograft models and mouse models of primary AML. CKMT1 inhibition altered mitochondrial respiration and ATP production, an effect that was abrogated by phosphocreatine-mediated reactivation of the arginine-creatine pathway. Targeting CKMT1 is thus a promising therapeutic strategy for this EVI1-driven AML subtype that is highly resistant to current treatment regimens.
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Identification of TWIST-interacting genes in prostate cancer. SCIENCE CHINA-LIFE SCIENCES 2017; 60:386-396. [DOI: 10.1007/s11427-016-0262-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
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Long-term exposure of MCF-7 breast cancer cells to ethanol stimulates oncogenic features. Int J Oncol 2016; 50:49-65. [PMID: 27959387 PMCID: PMC5182011 DOI: 10.3892/ijo.2016.3800] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/10/2016] [Indexed: 12/24/2022] Open
Abstract
Alcohol consumption is a risk factor for breast cancer. Little is known regarding the mechanism, although it is assumed that acetaldehyde or estrogen mediated pathways play a role. We previously showed that long-term exposure to 2.5 mM ethanol (blood alcohol ~0.012%) of MCF-12A, a human normal epithelial breast cell line, induced epithelial mesenchymal transition (EMT) and oncogenic transformation. In this study, we investigated in the human breast cancer cell line MCF-7, whether a similar exposure to ethanol at concentrations ranging up to peak blood levels in heavy drinkers would increase malignant progression. Short-term (1-week) incubation to ethanol at as low as 1-5 mM (corresponding to blood alcohol concentration of ~0.0048-0.024%) upregulated the stem cell related proteins Oct4 and Nanog, but they were reduced after exposure at 25 mM. Long-term (4-week) exposure to 25 mM ethanol upregulated the Oct4 and Nanog proteins, as well as the malignancy marker Ceacam6. DNA microarray analysis in cells exposed for 1 week showed upregulated expression of metallothionein genes, particularly MT1X. Long-term exposure upregulated expression of some malignancy related genes (STEAP4, SERPINA3, SAMD9, GDF15, KRT15, ITGB6, TP63, and PGR, as well as the CEACAM, interferon related, and HLA gene families). Some of these findings were validated by RT-PCR. A similar treatment also modulated numerous microRNAs (miRs) including one regulator of Oct4 as well as miRs involved in oncogenesis and/or malignancy, with only a few estrogen-induced miRs. Long-term 25 mM ethanol also induced a 5.6-fold upregulation of anchorage-independent growth, an indicator of malignant-like features. Exposure to acetaldehyde resulted in little or no effect comparable to that of ethanol. The previously shown alcohol induction of oncogenic transformation of normal breast cells is now complemented by the current results suggesting alcohol's potential involvement in malignant progression of breast cancer.
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Fontanillo M, Köhn M. Phosphatases: Their Roles in Cancer and Their Chemical Modulators. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:209-40. [PMID: 27236558 DOI: 10.1007/978-3-319-32805-8_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Phosphatases are involved in basically all cellular processes by dephosphorylating cellular components such as proteins, phospholipids and second messengers. They counteract kinases of which many are established oncogenes, and therefore kinases are one of the most important drug targets for targeted cancer therapy. Due to this relationship between kinases and phosphatases, phosphatases are traditionally assumed to be tumour suppressors. However, research findings over the last years prove that this simplification is incorrect, as bona-fide and putative phosphatase oncogenes have been identified. We describe here the role of phosphatases in cancer, tumour suppressors and oncogenes, and their chemical modulators, and discuss new approaches and opportunities for phosphatases as drug targets.
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Affiliation(s)
- Miriam Fontanillo
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Maja Köhn
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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Milioli HH, Vimieiro R, Riveros C, Tishchenko I, Berretta R, Moscato P. The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set. PLoS One 2015; 10:e0129711. [PMID: 26132585 PMCID: PMC4488510 DOI: 10.1371/journal.pone.0129711] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/12/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The prediction of breast cancer intrinsic subtypes has been introduced as a valuable strategy to determine patient diagnosis and prognosis, and therapy response. The PAM50 method, based on the expression levels of 50 genes, uses a single sample predictor model to assign subtype labels to samples. Intrinsic errors reported within this assay demonstrate the challenge of identifying and understanding the breast cancer groups. In this study, we aim to: a) identify novel biomarkers for subtype individuation by exploring the competence of a newly proposed method named CM1 score, and b) apply an ensemble learning, as opposed to the use of a single classifier, for sample subtype assignment. The overarching objective is to improve class prediction. METHODS AND FINDINGS The microarray transcriptome data sets used in this study are: the METABRIC breast cancer data recorded for over 2000 patients, and the public integrated source from ROCK database with 1570 samples. We first computed the CM1 score to identify the probes with highly discriminative patterns of expression across samples of each intrinsic subtype. We further assessed the ability of 42 selected probes on assigning correct subtype labels using 24 different classifiers from the Weka software suite. For comparison, the same method was applied on the list of 50 genes from the PAM50 method. CONCLUSIONS The CM1 score portrayed 30 novel biomarkers for predicting breast cancer subtypes, with the confirmation of the role of 12 well-established genes. Intrinsic subtypes assigned using the CM1 list and the ensemble of classifiers are more consistent and homogeneous than the original PAM50 labels. The new subtypes show accurate distributions of current clinical markers ER, PR and HER2, and survival curves in the METABRIC and ROCK data sets. Remarkably, the paradoxical attribution of the original labels reinforces the limitations of employing a single sample classifiers to predict breast cancer intrinsic subtypes.
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Affiliation(s)
- Heloisa Helena Milioli
- Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Environmental and Life Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Renato Vimieiro
- Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Centro de Informática, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Carlos Riveros
- Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Inna Tishchenko
- Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Regina Berretta
- Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Pablo Moscato
- Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Electrical Engineering and Computer Science, The University of Newcastle, Callaghan, NSW, Australia
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Poitou C, Perret C, Mathieu F, Truong V, Blum Y, Durand H, Alili R, Chelghoum N, Pelloux V, Aron-Wisnewsky J, Torcivia A, Bouillot JL, Parks BW, Ninio E, Clément K, Tiret L. Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study. PLoS One 2015; 10:e0125718. [PMID: 25938420 PMCID: PMC4418598 DOI: 10.1371/journal.pone.0125718] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/17/2015] [Indexed: 11/30/2022] Open
Abstract
Background Bariatric surgery is associated to improvements in obesity-associated comorbidities thought to be mediated by a decrease of adipose inflammation. However, the molecular mechanisms behind these beneficial effects are poorly understood. Methodology/Principal Findings We analyzed RNA-seq expression profiles in adipose tissue from 22 obese women before and 3 months after surgery. Of 15,972 detected genes, 1214 were differentially expressed after surgery at a 5% false discovery rate. Upregulated genes were mostly involved in the basal cellular machinery. Downregulated genes were enriched in metabolic functions of adipose tissue. At baseline, 26 modules of coexpressed genes were identified. The four most stable modules reflected the innate and adaptive immune responses of adipose tissue. A first module reflecting a non-specific signature of innate immune cells, mainly macrophages, was highly conserved after surgery with the exception of DUSP2 and CD300C. A second module reflected the adaptive immune response elicited by T lymphocytes; after surgery, a disconnection was observed between genes involved in T-cell signaling and mediators of the signal transduction such as CXCR1, CXCR2, GPR97, CCR7 and IL7R. A third module reflected neutrophil-mediated inflammation; after surgery, several genes were dissociated from the module, including S100A8, S100A12, CD300E, VNN2, TUBB1 and FAM65B. We also identified a dense network of 19 genes involved in the interferon-signaling pathway which was strongly preserved after surgery, with the exception of DDX60, an antiviral factor involved in RIG-I-mediated interferon signaling. A similar loss of connection was observed in lean mice compared to their obese counterparts. Conclusions/Significance These results suggest that improvements of the inflammatory state following surgery might be explained by a disruption of immuno-inflammatory cascades involving a few crucial molecules which could serve as potential therapeutic targets.
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Affiliation(s)
- Christine Poitou
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Claire Perret
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - François Mathieu
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - Vinh Truong
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - Yuna Blum
- Department of Medicine/Division of Cardiology, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Hervé Durand
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - Rohia Alili
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Nadjim Chelghoum
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Post-Genomic Platform of Pitié-Salpêtrière (P3S), F-75013, Paris, France
| | - Véronique Pelloux
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Judith Aron-Wisnewsky
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Adriana Torcivia
- Assistance Publique-Hôpitaux de Paris, Department of Visceral Surgery, Pitié-Salpêtrière Hospital, F-75013, Paris, France
| | - Jean-Luc Bouillot
- Assistance Publique-Hôpitaux de Paris, Department of General, Digestive and Metabolic Surgery, Ambroise-Paré Hospital, F- 92100, Boulogne-Billancourt, France
| | - Brian W. Parks
- Department of Medicine/Division of Cardiology, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Ewa Ninio
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
| | - Karine Clément
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Nutriomics team, F-75005, Paris, France
| | - Laurence Tiret
- Institute of Cardiometabolism And Nutrition (ICAN), Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Nutrition Department, F-75013, Paris, France
- Sorbonne Universités, University Pierre et Marie Curie (UPMC), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1166, Genomics and Pathophysiology of Cardiovascular Diseases team, F-75013, Paris, France
- * E-mail:
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Systematic identification of molecular links between core and candidate genes in breast cancer. J Mol Biol 2015; 427:1436-1450. [PMID: 25640309 DOI: 10.1016/j.jmb.2015.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/22/2015] [Accepted: 01/24/2015] [Indexed: 01/07/2023]
Abstract
Despite the remarkable progress achieved in the identification of specific genes involved in breast cancer (BC), our understanding of their complex functioning is still limited. In this manuscript, we systematically explore the existence of direct physical interactions between the products of BC core and associated genes. Our aim is to generate a protein interaction network of BC-associated gene products and suggest potential molecular mechanisms to unveil their role in the disease. In total, we report 599 novel high-confidence interactions among 44 BC core, 54 BC candidate/associated and 96 newly identified proteins. Our findings indicate that this network-based approach is indeed a robust inference tool to pinpoint new potential players and gain insight into the underlying mechanisms of those proteins with previously unknown roles in BC. To illustrate the power of our approach, we provide initial validation of two BC-associated proteins on the alteration of DNA damage response as a result of specific re-wiring interactions. Overall, our BC-related network may serve as a framework to integrate clinical and molecular data and foster novel global therapeutic strategies.
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Zhang Y, Baysac KC, Yee LF, Saporita AJ, Weber JD. Elevated DDX21 regulates c-Jun activity and rRNA processing in human breast cancers. Breast Cancer Res 2014; 16:449. [PMID: 25260534 PMCID: PMC4303128 DOI: 10.1186/s13058-014-0449-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 09/19/2014] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION The DDX21 RNA helicase has been shown to be a nucleolar and nuclear protein involved in ribosome RNA processing and AP-1 transcription. DDX21 is highly expressed in colon cancer, lymphomas, and some breast cancers, but little is known about how DDX21 might promote tumorigenesis. METHODS Immunohistochemistry was performed on a breast cancer tissue array of 187 patients. In order to study the subcellular localization of DDX21 in both tumor tissue and tumor cell lines, indirect immunofluorescence was applied. The effect of DDX21 knockdown was measured by cellular apoptosis, rRNA processing assays, soft agar growth and mouse xenograft imaging. AP-1 transcriptional activity was analyzed with a luciferase reporter and bioluminescence imaging, as well as qRT-PCR analysis of downstream target, cyclin D1, to determine the mechanism of action for DDX21 in breast tumorigenesis. RESULTS Herein, we show that DDX21 is highly expressed in breast cancer tissues and established cell lines. A significant number of mammary tumor tissues and established breast cancer cell lines exhibit nuclear but not nucleolar localization of DDX21. The protein expression level of DDX21 correlates with cell proliferation rate and is markedly induced by EGF signaling. Mechanistically, DDX21 is required for the phosphorylation of c-Jun on Ser73 and DDX21 deficiency markedly reduces the transcriptional activity of AP-1. Additionally, DDX21 promotes rRNA processing in multiple breast cancer cell lines. Tumor cells expressing high levels of endogenous DDX21 undergo apoptosis after acute DDX21 knockdown, resulting in significant reduction of tumorigenicity in vitro and in vivo. CONCLUSIONS Our findings indicate that DDX21 expression in breast cancer cells can promote AP-1 activity and rRNA processing, and thus, promote tumorigenesis by two independent mechanisms. DDX21 could serve as a marker for a subset of breast cancer patients with higher proliferation potential and may be used as a therapeutic target for a subset of breast cancer patients.
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Rosso M, Lapyckyj L, Amiano N, Besso MJ, Sánchez M, Chuluyan E, Vazquez-Levin MH. Secretory Leukocyte Protease Inhibitor (SLPI) expression downregulates E-cadherin, induces β-catenin re-localisation and triggers apoptosis-related events in breast cancer cells. Biol Cell 2014; 106:308-22. [PMID: 25039920 DOI: 10.1111/boc.201300075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 07/01/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND INFORMATION Epithelial cadherin (E-cadherin) is involved in cell-cell adhesion through its extracellular domain, whereas the intracellular domain interacts with adaptor proteins, i.e. β-catenin, links E-cadherin to the actin cytoskeleton and participates in signal transduction events. E-cadherin protects mammary epithelial cells from apoptosis and its loss during tumour progression has been documented. Secretory Leukocyte Protease Inhibitor (SLPI) has anti- and pro-tumourigenic activities but its role in breast cancer has not been fully elucidated. Notwithstanding its relevance, how SLPI affects E-cadherin in breast cancer is still unknown. This study evaluated the effect of SLPI upon E-cadherin/β-catenin expression and apoptosis-related markers in murine (F3II) and human (MCF-7) breast tumour cells either treated with exogenous recombinant human SLPI (rhSLPI) or stably transfected with a plasmid encoding its sequence. RESULTS Addition of rhSLPI to F3II cells caused a decrease (P < 0.05) in E-cadherin transcript and protein levels. Similar results were observed in SLPI-stable F3II transfectants (2C1), and treatment of 2C1 cells with a siRNA toward SLPI restored E-cadherin to control levels. SLPI-expressing cells showed disruption of E-cadherin/β-catenin complex and increased (P < 0.05) percentage of cells depicting nuclear β-catenin localisation. Associated to these changes, 2C1 cells showed increased Bax/Bcl-2 ratio and p21 protein levels, decreased c-Myc protein levels and decreased Cyclin D1 and Claudin-1 transcript levels. No differences in N- and P-cadherin were observed between SLPI-transfected cells and controls. Addition of rhSLPI to MCF-7 cells or stable transfection with SLPI caused a decrease (P < 0.05) in E-cadherin expression (transcript/protein) and its redistribution to the cytoplasm, as well as β-catenin re-localisation to the cell nucleus. CONCLUSIONS Expression of SLPI was associated to a decrease in E-cadherin expression and re-localisation of E-cadherin to the cell cytoplasm and β-catenin to the cell cytoplasm and nucleus, and had pro-apoptotic and cell cycle-arrest effects.
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Affiliation(s)
- Marina Rosso
- Instituto de Biología & Medicina Experimental (IBYME), National Research Council of Argentina (CONICET), Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina
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Bonzheim I, Irmler M, Klier-Richter M, Steinhilber J, Anastasov N, Schäfer S, Adam P, Beckers J, Raffeld M, Fend F, Quintanilla-Martinez L. Identification of C/EBPβ target genes in ALK+ anaplastic large cell lymphoma (ALCL) by gene expression profiling and chromatin immunoprecipitation. PLoS One 2013; 8:e64544. [PMID: 23741337 PMCID: PMC3669320 DOI: 10.1371/journal.pone.0064544] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/16/2013] [Indexed: 12/16/2022] Open
Abstract
C/EBPβ (CCAAT enhancer binding protein) is a transcription factor that plays a crucial role in survival and transformation of ALK+ anaplastic large cell lymphoma (ALCL). The aim of this study was to identify the downstream targets of C/EBPβ responsible for ALK-mediated oncogenesis. C/EBPβ was knocked down in ALK+ ALCL cell lines with a C/EBPβ-shRNA, followed by gene expression profiling (GEP). GEP analysis revealed a reproducible signature of genes that were significantly regulated by C/EBPβ. Classification into biological categories revealed overrepresentation of genes involved in the immune response, apoptosis and cell proliferation. Transcriptional regulation by C/EBPβ was found in 6 of 11 (BCL2A1, G0S2, TRIB1, S100A9, DDX21 and DDIT4) genes investigated by chromatin immunoprecipitation. We demonstrated that BCL2A1, G0S2 and DDX21 play a crucial role in survival and proliferation of ALK+ ALCL cells. DDX21, a gene involved in rRNA biogenesis, was found differentially overexpressed in primary ALK+ ALCL cases. All three candidate genes were validated in primary ALCL cases by either immunohistochemistry or RT-qPCR. In conclusion, we identified and validated several key C/EBPβ-regulated genes with major impact on survival and cell growth in ALK+ ALCL, supporting the central role of C/EBPβ in ALK-mediated oncogenesis.
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MESH Headings
- CCAAT-Enhancer-Binding Protein-beta/antagonists & inhibitors
- CCAAT-Enhancer-Binding Protein-beta/genetics
- CCAAT-Enhancer-Binding Protein-beta/metabolism
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Cell Survival/genetics
- Chromatin Immunoprecipitation
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphoma, Large-Cell, Anaplastic/genetics
- Lymphoma, Large-Cell, Anaplastic/metabolism
- Lymphoma, Large-Cell, Anaplastic/pathology
- Minor Histocompatibility Antigens
- Promoter Regions, Genetic
- Protein Binding
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Signal Transduction
- Transcription, Genetic
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Affiliation(s)
- Irina Bonzheim
- Institute of Pathology and Neuropathology, University Hospital Tübingen and Comprehensive Cancer Center, Eberhard-Karls-University, Tübingen, Germany
- Institute of Pathology, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| | - Margit Klier-Richter
- Institute of Pathology and Neuropathology, University Hospital Tübingen and Comprehensive Cancer Center, Eberhard-Karls-University, Tübingen, Germany
- Institute of Pathology, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| | - Julia Steinhilber
- Institute of Pathology and Neuropathology, University Hospital Tübingen and Comprehensive Cancer Center, Eberhard-Karls-University, Tübingen, Germany
| | - Nataša Anastasov
- Institute of Pathology, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabine Schäfer
- Institute of Pathology and Neuropathology, University Hospital Tübingen and Comprehensive Cancer Center, Eberhard-Karls-University, Tübingen, Germany
| | - Patrick Adam
- Institute of Pathology and Neuropathology, University Hospital Tübingen and Comprehensive Cancer Center, Eberhard-Karls-University, Tübingen, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Experimental Genetics, Technische Universität München, Freising-Weihenstephan, Germany
| | - Mark Raffeld
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen and Comprehensive Cancer Center, Eberhard-Karls-University, Tübingen, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology, University Hospital Tübingen and Comprehensive Cancer Center, Eberhard-Karls-University, Tübingen, Germany
- Institute of Pathology, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
- * E-mail:
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Penna E, Orso F, Cimino D, Vercellino I, Grassi E, Quaglino E, Turco E, Taverna D. miR-214 coordinates melanoma progression by upregulating ALCAM through TFAP2 and miR-148b downmodulation. Cancer Res 2013; 73:4098-111. [PMID: 23667173 DOI: 10.1158/0008-5472.can-12-3686] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Malignant melanoma is one of the most aggressive human cancers, but the mechanisms governing its metastatic dissemination are not fully understood. Upregulation of miR-214 and ALCAM and the loss of TFAP2 expression have been implicated in this process, with TFAP2 a direct target of miR-214. Here, we link miR-214 and ALCAM as well as identify a core role for miR-214 in organizing melanoma metastasis. miR-214 upregulated ALCAM, acting transcriptionally through TFAP2 and also posttranscriptionally through miR-148b (itself controlled by TFAP2), both negative regulators of ALCAM. We also identified several miR-214-mediated prometastatic functions directly promoted by ALCAM. Silencing ALCAM in miR-214-overexpressing melanoma cells reduced cell migration and invasion without affecting growth or anoikis in vitro, and it also impaired extravasation and metastasis formation in vivo. Conversely, cell migration and extravasation was reduced in miR-214-overexpressing cells by upregulation of either miR-148b or TFAP2. These findings were consistent with patterns of expression of miR-214, ALCAM, and miR-148b in human melanoma specimens. Overall, our results define a pathway involving miR-214, miR-148b, TFAP2, and ALCAM that is critical for establishing distant metastases in melanoma.
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Affiliation(s)
- Elisa Penna
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
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Biological features of core networks that result from a high-fat diet in hepatic and pulmonary tissues in mammary tumour-bearing, obesity-resistant mice. Br J Nutr 2012; 110:241-55. [DOI: 10.1017/s0007114512004965] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We previously demonstrated that the chronic consumption of a high-fat diet (HFD) promotes lung and liver metastases of 4T1 mammary carcinoma cells in obesity-resistant BALB/c mice. To examine early transcriptional responses to tumour progression in the liver and lungs of HFD-fed mice, 4-week-old female BALB/c mice were divided into four groups: sham-injected, control diet (CD)-fed; sham-injected, HFD-fed (SH); 4T1 cell-injected, CD-fed (TC); 4T1 cell-injected, HFD-fed (TH). Following 16 weeks of either a CD or HFD, 4T1 cells were injected into the mammary fat pads of mice in the TC and TH groups and all mice were continuously fed identical diets. At 14 d post-injection, RNA was isolated from hepatic and pulmonary tissues for microarray analysis of mRNA expression. Functional annotation and core network analyses were conducted for the TH/SH Unique gene set. Inflammation in hepatic tissues and cell mitosis in pulmonary tissues were the most significant biological functions in the TH/SH Unique gene set. The biological core networks of the hepatic TH/SH Unique gene set were characterised as those genes involved in the activation of acute inflammatory responses (Orm1, Lbp, Hp and Cfb), disordered lipid metabolism and deregulated cell cycle progression. Networks of the pulmonary Unique gene set displayed the deregulation of cell cycle progression (Cdc20, Cdk1 and Bub1b). These HFD-influenced alterations may have led to favourable conditions for the formation of both pro-inflammatory and pro-mitotic microenvironments in the target organs that promote immune cell infiltration and differentiation, as well as the infiltration and proliferation of metastatic tumour cells.
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Qian XL, Li YQ, Gu F, Liu FF, Li WD, Zhang XM, Fu L. Overexpression of ubiquitous mitochondrial creatine kinase (uMtCK) accelerates tumor growth by inhibiting apoptosis of breast cancer cells and is associated with a poor prognosis in breast cancer patients. Biochem Biophys Res Commun 2012; 427:60-6. [PMID: 22982673 DOI: 10.1016/j.bbrc.2012.08.147] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 08/31/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND Ubiquitous mitochondrial creatine kinase (uMtCK), a mitochondrial isoenzyme of creatine kinase (CK), is a central controller of cellular energy homeostasis. Overexpression of uMtCK has been reported to be associated with a poor prognosis for several tumors. The aim of this study was to assess its association with breast cancer (BCa) and to further investigate its underlying mechanisms. METHOD We first detected uMtCK expression by immunohistochemistry in human BCa tissues and assessed the association with the prognosis of patients. We then evaluated uMtCK expression in crowded and normal condition cultures of several human BCa cell lines. After two stable clones of the MDA-MB-231 cell line with high expression of uMtCK were established, cell growth, apoptosis and mitochondrial apoptotic pathway protein expression were measured in these clones. Finally, tumorigenicity of the above cells was assessed using nude mice to explore the relationship between uMtCK expression and tumor progression. RESULTS uMtCK expression was detected in 85.5% (47 of 55) of the invasive ductal carcinomas of breast tissue, not otherwise specified (IDC-NOS). Expression in BCa tissue was significantly associated with reduced progression-free survival (PFS; P=0.019) and overall survival (OS; P=0.022) of the patients. Up-regulation of uMtCK expression was identified in crowded BCa cells in culture, and the number of apoptotic cells was significantly decreased in uMtCK transfected MDA-MB-231 cell clones (P<0.01). Stabilization of the mitochondrial membrane potential (ΔΨm) and down regulation of cytochrome c (cyt c) and activated caspase 9, two components of mitochondrial apoptotic pathway proteins, were also identified in the same clones when cells were crowded in culture. In vivo studies revealed that the transfected tumor cells with uMtCK overexpression induced faster tumor growth in nude mice, along with accelerated animal body weight loss and a significantly lower tumor apoptotic index (AI) (P<0.001). CONCLUSION The results indicated that uMtCK expression is associated with a poor prognosis in BCa and might serve as a tumor marker. In vivo and In vitro evidence suggests that uMtCK overexpression promotes tumor growth by inhibiting apoptosis of tumor cells through stabilizing ΔΨm and down regulating mitochondrial apoptotic pathway proteins. Exploration of therapeutic agents targeting the expression of uMtCK may have practical value for BCa patients.
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Affiliation(s)
- Xiao-Long Qian
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
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50
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Abstract
Oestrogen receptor alpha (ERα) is a ligand-dependent transcription factor that mediates oestrogen effects in hormone-responsive cells. Following oestrogenic activation, ERα directly regulates the transcription of target genes via DNA binding. MicroRNAs (miRNAs) represent a class of small noncoding RNAs that function as negative regulators of protein-coding gene expression. They are found aberrantly expressed or mutated in cancer, suggesting their crucial role as either oncogenes or tumour suppressor genes. Here, we analysed changes in miRNA expression in response to oestrogen in hormone-responsive breast cancer MCF-7 and ZR-75.1 cells by microarray-mediated expression profiling. This led to the identification of 172 miRNAs up- or down-regulated by ERα in response to 17β-oestradiol, of which 52 are similarly regulated by the hormone in the two cell models investigated. To identify mechanisms by which ERα exerts its effects on oestrogen-responsive miRNA genes, the oestrogen-dependent miRNA expression profiles were integrated with global in vivo ERα binding site mapping in the genome by ChIP-Seq. In addition, data from miRNA and messenger RNA (mRNA) expression profiles obtained under identical experimental conditions were compared to identify relevant miRNA target transcripts. Results show that miRNAs modulated by ERα represent a novel genomic pathway to impact oestrogen-dependent processes that affect hormone-responsive breast cancer cell behaviour. MiRNome analysis in tumour tissues from breast cancer patients confirmed a strong association between expression of these small RNAs and clinical outcome of the disease, although this appears to involve only marginally the oestrogen-regulated miRNAs identified in this study.
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