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Baek SH, Foer D, Cahill KN, Israel E, Maiorino E, Röhl A, Boyce JA, Weiss ST. Systems Approaches to Treatment Response to Imatinib in Severe Asthma: A Pilot Study. J Pers Med 2021; 11:240. [PMID: 33805900 PMCID: PMC8064376 DOI: 10.3390/jpm11040240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/23/2022] Open
Abstract
There is an acute need for advances in pharmacologic therapies and a better understanding of novel drug targets for severe asthma. Imatinib, a tyrosine kinase inhibitor, has been shown to improve forced expiratory volume in 1 s (FEV1) in a clinical trial of patients with severe asthma. In a pilot study, we applied systems biology approaches to epithelium gene expression from these clinical trial patients treated with imatinib to better understand lung function response with imatinib treatment. Bronchial brushings from ten imatinib-treated patient samples and 14 placebo-treated patient samples were analyzed. We used personalized perturbation profiles (PEEPs) to characterize gene expression patterns at the individual patient level. We found that strong responders-patients with greater than 20% increase in FEV1-uniquely shared multiple downregulated mitochondrial-related pathways. In comparison, weak responders (5-10% FEV1 increase), and non-responders to imatinib shared none of these pathways. The use of PEEP highlights its potential for application as a systems biology tool to develop individual-level approaches to predicting disease phenotypes and response to treatment in populations needing innovative therapies. These results support a role for mitochondrial pathways in airflow limitation in severe asthma and as potential therapeutic targets in larger clinical trials.
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Affiliation(s)
- Seung Han Baek
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (S.H.B.); (E.M.); (A.R.); (S.T.W.)
| | - Dinah Foer
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (E.I.); (J.A.B.)
| | - Katherine N. Cahill
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
| | - Elliot Israel
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (E.I.); (J.A.B.)
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Enrico Maiorino
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (S.H.B.); (E.M.); (A.R.); (S.T.W.)
| | - Annika Röhl
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (S.H.B.); (E.M.); (A.R.); (S.T.W.)
| | - Joshua A. Boyce
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (E.I.); (J.A.B.)
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA; (S.H.B.); (E.M.); (A.R.); (S.T.W.)
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Abstract
BACKGROUND This study aimed to investigate the expression level of X-linked 4 (BEX4) in patients with gastric cancer (GC) and to investigate the prognostic significance of BEX4. METHODS The mRNA expression of BEX4 was analyzed using the Cancer Genome Atlas (TCGA) datasets. The relationship between the expression of BEX4 and GC patient survival was assessed using a Kaplan-Meier plot and Log Rank test. Multivariate cox regression analysis was used to evaluate prognostic factor. The diagnostic value of BEX4 expression in GC tissue was determined through receiver operating characteristic (ROC) curve analysis. Gene set enrichment analysis (GSEA) was used to explore BEX-4 related signaling pathways in GC. Furthermore, the Human Protein Atlas (HPA) database and GSE62254 dataset were used for further validation. RESULTS BEX4 was expressed at lower level in GC tissues than normal gastric tissues. The lower expression of BEX4 was also validated at protein level in HPA database. The area under the ROC curve for BEX4 expression in normal gastric tissue and GC was 0.791, which presented modest diagnostic value. Kaplan-Meier survival analysis revealed that patients in low BEX4 expression group had a worse prognosis than those with high BEX4 expression (P = .009). Multivariate analysis showed that BEX4 is an independent risk factor for overall survival both in TCGA and GSE62254 (P = .0142, .013, respectively). GSEA identified that the expression of BEX4 was related to DNA replication, RNA polymerase, cell cycle, and P53 signaling pathway. CONCLUSION BEX4 is expressed at low levels in GC. BEX4 expression independently predicted poor OS for GC. It is a promising independent molecular predictor for the diagnosis and prognosis of GC.
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Doi T, Ogawa H, Tanaka Y, Hayashi Y, Maniwa Y. Bex1 significantly contributes to the proliferation and invasiveness of malignant tumor cells. Oncol Lett 2020; 20:362. [PMID: 33133262 PMCID: PMC7590424 DOI: 10.3892/ol.2020.12226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023] Open
Abstract
Invasion has a significant role in cancer progression, including expansion to surrounding tissue and metastasis. Previously, we assessed the invasive ability of cancer cells using an easy-to-prepare double-layered collagen gel hemisphere (DL-CGH) method by which cancer cell invasion can be easily visualized. The present study examined multiple lung adenocarcinoma and malignant pleural mesothelioma (MPM) cell lines using the DL-CGH method and identified inherently invasive cell lines. Next, by comparing gene expression between invasive and non-invasive cells by cDNA microarray, the potential candidate gene brain-expressed x-linked protein 1 (Bex1) was identified to be involved in cancer invasion, as it was highly expressed in the invasive cell lines. Downregulation of Bex1 suppressed the invasion and proliferation of the invasive tumor cell lines. The findings of the present study suggested that Bex1 may promote metastasis in vivo and could be a potential oncogene and molecular therapeutic target in lung adenocarcinoma and MPM.
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Affiliation(s)
- Takefumi Doi
- Division of Thoracic Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Hiroyuki Ogawa
- Department of Thoracic Surgery, Hyogo Cancer Center, Akashi, Hyogo 673-8558, Japan
| | - Yugo Tanaka
- Division of Thoracic Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Yoshitake Hayashi
- Division of Molecular Medicine and Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Yoshimasa Maniwa
- Division of Thoracic Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
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Tan Y, Hu Y, Xiao Q, Tang Y, Chen H, He J, Chen L, Jiang K, Wang Z, Yuan Y, Ding K. Silencing of brain-expressed X-linked 2 (BEX2) promotes colorectal cancer metastasis through the Hedgehog signaling pathway. Int J Biol Sci 2020; 16:228-238. [PMID: 31929751 PMCID: PMC6949152 DOI: 10.7150/ijbs.38431] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022] Open
Abstract
The incidence of colorectal cancer is increasing, and cancer metastasis is one of the major causes of poor outcomes. BEX2 has been reported to be involved in tumor development in several types of cancer, but its role in metastatic colorectal cancer remains largely undefined. Herein, we demonstrated that BEX2 knockout resulted in enhanced migratory and metastatic potential in colorectal cancer cells both in vitro and in vivo, and re-expression of BEX2 in knockout cells could reverse the enhanced migratory capacity. RNA-Seq results indicated that the hedgehog signaling pathway was activated after BEX2 knockout; moreover, the hedgehog signaling inhibitors, GANT61 and GDC-0449 could reverse the migratory enhancement of BEX2-/- colorectal cancer cells. We also demonstrated that the nuclear translocation of Zic2 after BEX2 silencing could activate the hedgehog signaling pathway, while Zic2 knockdown abrogated the migratory enhancement of BEX2-/- cells and inhibited the hedgehog signaling pathway. In summary, our findings suggest that BEX2 negatively modulates the hedgehog signaling pathway by retaining Zic2 in the cytoplasm in colorectal cancer cells, thereby inhibiting migration and metastasis of colorectal cancer cells.
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Affiliation(s)
- Yinuo Tan
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yeting Hu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Qian Xiao
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yang Tang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Haiyan Chen
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Jinjie He
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Liubo Chen
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Kai Jiang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Zhanhuai Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Kefeng Ding
- Department of Colorectal Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
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5
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Judd J, Lovas J, Huang GN. Defined factors to reactivate cell cycle activity in adult mouse cardiomyocytes. Sci Rep 2019; 9:18830. [PMID: 31827131 PMCID: PMC6906479 DOI: 10.1038/s41598-019-55027-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 11/22/2019] [Indexed: 12/11/2022] Open
Abstract
Adult mammalian cardiomyocytes exit the cell cycle during the neonatal period, commensurate with the loss of regenerative capacity in adult mammalian hearts. We established conditions for long-term culture of adult mouse cardiomyocytes that are genetically labeled with fluorescence. This technique permits reliable analyses of proliferation of pre-existing cardiomyocytes without complications from cardiomyocyte marker expression loss due to dedifferentiation or significant contribution from cardiac progenitor cell expansion and differentiation in culture. Using this system, we took a candidate gene approach to screen for fetal-specific proliferative gene programs that can induce proliferation of adult mouse cardiomyocytes. Using pooled gene delivery and subtractive gene elimination, we identified a novel functional interaction between E2f Transcription Factor 2 (E2f2) and Brain Expressed X-Linked (Bex)/Transcription elongation factor A-like (Tceal) superfamily members Bex1 and Tceal8. Specifically, Bex1 and Tceal8 both preserved cell viability during E2f2-induced cell cycle re-entry. Although Tceal8 inhibited E2f2-induced S-phase re-entry, Bex1 facilitated DNA synthesis while inhibiting cell death. In sum, our study provides a valuable method for adult cardiomyocyte proliferation research and suggests that Bex family proteins may function in modulating cell proliferation and death decisions during cardiomyocyte development and maturation.
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Affiliation(s)
- Justin Judd
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jonathan Lovas
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Guo N Huang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Department of Physiology, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94158, USA.
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6
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Zhang ZH, Luan ZY, Han F, Chen HQ, Liu WB, Liu JY, Cao J. Diagnostic and prognostic value of the BEX family in lung adenocarcinoma. Oncol Lett 2019; 18:5523-5533. [PMID: 31612060 PMCID: PMC6781490 DOI: 10.3892/ol.2019.10905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/23/2019] [Indexed: 02/07/2023] Open
Abstract
Previous studies have demonstrated that members of the brain-expressed X-linked (BEX) family participate in a wide range of biological functions in normal and tumor tissues. However, their role and clinical significance in lung adenocarcinoma (LUAD) remains unclear. The present study investigated The Cancer Genome Atlas data and revealed that the BEX family was downregulated in LUAD tissues compared with adjacent non-cancerous tissues. Additionally, analysis of LUAD cohorts from the Oncomine database revealed similar results. Furthermore, the expression of BEX members was significantly decreased in several LUAD cell lines compared with normal lung epithelial cells in vitro. The aforementioned data mining and in vitro results suggested that the BEX family may be involved in the development of LUAD. Furthermore, receiver operating characteristic curve analysis revealed that BEX members exhibited high sensitivity and specificity for the diagnosis of patients with LUAD. The low expression levels of BEX1, BEX4 and BEX5 were associated with certain pathologic features, particularly in advanced LUAD. Survival analysis demonstrated that BEX members, particularly BEX4, were involved in the prognosis of patients with LUAD at early and late clinical stages. The results obtained in the current study suggested that BEX members may serve as potential tumor biomarkers for the diagnosis and prognosis of patients with LUAD.
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Affiliation(s)
- Zhong-Hao Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Zhi-Yu Luan
- Department of Medical Affairs, Chinese PLA No. 964 Hospital, Changchun, Jilin 130062, P.R. China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Hong-Qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China
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7
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Jiang K, Jiao Y, Liu Y, Fu D, Geng H, Chen L, Chen H, Shen X, Sun L, Ding K. HNF6 promotes tumor growth in colorectal cancer and enhances liver metastasis in mouse model. J Cell Physiol 2018; 234:3675-3684. [PMID: 30256389 DOI: 10.1002/jcp.27140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/05/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Kai Jiang
- Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education, Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
- Department of Surgical Oncology The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Yurong Jiao
- Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education, Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
- Department of Surgical Oncology The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Yue Liu
- Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education, Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
- Department of Surgical Oncology The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Dongliang Fu
- Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education, Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
- Department of Surgical Oncology The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Haitao Geng
- Department of Oncology Binzhou Medical University Hospital Binzhou China
| | - Liubo Chen
- Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education, Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
- Department of Surgical Oncology The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Haiyan Chen
- Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education, Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
- Department of Surgical Oncology The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Xiangfeng Shen
- Department of Mastopathy Zhejiang Provincial Hospital of TCM Hangzhou China
| | - Lifeng Sun
- Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education, Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Kefeng Ding
- Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education, Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
- Department of Surgical Oncology The Second Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
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8
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Chen H, Xiao Q, Hu Y, Chen L, Jiang K, Tang Y, Tan Y, Hu W, Wang Z, He J, Liu Y, Cai Y, Yang Q, Ding K. ANGPTL1 attenuates colorectal cancer metastasis by up-regulating microRNA-138. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:78. [PMID: 28606130 PMCID: PMC5467265 DOI: 10.1186/s13046-017-0548-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 06/04/2017] [Indexed: 01/05/2023]
Abstract
Background Angiopoietin-like protein 1 (ANGPTL1) has been reported to suppress migration and invasion in lung and breast cancer, acting as a novel tumor suppressor candidate. Nevertheless, its effects on colorectal cancer (CRC) remain poorly defined. In this study, we aim to demonstrate the biological function of ANGPTL1 in CRC cells. Methods We explored ANGPTL1 mRNA expression in human CRC tissues and its association with prognosis. CRC cell lines overexpressing ANGPTL1 or with ANGPTL1 knocked down were constructed and analyzed for changes in proliferation, colony formation, migration and invasion. ANGPTL1-regulated microRNAs were analyzed, and microRNA inhibitor and mimics were used to explore the role of microRNA in ANGPTL1-associated biological function. Results ANGPTL1 mRNA expression was down-regulated in CRC tissues, and high ANGPTL1 expression predicted better survival in CRC patients. ANGPTL1 overexpression resulted in suppressed migration and invasion in vitro, and it prolonged overall survival in mouse models. By contrast, its down-regulation enhanced migration and invasion of CRC cells. MicroRNA-138 expression was positively correlated with ANGPTL1 mRNA level in CRC tissues and up-regulated by ANGPTL1 in CRC cells. In addition, the microRNA-138 inhibitor or mimics could reverse or promote the ANGPTL1-mediated inhibition of the migratory capacity of CRC cells, respectively. Conclusions This study is the first to demonstrate the biological function of ANGPTL1 in CRC cells. ANGPTL1 expression was down-regulated in CRC tissues and inversely correlated with poor survival. ANGPTL1 repressed migration and invasion of CRC cells, and microRNA-138 was involved in this process. Electronic supplementary material The online version of this article (doi:10.1186/s13046-017-0548-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haiyan Chen
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Qian Xiao
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Yeting Hu
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Liubo Chen
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Kai Jiang
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Yang Tang
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Yinuo Tan
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Wangxiong Hu
- The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Zhanhuai Wang
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Jinjie He
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Yue Liu
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Yibo Cai
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Qi Yang
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China.,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China
| | - Kefeng Ding
- Department of Surgical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, Zhejiang, 310009, China. .,The Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, The Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Hangzhou, Zhejiang, China.
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9
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Gao M, Zhao B, Chen M, Liu Y, Xu M, Wang Z, Liu S, Zhang C. Nrf-2-driven long noncoding RNA ODRUL contributes to modulating silver nanoparticle-induced effects on erythroid cells. Biomaterials 2017; 130:14-27. [DOI: 10.1016/j.biomaterials.2017.03.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 02/07/2023]
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10
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Hu Y, Xiao Q, Chen H, He J, Tan Y, Liu Y, Wang Z, Yang Q, Shen X, Huang Y, Yuan Y, Ding K. BEX2 promotes tumor proliferation in colorectal cancer. Int J Biol Sci 2017; 13:286-294. [PMID: 28367093 PMCID: PMC5370436 DOI: 10.7150/ijbs.15171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022] Open
Abstract
BEX2 has been suggested to promote the tumor growth in breast cancer and glioblastoma, while inhibit the proliferation of glioma cells. Thus, the role of BEX2 in tumor was still in debate. Additionally, the biological functions of BEX2 in colorectal cancer (CRC) have not yet been clarified. Here, we reported that BEX2 was overexpressed in advanced CRC from both the GSE14333 database and fresh CRC tissue specimens, and positively correlated with clinical staging. Knockdown of BEX2 significantly decreased the in vitro proliferation of SW620 colorectal cancer cells, suppressed subcutaneous xenograft growth and enhanced the survival of mice with cecal tumors. These effects were mainly mediated by the JNK/c-Jun pathway. Knockdown of BEX2 inhibited JNK/c-Jun phosphorylation, while BEX2 overexpression activated JNK/c-Jun phosphorylation. Moreover, the administration of the JNK-specific inhibitor SP600125 to SW620 with BEX2 overexpression abolished the effect of BEX2 on SW620 cell proliferation. This study reveals that BEX2 promotes colorectal cancer cell proliferation via the JNK/c-Jun pathway, suggesting BEX2 as a potential candidate target for the treatment of CRC.
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Affiliation(s)
- Yeting Hu
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qian Xiao
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haiyan Chen
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jinjie He
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinuo Tan
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yue Liu
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhanhuai Wang
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qi Yang
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiangfeng Shen
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Huang
- Laboratory Animal Research Center, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Ying Yuan
- Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kefeng Ding
- Department of Surgical Oncology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China;; Key Laboratory of Cancer Prevention and Intervention of the China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences of Zhejiang Province, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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11
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Zook P, Pathak HB, Belinsky MG, Gersz L, Devarajan K, Zhou Y, Godwin AK, von Mehren M, Rink L. Combination of Imatinib Mesylate and AKT Inhibitor Provides Synergistic Effects in Preclinical Study of Gastrointestinal Stromal Tumor. Clin Cancer Res 2016; 23:171-180. [PMID: 27370604 DOI: 10.1158/1078-0432.ccr-16-0529] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/31/2016] [Accepted: 06/16/2016] [Indexed: 12/30/2022]
Abstract
PURPOSE Gastrointestinal stromal tumors (GIST) generally harbor activating mutations in the receptor tyrosine kinase KIT or in the related platelet-derived growth factor receptor alpha (PDGFRA). GIST treated with imatinib mesylate or second-line therapies that target mutant forms of these receptors generally escape disease control and progress over time. Inhibiting additional molecular targets may provide more substantial disease control. Recent studies have implicated the PI3K/AKT pathway in the survival of imatinib mesylate-resistant GIST cell lines and tumors. EXPERIMENTAL DESIGN Here, we performed in vitro and in vivo studies evaluating the novel combination of imatinib mesylate with the AKT inhibitor MK-2206 in GIST. Whole-transcriptome sequencing (WTS) of xenografts was performed to explore the molecular aspects of tumor response to this novel combination and to potentially identify additional therapeutic targets in GIST. RESULTS This drug combination demonstrated significant synergistic effects in a panel of imatinib mesylate-sensitive and -resistant GIST cell lines. Furthermore, combination therapy provided significantly greater efficacy, as measured by tumor response and animal survival, in imatinib mesylate-sensitive GIST xenografts as compared with treatment with imatinib mesylate or MK-2206 alone. WTS implicated two neural genes, brain expressed X-linked 1 and neuronal pentraxin I, whose expression was significantly upregulated in combination-treated tumors compared with tumors treated with the two monotherapies. CONCLUSIONS These studies provide strong preclinical justification for combining imatinib mesylate with an AKT inhibitor as a front-line therapy in GIST. In addition, the WTS implicated the BCL-2/BAX/BAD apoptotic pathway as a potential mechanism for this enhanced combination effect. Clin Cancer Res; 23(1); 171-80. ©2016 AACR.
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Affiliation(s)
- Phillip Zook
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Harsh B Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Martin G Belinsky
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Lawrence Gersz
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Karthik Devarajan
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Yan Zhou
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Margaret von Mehren
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Lori Rink
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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12
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Gao W, Li JZH, Chen SQ, Chu CY, Chan JYW, Wong TS. Decreased brain-expressed X-linked 4 (BEX4) expression promotes growth of oral squamous cell carcinoma. J Exp Clin Cancer Res 2016; 35:92. [PMID: 27297407 PMCID: PMC4906687 DOI: 10.1186/s13046-016-0355-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/03/2016] [Indexed: 11/29/2022] Open
Abstract
Background Brain-expressed X-linked (BEX) 4 is a member of BEX family. The functional role of BEX4 in oral squamous cell carcinoma (OSCC) remains unknown. Methods Expression level of BEX family members (BEX1-5) in OSCC tissues and the paired normal epithelial were examined. Functions of epigenetic changes (DNA methylation and histone modifications) on BEX4 suppression in OSCC were examined by zebularine and trichostatin A (TSA) treatment on OSCC cell lines. Lentivector containing full-length BEX4 was used to generate OSCC cell lines with stable BEX4 expression. Effects of BEX4 expression on OSCC proliferation were monitored with xCELLigence RTCA real-time cell analyzer. BEX4-overexpressing CAL27 was implanted into nude mice to evaluate the effects on tumor growth in vivo. The signaling pathways regulated by BEX4 in OSCC was explored using human whole-transcript expression microarray. Results Among the 5 BEX family members, BEX1 and BEX4 showed significant down-regulation in OSCC (P < 0.001). BEX3, in comparison, was overexpressed in the primary tumor. BEX4 expression in OSCC cell lines was re-activated after zebularine and TSA treatment. High BEX4 expression could suppress proliferation of OSCC in vitro. Subcutaneous tumor volume of BEX4-overexpressing CAL27 was remarkably reduced in nude mice. Microarray experiment showed that S100A family members (S100A7, S100A7A, S100A8, S100A9 & S100A12) might be the downstream targets of BEX4 in OSCC. Conclusions BEX4 functions as tumor suppressor by inhibiting proliferation and growth of oral cancer. Decreased BEX4 contributes to the increased proliferative propensity of OSCC.
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Affiliation(s)
- Wei Gao
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
| | - John Zeng-Hong Li
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China.,Department of Otolaryngology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Si-Qi Chen
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
| | - Chiao-Yun Chu
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
| | - Jimmy Yu-Wai Chan
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
| | - Thian-Sze Wong
- Department of Surgery, The University of Hong Kong, Hong Kong SAR, China.
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BEX1 acts as a tumor suppressor in acute myeloid leukemia. Oncotarget 2016; 6:21395-405. [PMID: 26046670 PMCID: PMC4673273 DOI: 10.18632/oncotarget.4095] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/12/2015] [Indexed: 12/25/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease of the myeloid lineage. About 35% of AML patients carry an oncogenic FLT3 mutant making FLT3 an attractive target for treatment of AML. Major problems in the development of FLT3 inhibitors include lack of specificity, poor response and development of a resistant phenotype upon treatment. Further understanding of FLT3 signaling and discovery of novel regulators will therefore help to determine additional pharmacological targets in FLT3-driven AML. In this report, we identified BEX1 as a novel regulator of oncogenic FLT3-ITD-driven AML. We showed that BEX1 expression was down-regulated in a group of AML patients carrying FLT3-ITD. Loss of BEX1 expression resulted in poor overall survival (hazard ratio, HR = 2.242, p = 0.0011). Overexpression of BEX1 in mouse pro-B and myeloid cells resulted in decreased FLT3-ITD-dependent cell proliferation, colony and tumor formation, and in increased apoptosis in vitro and in vivo. BEX1 localized to the cytosolic compartment of cells and significantly decreased FLT3-ITD-induced AKT phosphorylation without affecting ERK1/2 or STAT5 phosphorylation. Our data suggest that the loss of BEX1 expression in FLT3-ITD driven AML potentiates oncogenic signaling and leads to decreased overall survival of the patients.
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14
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Epithelial Cell Transforming 2 and Aurora Kinase B Modulate Formation of Stress Granule–Containing Transcripts from Diverse Cellular Pathways in Astrocytoma Cells. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:1674-87. [DOI: 10.1016/j.ajpath.2016.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 01/26/2016] [Accepted: 02/18/2016] [Indexed: 12/12/2022]
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15
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Brain expressed and X-linked (Bex) proteins are intrinsically disordered proteins (IDPs) and form new signaling hubs. PLoS One 2015; 10:e0117206. [PMID: 25612294 PMCID: PMC4303428 DOI: 10.1371/journal.pone.0117206] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/20/2014] [Indexed: 11/19/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are abundant in complex organisms. Due to their promiscuous nature and their ability to adopt several conformations IDPs constitute important points of network regulation. The family of Brain Expressed and X-linked (Bex) proteins consists of 5 members in humans (Bex1-5). Recent reports have implicated Bex proteins in transcriptional regulation and signaling pathways involved in neurodegeneration, cancer, cell cycle and tumor growth. However, structural and biophysical data for this protein family is almost non-existent. We used bioinformatics analyses to show that Bex proteins contain long regions of intrinsic disorder which are conserved across all members. Moreover, we confirmed the intrinsic disorder by circular dichroism spectroscopy of Bex1 after expression and purification in E. coli. These observations strongly suggest that Bex proteins constitute a new group of IDPs. Based on these findings, together with the demonstrated promiscuity of Bex proteins and their involvement in different signaling pathways, we propose that Bex family members play important roles in the formation of protein network hubs.
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Capurro A, Bodea LG, Schaefer P, Luthi-Carter R, Perreau VM. Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis. Front Neurosci 2015; 8:441. [PMID: 25620908 PMCID: PMC4288238 DOI: 10.3389/fnins.2014.00441] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/15/2014] [Indexed: 01/09/2023] Open
Abstract
The characterization of molecular changes in diseased tissues gives insight into pathophysiological mechanisms and is important for therapeutic development. Genome-wide gene expression analysis has proven valuable for identifying biological processes in neurodegenerative diseases using post mortem human brain tissue and numerous datasets are publically available. However, many studies utilize heterogeneous tissue samples consisting of multiple cell types, all of which contribute to global gene expression values, confounding biological interpretation of the data. In particular, changes in numbers of neuronal and glial cells occurring in neurodegeneration confound transcriptomic analyses, particularly in human brain tissues where sample availability and controls are limited. To identify cell specific gene expression changes in neurodegenerative disease, we have applied our recently published computational deconvolution method, population specific expression analysis (PSEA). PSEA estimates cell-type-specific expression values using reference expression measures, which in the case of brain tissue comprises mRNAs with cell-type-specific expression in neurons, astrocytes, oligodendrocytes and microglia. As an exercise in PSEA implementation and hypothesis development regarding neurodegenerative diseases, we applied PSEA to Parkinson's and Huntington's disease (PD, HD) datasets. Genes identified as differentially expressed in substantia nigra pars compacta neurons by PSEA were validated using external laser capture microdissection data. Network analysis and Annotation Clustering (DAVID) identified molecular processes implicated by differential gene expression in specific cell types. The results of these analyses provided new insights into the implementation of PSEA in brain tissues and additional refinement of molecular signatures in human HD and PD.
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Affiliation(s)
- Alberto Capurro
- Department of Cell Physiology and Pharmacology, University of Leicester Leicester, UK
| | - Liviu-Gabriel Bodea
- Neural Regeneration Unit, Institute of Reconstructive Neurobiology, University of Bonn Bonn, Germany ; Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland St Lucia, QLD, Australia
| | | | - Ruth Luthi-Carter
- Department of Cell Physiology and Pharmacology, University of Leicester Leicester, UK
| | - Victoria M Perreau
- The Bioinformatics Core and The Synaptic Neurobiology Laboratory, The Florey Institute of Neuroscience and Mental Health Parkville, VIC, Australia
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