1
|
Piemonte KM, Webb BM, Bobbitt JR, Majmudar PR, Cuellar-Vite L, Bryson BL, Latina NC, Seachrist DD, Keri RA. Disruption of CDK7 signaling leads to catastrophic chromosomal instability coupled with a loss of condensin-mediated chromatin compaction. J Biol Chem 2023; 299:104834. [PMID: 37201585 PMCID: PMC10300262 DOI: 10.1016/j.jbc.2023.104834] [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: 04/20/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/20/2023] Open
Abstract
Chromatin organization is highly dynamic and modulates DNA replication, transcription, and chromosome segregation. Condensin is essential for chromosome assembly during mitosis and meiosis, as well as maintenance of chromosome structure during interphase. While it is well established that sustained condensin expression is necessary to ensure chromosome stability, the mechanisms that control its expression are not yet known. Herein, we report that disruption of cyclin-dependent kinase 7 (CDK7), the core catalytic subunit of CDK-activating kinase, leads to reduced transcription of several condensin subunits, including structural maintenance of chromosomes 2 (SMC2). Live and static microscopy revealed that inhibiting CDK7 signaling prolongs mitosis and induces chromatin bridge formation, DNA double-strand breaks, and abnormal nuclear features, all of which are indicative of mitotic catastrophe and chromosome instability. Affirming the importance of condensin regulation by CDK7, genetic suppression of the expression of SMC2, a core subunit of this complex, phenocopies CDK7 inhibition. Moreover, analysis of genome-wide chromatin conformation using Hi-C revealed that sustained activity of CDK7 is necessary to maintain chromatin sublooping, a function that is ascribed to condensin. Notably, the regulation of condensin subunit gene expression is independent of superenhancers. Together, these studies reveal a new role for CDK7 in sustaining chromatin configuration by ensuring the expression of condensin genes, including SMC2.
Collapse
Affiliation(s)
- Katrina M Piemonte
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Bryan M Webb
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jessica R Bobbitt
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Parth R Majmudar
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Leslie Cuellar-Vite
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Benjamin L Bryson
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Nicholas C Latina
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ruth A Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of General Medical Sciences-Oncology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
| |
Collapse
|
2
|
Roberts MS, Sahni JM, Schrock MS, Piemonte KM, Weber-Bonk KL, Seachrist DD, Avril S, Anstine LJ, Singh S, Sizemore ST, Varadan V, Summers MK, Keri RA. LIN9 and NEK2 Are Core Regulators of Mitotic Fidelity That Can Be Therapeutically Targeted to Overcome Taxane Resistance. Cancer Res 2020; 80:1693-1706. [PMID: 32054769 PMCID: PMC7165041 DOI: 10.1158/0008-5472.can-19-3466] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/07/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
A significant therapeutic challenge for patients with cancer is resistance to chemotherapies such as taxanes. Overexpression of LIN9, a transcriptional regulator of cell-cycle progression, occurs in 65% of patients with triple-negative breast cancer (TNBC), a disease commonly treated with these drugs. Here, we report that LIN9 is further elevated with acquisition of taxane resistance. Inhibiting LIN9 genetically or by suppressing its expression with a global BET inhibitor restored taxane sensitivity by inducing mitotic progression errors and apoptosis. While sustained LIN9 is necessary to maintain taxane resistance, there are no inhibitors that directly repress its function. Hence, we sought to discover a druggable downstream transcriptional target of LIN9. Using a computational approach, we identified NIMA-related kinase 2 (NEK2), a regulator of centrosome separation that is also elevated in taxane-resistant cells. High expression of NEK2 was predictive of low survival rates in patients who had residual disease following treatment with taxanes plus an anthracycline, suggesting a role for this kinase in modulating taxane sensitivity. Like LIN9, genetic or pharmacologic blockade of NEK2 activity in the presence of paclitaxel synergistically induced mitotic abnormalities in nearly 100% of cells and completely restored sensitivity to paclitaxel, in vitro. In addition, suppressing NEK2 activity with two distinct small molecules potentiated taxane response in multiple in vivo models of TNBC, including a patient-derived xenograft, without inducing toxicity. These data demonstrate that the LIN9/NEK2 pathway is a therapeutically targetable mediator of taxane resistance that can be leveraged to improve response to this core chemotherapy. SIGNIFICANCE: Resistance to chemotherapy is a major hurdle for treating patients with cancer. Combining NEK2 inhibitors with taxanes may be a viable approach for improving patient outcomes by enhancing mitotic defects induced by taxanes alone.
Collapse
Affiliation(s)
- Melyssa S Roberts
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | - Jennifer M Sahni
- Department of Pathology, School of Medicine, New York University, New York, New York
| | - Morgan S Schrock
- Department of Radiation Oncology, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University Medical Center, Columbus, Ohio
| | - Katrina M Piemonte
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | | | - Darcie D Seachrist
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | - Stefanie Avril
- Department of Pathology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Lindsey J Anstine
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | - Salendra Singh
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Steven T Sizemore
- Department of Radiation Oncology, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University Medical Center, Columbus, Ohio
| | - Vinay Varadan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Matthew K Summers
- Department of Radiation Oncology, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University Medical Center, Columbus, Ohio
| | - Ruth A Keri
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| |
Collapse
|
3
|
Wang N, Dong Q, Zhou XN. LMO4 promotes the invasion and proliferation of gastric cancer by activating PI3K-Akt-mTOR signaling. Am J Transl Res 2019; 11:6534-6543. [PMID: 31737204 PMCID: PMC6834506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/21/2019] [Indexed: 06/10/2023]
Abstract
This study assessed the biological functions of LIM-domain-only 4 (LMO4) in gastric cancer (GC) and investigated the underlying molecular mechanisms. It was found that the expression of LMO4 was significantly upregulated in GC tissues and closely associated with clinicopathological factors, overall survival and disease-free survival of patients. After knockdown of LMO4 in MGC-803 and SGC-7901 cells, invasion and proliferation were obviously suppressed. Furthermore, LMO4 knockdown suppressed the phosphorylation of phosphatidylinositol 3-kinase (PI3K), Akt and mammalian target of rapamycin (mTOR). Miltefosine, the inhibitor of PI3K/Akt, and dactolisib, the inhibitor of mTOR, abrogated recombinant LMO4-induced GC cell invasion and proliferation. These results suggest that LMO4 promotes GC cell invasion and proliferation mainly through PI3K-Akt-mTOR signaling. LMO4 may serve as a potential therapeutic target for GC in the future.
Collapse
Affiliation(s)
- Ning Wang
- Department of Gastroenterology, The First Ward, Shijiazhuang First HospitalShijiazhuang 050011, Hebei, P. R. China
| | - Qing Dong
- Department of Oncology, The Fifth Ward, Shijiazhuang First HospitalShijiazhuang 050011, Hebei, P. R. China
| | - Xiao-Na Zhou
- Department of Gastroenterology, The First Ward, Shijiazhuang First HospitalShijiazhuang 050011, Hebei, P. R. China
| |
Collapse
|
4
|
Postmortem vs. neoplastic gene expression: Clues to cancer development and therapy. Med Hypotheses 2019; 133:109381. [PMID: 31476667 DOI: 10.1016/j.mehy.2019.109381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/22/2019] [Indexed: 11/22/2022]
Abstract
Organismal death does not immediately end gene expression. Studies of postmortem gene expression in zebrafish and mice and in the myocardium, liver, prostate, pericardial fluid, and blood of human cadavers have identified genes whose expression is increased after organismal death. Cancer can be considered a form of "un-death" since excessively proliferating cells are typically unusually resistant to apoptosis (programmed cell death), and are subject to strong selective pressure for "uncontrolled life." The changes in gene expression observed in organismal death, particularly in mammals (mice and humans), can be compared to that observed in human neoplasia, and the comparison of these expression patterns can inform us about human cancer. Here we present a hypothesis based on the following three tenets: (a) there will be distinct and opposing patterns of gene expression between the postmortem state and cancer with respect to key physiological outputs such as growth, apoptosis, invasion, and prognosis; (b) cancer cells considered more aggressive (e.g., derived from a metastasis and/or resistant to agents that suppress growth or induce apoptosis) will exhibit expression of relevant genes more unlike that of the postmortem condition while less aggressive neoplastic cells will exhibit gene expression more similar to the postmortem condition; and (c) targeting gene expression in cancer to produce a more postmortem-like pattern will promote less tumorigenic and less aggressive cell phenotypes. To evaluate components (a) and (b) of our hypothesis, we focus on previously published gene expression data from colorectal cancer (CRC) and colonic adenoma cells and compare that to postmortem expression data. This preliminary analysis in general supports our hypothesis, with more aggressive neoplastic cell types exhibiting gene expression patterns most unlike that found in the postmortem condition; this suggests that cancer and the postmortem condition represent opposing ends of a gene expression spectrum in the balance between life and death. Subsequently, we discuss the possibilities for further testing of the hypothesis, particularly for part (c), and we also discuss the possible implications of the hypothesis for cancer therapeutics.
Collapse
|
5
|
The LIM domain binding protein 1, Ldb1, has distinct roles in Neu-induced mammary tumorigenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1590-1597. [DOI: 10.1016/j.bbamcr.2018.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/07/2018] [Accepted: 08/14/2018] [Indexed: 01/15/2023]
|
6
|
LMO1 functions as an oncogene by regulating TTK expression and correlates with neuroendocrine differentiation of lung cancer. Oncotarget 2018; 9:29601-29618. [PMID: 30038707 PMCID: PMC6049873 DOI: 10.18632/oncotarget.25642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/24/2018] [Indexed: 11/25/2022] Open
Abstract
LMO1 encodes a protein containing a cysteine-rich LIM domain involved in protein-protein interactions. Recent studies have shown that LMO1 functions as an oncogene in several cancer types, including non-small cell lung cancer (NSCLC). However, the function of LMO1 in other histological subtypes of lung cancer, such as small cell lung cancer (SCLC), was not investigated. In analyzing the expression of LMO1 across a panel of lung cell lines, we found that LMO1 expression levels were significantly and dramatically higher in SCLC cells, an aggressive neuroendocrine subtype of lung cancer, relative to NSCLC and normal lung cells. In NSCLC cells, LMO1 mRNA levels were significantly correlated with expression of neuroendocrine differentiation markers. Our in vitro investigations indicated that LMO1 had the general property of promoting cell proliferation in lung cancer cells representing different histological subtypes, suggesting a general oncogenic function of LMO1 in lung cancer. In investigating the clinical relevance of LMO1 as an oncogene, we found that a high tumor level of the LMO1 mRNA was an independent predictor of poor patient survival. These results suggest that LMO1 acts as an oncogene, with expression correlated with neuroendocrine differentiation of lung cancer, and that it is a determinant of lung cancer aggressiveness and prognosis. By combining gene expression correlations with patient survival and functional in vitro investigations, we further identified TTK as mediating the oncogenic function of LMO1 in lung cancer cells.
Collapse
|
7
|
de Alcantara Filho PR, Mangone FR, Pavanelli AC, de Bessa Garcia SA, Nonogaki S, de Toledo Osório CAB, de Andrade VP, Nagai MA. Gene expression profiling of triple-negative breast tumors with different expression of secreted protein acidic and cysteine rich (SPARC). BREAST CANCER MANAGEMENT 2018. [DOI: 10.2217/bmt-2017-0019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To determine the expression signature of triple-negative breast cancer (TNBC) with differences of secreted protein acidic and rich in cysteine expression and clinical behavior. Patients, materials & methods: cDNA microarray analysis was performed to determine the expression profiling of TNBC, characterized regarding secreted protein acidic and rich in cysteine expression status. Immunohistochemistry analysis on tissue microarrays containing an independent cohort of TNBC was performed for validation. Results: Negative staining of SOHLH2 and positive staining of DNAJC12 and LIM1 was correlated with a poor outcome of the patients. Conclusion: Our findings provide new information on transcriptome changes associated with the clinical behavior of TNBC that may serve as a potential tool for the identification and characterization of new candidate biomarkers.
Collapse
Affiliation(s)
- Paulo R de Alcantara Filho
- Discipline of Oncology, Department of Radiology & Oncology, Faculty of Medicine, University of São Paulo, 01246–903, São Paulo, Brazil
- Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), 01246–000, São Paulo, Brazil
- Department of Breast Surgery, A. C. Camargo Cancer Center, 01509-020, São Paulo, Brazil
| | - Flavia R Mangone
- Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), 01246–000, São Paulo, Brazil
| | - Ana C Pavanelli
- Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), 01246–000, São Paulo, Brazil
| | - Simone A de Bessa Garcia
- Discipline of Oncology, Department of Radiology & Oncology, Faculty of Medicine, University of São Paulo, 01246–903, São Paulo, Brazil
- Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), 01246–000, São Paulo, Brazil
| | - Suely Nonogaki
- Department of Pathology, A. C. Camargo Cancer Center, 01509-020, São Paulo, Brazil
| | | | - Victor P de Andrade
- Department of Pathology, A. C. Camargo Cancer Center, 01509-020, São Paulo, Brazil
| | - Maria A Nagai
- Discipline of Oncology, Department of Radiology & Oncology, Faculty of Medicine, University of São Paulo, 01246–903, São Paulo, Brazil
- Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), 01246–000, São Paulo, Brazil
| |
Collapse
|
8
|
Dharanipragada P, Vogeti S, Parekh N. iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization. PLoS One 2018; 13:e0195334. [PMID: 29621297 PMCID: PMC5886540 DOI: 10.1371/journal.pone.0195334] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/20/2018] [Indexed: 12/14/2022] Open
Abstract
Discovery of copy number variations (CNVs), a major category of structural variations, have dramatically changed our understanding of differences between individuals and provide an alternate paradigm for the genetic basis of human diseases. CNVs include both copy gain and copy loss events and their detection genome-wide is now possible using high-throughput, low-cost next generation sequencing (NGS) methods. However, accurate detection of CNVs from NGS data is not straightforward due to non-uniform coverage of reads resulting from various systemic biases. We have developed an integrated platform, iCopyDAV, to handle some of these issues in CNV detection in whole genome NGS data. It has a modular framework comprising five major modules: data pre-treatment, segmentation, variant calling, annotation and visualization. An important feature of iCopyDAV is the functional annotation module that enables the user to identify and prioritize CNVs encompassing various functional elements, genomic features and disease-associations. Parallelization of the segmentation algorithms makes the iCopyDAV platform even accessible on a desktop. Here we show the effect of sequencing coverage, read length, bin size, data pre-treatment and segmentation approaches on accurate detection of the complete spectrum of CNVs. Performance of iCopyDAV is evaluated on both simulated data and real data for different sequencing depths. It is an open-source integrated pipeline available at https://github.com/vogetihrsh/icopydav and as Docker’s image at http://bioinf.iiit.ac.in/icopydav/.
Collapse
Affiliation(s)
- Prashanthi Dharanipragada
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Sriharsha Vogeti
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Nita Parekh
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
- * E-mail:
| |
Collapse
|
9
|
Ding K, Wu Z, Li X, Sheng Y, Wang X, Tan S. LMO4 mediates trastuzumab resistance in HER2 positive breast cancer cells. Am J Cancer Res 2018; 8:594-609. [PMID: 29736306 PMCID: PMC5934551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/04/2018] [Indexed: 06/08/2023] Open
Abstract
Breast cancer is the leading cause of cancer-related mortality in women worldwide. Trastuzumab (Herceptin) is an effective antibody drug for HER2 positive breast cancer; de novo or acquired trastuzumab resistance retarded the use of trastuzumab for at least 70% of HER2 positive breast cancers. In this study, we reported LMO4 (a member of LIM-only proteins) promoted trastuzumab resistance in human breast cancer cells. Over-expression of LMO4 was observed in acquired trastuzumab resistance breast cancer cells SKBR3 HR and BT474 HR. Depletion of LMO4 partly abolished the trastuzumab resistance of SKBR3 HR and BT474 HR cells. Forced expression of LMO4 significantly increased trastuzumab resistance of HER2 positive breast cancer cells both in vitro and in vivo. BCL-2 was regulated by LMO4 and mediated the promoting role of LMO4 in trastuzumab resistance of HER2 positive breast cancer cells. High level of LMO4 was associated with worse clinicopathological parameters (including tumor size and histological grade) and lower survival rate in HER2 positive breast cancer patients. LMO4 therefore could be used as a target to develop diagnostic and therapeutic methods for human HER2 positive breast cancer.
Collapse
Affiliation(s)
- Keshuo Ding
- Department of Pathology, Anhui Medical UniversityHefei, Anhui, P. R. China
| | - Zhengsheng Wu
- Department of Pathology, Anhui Medical UniversityHefei, Anhui, P. R. China
| | - Xiaocan Li
- Department of Pathology, The Second Hospital of Anhui Medical UniversityHefei, Anhui, P. R. China
| | - Youjing Sheng
- Department of Pathology, Anhui Medical UniversityHefei, Anhui, P. R. China
| | - Xiaonan Wang
- Laboratory of Pathogenic Microbiology and Immunology, Anhui Medical UniversityHefei, Anhui, P. R. China
| | - Sheng Tan
- Laboratory of Molecular Tumor Pathology, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of ChinaHefei, Anhui, P. R. China
| |
Collapse
|
10
|
Tolbert VP, Coggins GE, Maris JM. Genetic susceptibility to neuroblastoma. Curr Opin Genet Dev 2017; 42:81-90. [PMID: 28458126 DOI: 10.1016/j.gde.2017.03.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 12/11/2022]
Abstract
Until recently, the genetic basis of neuroblastoma, a heterogeneous neoplasm arising from the developing sympathetic nervous system, remained undefined. The discovery of gain-of-function mutations in the ALK receptor tyrosine kinase gene as the major cause of familial neuroblastoma led to the discovery of identical somatic mutations and rapid advancement of ALK as a tractable therapeutic target. Inactivating mutations in a master regulator of neural crest development, PHOX2B, have also been identified in a subset of familial neuroblastomas. Other high penetrance susceptibility alleles likely exist, but together these heritable mutations account for less than 10% of neuroblastoma cases. A genome-wide association study of a large neuroblastoma cohort identified common and rare polymorphisms highly associated with the disease. Ongoing resequencing efforts aim to further define the genetic landscape of neuroblastoma.
Collapse
Affiliation(s)
- Vanessa P Tolbert
- University of California San Francisco School of Medicine, United States
| | | | - John M Maris
- University of Pennsylvania, United States; Children's Hospital of Philadelphia, United States.
| |
Collapse
|
11
|
Simonik EA, Cai Y, Kimmelshue KN, Brantley-Sieders DM, Loomans HA, Andl CD, Westlake GM, Youngblood VM, Chen J, Yarbrough WG, Brown BT, Nagarajan L, Brandt SJ. LIM-Only Protein 4 (LMO4) and LIM Domain Binding Protein 1 (LDB1) Promote Growth and Metastasis of Human Head and Neck Cancer (LMO4 and LDB1 in Head and Neck Cancer). PLoS One 2016; 11:e0164804. [PMID: 27780223 PMCID: PMC5079595 DOI: 10.1371/journal.pone.0164804] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/01/2016] [Indexed: 12/18/2022] Open
Abstract
Squamous cell carcinoma of the head and neck (HNSCC) accounts for more than 300,000 deaths worldwide per year as a consequence of tumor cell invasion of adjacent structures or metastasis. LIM-only protein 4 (LMO4) and LIM-domain binding protein 1 (LDB1), two directly interacting transcriptional adaptors that have important roles in normal epithelial cell differentiation, have been associated with increased metastasis, decreased differentiation, and shortened survival in carcinoma of the breast. Here, we implicate two LDB1-binding proteins, single-stranded binding protein 2 (SSBP2) and 3 (SSBP3), in controlling LMO4 and LDB1 protein abundance in HNSCC and in regulating specific tumor cell functions in this disease. First, we found that the relative abundance of LMO4, LDB1, and the two SSBPs correlated very significantly in a panel of human HNSCC cell lines. Second, expression of these proteins in tumor primaries and lymph nodes involved by metastasis were concordant in 3 of 3 sets of tissue. Third, using a Matrigel invasion and organotypic reconstruct assay, CRISPR/Cas9-mediated deletion of LDB1 in the VU-SCC-1729 cell line, which is highly invasive of basement membrane and cellular monolayers, reduced tumor cell invasiveness and migration, as well as proliferation on tissue culture plastic. Finally, inactivation of the LDB1 gene in these cells decreased growth and vascularization of xenografted human tumor cells in vivo. These data show that LMO4, LDB1, and SSBP2 and/or SSBP3 regulate metastasis, proliferation, and angiogenesis in HNSCC and provide the first evidence that SSBPs control LMO4 and LDB1 protein abundance in a cancer context.
Collapse
Affiliation(s)
- Elizabeth A. Simonik
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Ying Cai
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Katherine N. Kimmelshue
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Dana M. Brantley-Sieders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Holli A. Loomans
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Claudia D. Andl
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Grant M. Westlake
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Victoria M. Youngblood
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Jin Chen
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Cell & Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
- VA Tennessee Valley Healthcare System, Nashville, TN, United States of America
| | - Wendell G. Yarbrough
- Department of Otolaryngology and Barry Baker Laboratory for Head and Neck Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Brandee T. Brown
- Department of Otolaryngology and Barry Baker Laboratory for Head and Neck Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Lalitha Nagarajan
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - Stephen J. Brandt
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Cell & Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
- VA Tennessee Valley Healthcare System, Nashville, TN, United States of America
- * E-mail:
| |
Collapse
|
12
|
Sahni JM, Gayle SS, Bonk KLW, Vite LC, Yori JL, Webb B, Ramos EK, Seachrist DD, Landis MD, Chang JC, Bradner JE, Keri RA. Bromodomain and Extraterminal Protein Inhibition Blocks Growth of Triple-negative Breast Cancers through the Suppression of Aurora Kinases. J Biol Chem 2016; 291:23756-23768. [PMID: 27650498 DOI: 10.1074/jbc.m116.738666] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 12/15/2022] Open
Abstract
Bromodomain and extraterminal (BET) proteins are epigenetic "readers" that recognize acetylated histones and mark areas of the genome for transcription. BRD4, a BET family member protein, has been implicated in a number of types of cancer, and BET protein inhibitors (BETi) are efficacious in many preclinical cancer models. However, the drivers of response to BETi vary depending on tumor type, and little is known regarding the target genes conveying BETi activity in triple-negative breast cancer (TNBC). Here, we show that BETi repress growth of multiple in vitro and in vivo models of TNBC by inducing two terminal responses: apoptosis and senescence. Unlike in other cancers, response to BETi in TNBC is not dependent upon suppression of MYC Instead, both end points are preceded by the appearance of polyploid cells caused by the suppression of Aurora kinases A and B (AURKA/B), which are critical mediators of mitosis. In addition, AURKA/B inhibitors phenocopy the effects of BETi. These results indicate that Aurora kinases play an important role in the growth suppressive activity of BETi in TNBC. Elucidating the mechanism of response to BETi in TNBC should 1) facilitate the prediction of how distinct TNBC tumors will respond to BETi and 2) inform the rational design of drug combination therapies.
Collapse
Affiliation(s)
| | | | | | | | | | - Bryan Webb
- From the Departments of Pharmacology and
| | | | | | - Melissa D Landis
- the Methodist Cancer Center, Houston Methodist Hospital, Houston, Texas 77030, and
| | - Jenny C Chang
- the Methodist Cancer Center, Houston Methodist Hospital, Houston, Texas 77030, and
| | - James E Bradner
- the Dana-Farber Cancer Institute, Boston, Massachusetts 02115
| | - Ruth A Keri
- From the Departments of Pharmacology and .,Genetics and Genome Sciences and General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, Ohio 44106
| |
Collapse
|
13
|
Han MR, Long J, Choi JY, Low SK, Kweon SS, Zheng Y, Cai Q, Shi J, Guo X, Matsuo K, Iwasaki M, Shen CY, Kim MK, Wen W, Li B, Takahashi A, Shin MH, Xiang YB, Ito H, Kasuga Y, Noh DY, Matsuda K, Park MH, Gao YT, Iwata H, Tsugane S, Park SK, Kubo M, Shu XO, Kang D, Zheng W. Genome-wide association study in East Asians identifies two novel breast cancer susceptibility loci. Hum Mol Genet 2016; 25:3361-3371. [PMID: 27354352 DOI: 10.1093/hmg/ddw164] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/04/2016] [Accepted: 05/20/2016] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is one of the most common malignancies among women worldwide. Genetic factors have been shown to play an important role in breast cancer aetiology. We conducted a two-stage genome-wide association study (GWAS) including 14 224 cases and 14 829 controls of East Asian women to search for novel genetic susceptibility loci for breast cancer. Single nucleotide polymorphisms (SNPs) in two loci were found to be associated with breast cancer risk at the genome-wide significance level. The first locus, represented by rs12118297 at 1p22.3 (near the LMO4 gene), was associated with breast cancer risk with odds ratio (OR) and (95% confidence interval (CI)) of 0.91 (0.88-0.94) and a P-value of 4.48 × 10- 8 This association was replicated in another study, DRIVE GAME-ON Consortium, including 16 003 cases and 41 335 controls of European ancestry (OR = 0.95, 95% CI = 0.91-0.99, P-value = 0.019). The second locus, rs16992204 at 21q22.12 (near the LINC00160 gene), was associated with breast cancer risk with OR (95% CI) of 1.13 (1.07-1.18) and a P-value of 4.63 × 10 - 8 The risk allele frequency for this SNP is zero in European-ancestry populations in 1000 Genomes Project and thus its association with breast cancer risk cannot be assessed in DRIVE GAME-ON Consortium. Functional annotation using the ENCODE data indicates that rs12118297 might be located in a repressed element and locus 21q22.12 may affect breast cancer risk through regulating LINC00160 expressions and interaction with oestrogen receptor signalling. Our findings provide additional insights into the genetics of breast cancer.
Collapse
Affiliation(s)
- Mi-Ryung Han
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jirong Long
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Siew-Kee Low
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama 351-0198, Japan
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju 61469, South Korea.,Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun 58128, South Korea
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Qiuyin Cai
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jiajun Shi
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Xingyi Guo
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan.,Department of Epidemiology, Nagoya University Graduates School of Medicine, Nagoya 464-8681, Japan
| | - Motoki Iwasaki
- Epidemiology Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo 104-0045, Japan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Taiwan Biobank, Academia Sinica, Taipei 115, Taiwan.,College of Public Health, China Medical University, Taichung 404, Taiwan
| | - Mi Kyung Kim
- Division of Cancer Epidemiology and Management, National Cancer Center, Gyeonggi-do 10408, South Korea
| | - Wanqing Wen
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama 351-0198, Japan
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju 61469, South Korea
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai 200032, China
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Yoshio Kasuga
- Department of Surgery, Nagano Matsushiro General Hospital, Nagano 381-1231, Japan
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea.,Department of Surgery, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, the University of Tokyo, Tokyo 108-8639, Japan
| | - Min Ho Park
- Department of Surgery, Chonnam National University Medical School, Gwangju 61469, South Korea
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai 200032, China
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Central Hospital, Nagoya 464-8681, Japan
| | - Shoichiro Tsugane
- Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo 104-0045, Japan
| | - Sue K Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama 351-0198, Japan
| | - Xiao-Ou Shu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Wei Zheng
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| |
Collapse
|
14
|
Abstract
Oncogenic transcription factors are commonly activated in acute leukemias and subvert normal gene expression networks to reprogram hematopoietic progenitors into preleukemic stem cells, as exemplified by LIM-only 2 (LMO2) in T-cell acute lymphoblastic leukemia (T-ALL). Whether or not these oncoproteins interfere with other DNA-dependent processes is largely unexplored. Here, we show that LMO2 is recruited to DNA replication origins by interaction with three essential replication enzymes: DNA polymerase delta (POLD1), DNA primase (PRIM1), and minichromosome 6 (MCM6). Furthermore, tethering LMO2 to synthetic DNA sequences is sufficient to transform these sequences into origins of replication. We next addressed the importance of LMO2 in erythroid and thymocyte development, two lineages in which cell cycle and differentiation are tightly coordinated. Lowering LMO2 levels in erythroid progenitors delays G1-S progression and arrests erythropoietin-dependent cell growth while favoring terminal differentiation. Conversely, ectopic expression in thymocytes induces DNA replication and drives these cells into cell cycle, causing differentiation blockade. Our results define a novel role for LMO2 in directly promoting DNA synthesis and G1-S progression.
Collapse
|
15
|
GU HUI, LIU TONG, CAI XINZE, TONG YUXIN, LI YAN, WANG CHUNYU, LI FENG. Upregulated LMO1 in prostate cancer acts as a novel coactivator of the androgen receptor. Int J Oncol 2015; 47:2181-7. [DOI: 10.3892/ijo.2015.3195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/21/2015] [Indexed: 11/05/2022] Open
|
16
|
Krishnan N, Tonks NK. Anxious moments for the protein tyrosine phosphatase PTP1B. Trends Neurosci 2015; 38:462-5. [PMID: 26166619 DOI: 10.1016/j.tins.2015.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 11/16/2022]
Abstract
Chronic stress can lead to the development of anxiety and mood disorders. Thus, novel therapies for preventing adverse effects of stress are vitally important. Recently, the protein tyrosine phosphatase PTP1B was identified as a novel regulator of stress-induced anxiety. This opens up exciting opportunities to exploit PTP1B inhibitors as anxiolytics.
Collapse
Affiliation(s)
- Navasona Krishnan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Nicholas K Tonks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
| |
Collapse
|
17
|
Baron KD, Al-Zahrani K, Conway J, Labrèche C, Storbeck CJ, Visvader JE, Sabourin LA. Recruitment and activation of SLK at the leading edge of migrating cells requires Src family kinase activity and the LIM-only protein 4. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1683-92. [PMID: 25882817 DOI: 10.1016/j.bbamcr.2015.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/20/2015] [Accepted: 04/03/2015] [Indexed: 12/26/2022]
Abstract
The Ste20-like kinase SLK plays a pivotal role in cell migration and focal adhesion turnover and is regulated by the LIM domain-binding proteins Ldb1 and Ldb2. These adapter proteins have been demonstrated to interact with LMO4 in the organization of transcriptional complexes. Therefore, we have assessed the ability of LMO4 to also interact and regulate SLK activity. Our data show that LMO4 can directly bind to SLK and activate its kinase activity in vitro and in vivo. LMO4 can be co-precipitated with SLK following the induction of cell migration by scratch wounding and Cre-mediated deletion of LMO4 in conditional LMO4(fl/fl) fibroblasts inhibits cell migration and SLK activation. Deletion of LMO4 impairs Ldb1 and SLK recruitment to the leading edge of migrating cells. Supporting this, Src/Yes/Fyn-deficient cells (SYF) expressing very low levels of LMO4 do not recruit SLK to the leading edge. Re-expression of wildtype Myc-LMO4 in SYF cells, but not a mutant version, restores SLK localization and kinase activity. Overall, our data suggest that activation of SLK by haptotactic signals requires its recruitment to the leading edge by LMO4 in a Src-dependent manner. Furthermore, this establishes a novel cytosolic role for the transcriptional co-activator LMO4.
Collapse
Affiliation(s)
- Kyla D Baron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Khalid Al-Zahrani
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jillian Conway
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Cédrik Labrèche
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Christopher J Storbeck
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jane E Visvader
- Walter and Eliza Hall Institute Biotechnology Centre, Bundoora, Victoria 3086, Australia
| | - Luc A Sabourin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Ottawa Hospital Research Institute, Cancer Therapeutics, Ottawa, Ontario, Canada.
| |
Collapse
|
18
|
Joseph S, Kwan AH, Stokes PH, Mackay JP, Cubeddu L, Matthews JM. The structure of an LIM-only protein 4 (LMO4) and Deformed epidermal autoregulatory factor-1 (DEAF1) complex reveals a common mode of binding to LMO4. PLoS One 2014; 9:e109108. [PMID: 25310299 PMCID: PMC4195752 DOI: 10.1371/journal.pone.0109108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/27/2014] [Indexed: 12/23/2022] Open
Abstract
LIM-domain only protein 4 (LMO4) is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1), with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1) and C-terminal binding protein interacting protein (CtIP/RBBP8). Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2 and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways.
Collapse
Affiliation(s)
- Soumya Joseph
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Ann H. Kwan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Philippa H. Stokes
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Joel P. Mackay
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Liza Cubeddu
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
- School of Science and Health, University of Western Sydney, Campbelltown, NSW Australia
| | | |
Collapse
|
19
|
Salmans ML, Yu Z, Watanabe K, Cam E, Sun P, Smyth P, Dai X, Andersen B. The co-factor of LIM domains (CLIM/LDB/NLI) maintains basal mammary epithelial stem cells and promotes breast tumorigenesis. PLoS Genet 2014; 10:e1004520. [PMID: 25079073 PMCID: PMC4117441 DOI: 10.1371/journal.pgen.1004520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/03/2014] [Indexed: 12/20/2022] Open
Abstract
Mammary gland branching morphogenesis and ductal homeostasis relies on mammary stem cell function for the maintenance of basal and luminal cell compartments. The mechanisms of transcriptional regulation of the basal cell compartment are currently unknown. We explored these mechanisms in the basal cell compartment and identified the Co-factor of LIM domains (CLIM/LDB/NLI) as a transcriptional regulator that maintains these cells. Clims act within the basal cell compartment to promote branching morphogenesis by maintaining the number and proliferative potential of basal mammary epithelial stem cells. Clim2, in a complex with LMO4, supports mammary stem cells by directly targeting the Fgfr2 promoter in basal cells to increase its expression. Strikingly, Clims also coordinate basal-specific transcriptional programs to preserve luminal cell identity. These basal-derived cues inhibit epidermis-like differentiation of the luminal cell compartment and enhance the expression of luminal cell-specific oncogenes ErbB2 and ErbB3. Consistently, basal-expressed Clims promote the initiation and progression of breast cancer in the MMTV-PyMT tumor model, and the Clim-regulated branching morphogenesis gene network is a prognostic indicator of poor breast cancer outcome in humans. Recent advancements in mammary gland biology demonstrate conflicting models in maintenance of basal and luminal cell compartments by either unipotent or bipotent mammary stem cells. However, the molecular mechanisms underlying control of the basal cell compartment, including stem cells, remain poorly understood. Here we explore the currently unknown transcriptional mechanisms of basal stem cell (BSC) maintenance, in addition to addressing the role of the basal cell compartment in preserving luminal cell fate and promoting development of human breast tumors of luminal origin. We discover a novel function for the Co-factor of LIM domains (Clim) transcriptional regulator in promoting mammary gland branching morphogenesis and breast tumorigenesis through maintenance of the basal stem cell population. The transcriptional networks coordinated by Clims in basal mammary epithelial cells also preserve the identity of luminal epithelial cells, demonstrating a crosstalk between these two cellular compartments. Furthermore, we correlate developmental gene expression data with human breast cancer to investigate the role of developmental pathways during the initiation and progression of breast cancer. The gene regulatory networks identified during development, including those specifically coordinated by Clims, correlate with breast cancer patient outcome, suggesting these genes play an important role in the progression of breast cancer.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Carcinogenesis/genetics
- Cell Differentiation/genetics
- DNA-Binding Proteins/genetics
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- LIM Domain Proteins/genetics
- Mammary Glands, Human/metabolism
- Mammary Glands, Human/pathology
- Neoplasms, Basal Cell/genetics
- Neoplasms, Basal Cell/metabolism
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- Receptor, ErbB-2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Stem Cells/metabolism
- Stem Cells/pathology
- Transcription Factors/genetics
Collapse
Affiliation(s)
- Michael L. Salmans
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
| | - Zhengquan Yu
- State Key Laboratories for AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, PR China
| | - Kazuhide Watanabe
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Eric Cam
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Peng Sun
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Padhraic Smyth
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California, Irvine, Irvine, California, United States of America
| | - Xing Dai
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Bogi Andersen
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- Department of Medicine, University of California, Irvine, Irvine, California, United States of America
- * E-mail:
| |
Collapse
|
20
|
Liu F, You X, Wang Y, Liu Q, Liu Y, Zhang S, Chen L, Zhang X, Ye L. The oncoprotein HBXIP enhances angiogenesis and growth of breast cancer through modulating FGF8 and VEGF. Carcinogenesis 2014; 35:1144-1153. [DOI: 10.1093/carcin/bgu021] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
|
21
|
LIM-domain-only proteins: multifunctional nuclear transcription coregulators that interacts with diverse proteins. Mol Biol Rep 2013; 41:1067-73. [DOI: 10.1007/s11033-013-2952-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 12/20/2013] [Indexed: 02/07/2023]
|
22
|
Wang N, Wang X, Shi M, Shi H, Yan X, Li H, Wang S, Wang Y. LMO4 modulates proliferation and differentiation of 3T3-L1 preadipocytes. FEBS Lett 2013; 587:3032-7. [PMID: 23892074 DOI: 10.1016/j.febslet.2013.07.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/06/2013] [Accepted: 07/14/2013] [Indexed: 12/11/2022]
Abstract
Previous microarray analyses revealed that LMO4 is expressed in 3T3-L1 preadipocytes, however, its roles in adipogenesis are unknown. In the present study, using RT-PCR sequencing and quantitative real-time RT-PCR, we confirmed that LMO4 gene is expressed in 3T3-L1 preadipocytes and its expression peaks at the early stage of 3T3-L1 preadipocyte differentiation. Further analyses showed that LMO4 knockdown decreased the proliferation of 3T3-L1 preadipocytes, and attenuated the differentiation of 3T3-L1 preadipocytes, as evidenced by reduced lipid accumulation and down-regulation of PPARγ gene expression. Collectively, our findings indicate that LMO4 is a novel modulator of adipogenesis.
Collapse
Affiliation(s)
- Ning Wang
- College of Animal Science and Technology, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, Heilongjiang 150030, China.
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
LIM-domain proteins are a large family of proteins that are emerging as key molecules in a wide variety of human cancers. In particular, all members of the human LIM-domain-only (LMO) proteins, LMO1-4, which are required for many developmental processes, are implicated in the onset or the progression of several cancers, including T cell leukaemia, breast cancer and neuroblastoma. These small proteins contain two protein-interacting LIM domains but little additional sequence, and they seem to function by nucleating the formation of new transcriptional complexes and/or by disrupting existing transcriptional complexes to modulate gene expression programmes. Through these activities, the LMO proteins have important cellular roles in processes that are relevant to cancer such as self-renewal, cell cycle regulation and metastasis. These functions highlight the therapeutic potential of targeting these proteins in cancer.
Collapse
Affiliation(s)
- Jacqueline M Matthews
- School of Molecular Bioscience, The University of Sydney, New South Wales 2006, Australia. jacqui.matthews@ sydney.edu.au
| | | | | | | |
Collapse
|
24
|
Yue L, Li L, Liu F, Hu N, Zhang W, Bai X, Li Y, Zhang Y, Fu L, Zhang X, Ye L. The oncoprotein HBXIP activates transcriptional coregulatory protein LMO4 via Sp1 to promote proliferation of breast cancer cells. Carcinogenesis 2013; 34:927-35. [PMID: 23291272 PMCID: PMC3616668 DOI: 10.1093/carcin/bgs399] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B X-interacting protein (HBXIP) is an important oncoprotein that plays critical role in the development of cancer. In this study, we report that HBXIP activates LIM-only protein 4 (LMO4), a transcriptional coregulatory protein, in promotion of cell proliferation. We observed that the messenger RNA (mRNA) expression levels of HBXIP were positively associated with those of LMO4 in clinical breast cancer tissues. We further identified that HBXIP upregulated LMO4 at the levels of promoter, mRNA and protein in MCF-7 and LM-MCF-7 breast cancer cell lines. The expression of cyclin D1 and cyclin E, downstream effectors of LMO4, could be upregulated by HBXIP through LMO4. Then, chromatin immunoprecipitation (ChIP) assay revealed that HBXIP was able to interact with the promoter region of LMO4. Electrophoretic mobility shift assay showed that HBXIP occupied the -237/-206 region of LMO4 promoter containing Sp1 binding element. The mutant of Sp1 binding site in the LMO4 promoter impeded the interaction of HBXIP with the promoter. Co-immunoprecipitation, ChIP and luciferase reporter gene assays showed that HBXIP activated LMO4 promoter through binding to Sp1. In function, flow cytometry, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, 5-ethynyl-2'-deoxyuridine (EdU) incorporation assays and animal transplantation assays demonstrated that HBXIP-enhanced cell proliferation of breast cancer through upregulating LMO4 in vitro and in vivo. Thus, we concluded that oncoprotein HBXIP is able to activate the transcriptional coregulatory protein LMO4 through transcription factor Sp1 in promotion of proliferation of breast cancer cells. HBXIP may serve as a driver gene to activate transcription in the development of cancer.
Collapse
Affiliation(s)
- Lin Yue
- Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Identification of PADI2 as a potential breast cancer biomarker and therapeutic target. BMC Cancer 2012; 12:500. [PMID: 23110523 PMCID: PMC3571905 DOI: 10.1186/1471-2407-12-500] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 10/27/2012] [Indexed: 12/25/2022] Open
Abstract
Background We have recently reported that the expression of peptidylarginine deiminase 2 (PADI2) is regulated by EGF in mammary cancer cells and appears to play a role in the proliferation of normal mammary epithelium; however, the role of PADI2 in the pathogenesis of human breast cancer has yet to be investigated. Thus, the goals of this study were to examine whether PADI2 plays a role in mammary tumor progression, and whether the inhibition of PADI activity has anti-tumor effects. Methods RNA-seq data from a collection of 57 breast cancer cell lines was queried for PADI2 levels, and correlations with known subtype and HER2/ERBB2 status were evaluated. To examine PADI2 expression levels during breast cancer progression, the cell lines from the MCF10AT model were used. The efficacy of the PADI inhibitor, Cl-amidine, was tested in vitro using MCF10DCIS cells grown in 2D-monolayers and 3D-spheroids, and in vivo using MCF10DCIS tumor xenografts. Treated MCF10DCIS cells were examined by flow-cytometry to determine the extent of apoptosis and by RT2 Profiler PCR Cell Cycle Array to detect alterations in cell cycle associated genes. Results We show by RNA-seq that PADI2 mRNA expression is highly correlated with HER2/ERBB2 (p = 2.2 × 106) in luminal breast cancer cell lines. Using the MCF10AT model of breast cancer progression, we then demonstrate that PADI2 expression increases during the transition of normal mammary epithelium to fully malignant breast carcinomas, with a strong peak of PADI2 expression and activity being observed in the MCF10DCIS cell line, which models human comedo-DCIS lesions. Next, we show that a PADI inhibitor, Cl-amidine, strongly suppresses the growth of MCF10DCIS monolayers and tumor spheroids in culture. We then carried out preclinical studies in nude (nu/nu) mice and found that Cl-amidine also suppressed the growth of xenografted MCF10DCIS tumors by more than 3-fold. Lastly, we performed cell cycle array analysis of Cl-amidine treated and control MCF10DCIS cells, and found that the PADI inhibitor strongly affects the expression of several cell cycle genes implicated in tumor progression, including p21, GADD45α, and Ki67. Conclusion Together, these results suggest that PADI2 may function as an important new biomarker for HER2/ERBB2+ tumors and that Cl-amidine represents a new candidate for breast cancer therapy.
Collapse
|
26
|
Engström PG, Tommei D, Stricker SH, Ender C, Pollard SM, Bertone P. Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival. Genome Med 2012; 4:76. [PMID: 23046790 PMCID: PMC3556652 DOI: 10.1186/gm377] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/20/2012] [Accepted: 10/09/2012] [Indexed: 02/07/2023] Open
Abstract
Background Glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cells with neural stem (NS) cell characteristics. Using derivation methods developed for NS cells, it is possible to expand tumorigenic stem cells continuously in vitro. Although these glioblastoma-derived neural stem (GNS) cells are highly similar to normal NS cells, they harbor mutations typical of gliomas and initiate authentic tumors following orthotopic xenotransplantation. Here, we analyzed GNS and NS cell transcriptomes to identify gene expression alterations underlying the disease phenotype. Methods Sensitive measurements of gene expression were obtained by high-throughput sequencing of transcript tags (Tag-seq) on adherent GNS cell lines from three glioblastoma cases and two normal NS cell lines. Validation by quantitative real-time PCR was performed on 82 differentially expressed genes across a panel of 16 GNS and 6 NS cell lines. The molecular basis and prognostic relevance of expression differences were investigated by genetic characterization of GNS cells and comparison with public data for 867 glioma biopsies. Results Transcriptome analysis revealed major differences correlated with glioma histological grade, and identified misregulated genes of known significance in glioblastoma as well as novel candidates, including genes associated with other malignancies or glioma-related pathways. This analysis further detected several long non-coding RNAs with expression profiles similar to neighboring genes implicated in cancer. Quantitative PCR validation showed excellent agreement with Tag-seq data (median Pearson r = 0.91) and discerned a gene set robustly distinguishing GNS from NS cells across the 22 lines. These expression alterations include oncogene and tumor suppressor changes not detected by microarray profiling of tumor tissue samples, and facilitated the identification of a GNS expression signature strongly associated with patient survival (P = 1e-6, Cox model). Conclusions These results support the utility of GNS cell cultures as a model system for studying the molecular processes driving glioblastoma and the use of NS cells as reference controls. The association between a GNS expression signature and survival is consistent with the hypothesis that a cancer stem cell component drives tumor growth. We anticipate that analysis of normal and malignant stem cells will be an important complement to large-scale profiling of primary tumors.
Collapse
Affiliation(s)
- Pär G Engström
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Diva Tommei
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stefan H Stricker
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Christine Ender
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Steven M Pollard
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Paul Bertone
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK ; Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany ; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| |
Collapse
|
27
|
Zhou X, Sang M, Liu W, Gao W, Xing E, Lü W, Xu Y, Fan X, Jing S, Shan B. LMO4 inhibits p53-mediated proliferative inhibition of breast cancer cells through interacting p53. Life Sci 2012; 91:358-63. [PMID: 22906635 DOI: 10.1016/j.lfs.2012.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 07/14/2012] [Accepted: 08/02/2012] [Indexed: 02/07/2023]
Abstract
AIMS The LIM domain only proteins (LMOs) which consist of four members (LMO1-LMO4) are a family of nuclear transcription coregulators that are characterized by the exclusive presence of two tandem LIM domains and no other functional domains. They regulate gene transcription by functioning as "linker" or "scaffolding" proteins by virtue of their LIM domains and are involved in the formation of multiprotein complexes with several DNA-binding factors and transcriptional regulatory proteins. In the present study, we tried to find the physical interaction between p53 and LMO4, and the effect of LMO4 on p53-mediated proliferative inhibition of breast cancer cells. MAIN METHODS FCM analysis was developed to detect the apoptosis of breast cancer cells after adriamycin (ADR) treatment. RT-PCR and Western blot analysis were performed to detect the expression of LMO4 and p53-related genes and proteins. Immunoprecipitation assay was used to detect the interaction between LMO4 and p53. Colony formation assay was developed to detect the proliferation of breast cancer cells. KEY FINDINGS We found that p53 was induced, but LMO4 was down-regulated in response to ADR. We also found that enforced expression of p53 inhibited the expression of LMO4, suggesting that LMO4 is a direct transcriptional target of p53. Furthermore, LMO4 can interact with p53 and inhibit p53-mediated inhibition of colony formation of breast cancer MDA-MB-453 cells. SIGNIFICANCE The present study showed that LMO4 is a direct target of p53 and inhibits p53-mediated proliferative inhibition of breast cancer cells through interacting p53.
Collapse
Affiliation(s)
- Xinliang Zhou
- Research Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050017, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Schuit F, Van Lommel L, Granvik M, Goyvaerts L, de Faudeur G, Schraenen A, Lemaire K. β-cell-specific gene repression: a mechanism to protect against inappropriate or maladjusted insulin secretion? Diabetes 2012; 61:969-75. [PMID: 22517647 PMCID: PMC3331770 DOI: 10.2337/db11-1564] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Frans Schuit
- Gene Expression Unit, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium.
| | | | | | | | | | | | | |
Collapse
|
29
|
Kono Y, Inomata M, Hagiwara S, Hiratsuka T, Suzuki K, Koga H, Shiraishi N, Noguchi T, Kitano S. Antiproliferative effects of a new α-lipoic acid derivative, DHL-HisZnNa, in HT29 human colon cancer cellsin vitro. Expert Opin Ther Targets 2012; 16 Suppl 1:S103-9. [DOI: 10.1517/14728222.2011.640320] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
30
|
Novel amplifications in pediatric medulloblastoma identified by genome-wide copy number profiling. J Neurooncol 2011; 107:37-49. [PMID: 21979893 DOI: 10.1007/s11060-011-0716-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 09/16/2011] [Indexed: 12/21/2022]
Abstract
Medulloblastoma (MB) is a WHO grade IV, invasive embryonal CNS tumor that mainly affects children. The aggressiveness and response to therapy can vary considerably between cases, and despite treatment, ~30% of patients die within 2 years from diagnosis. Furthermore, the majority of survivors suffer long-term side-effects due to severe management modalities. Several distinct morphological features have been associated with differences in biological behavior, but improved molecular-based criteria that better reflect the underlying tumor biology are in great demand. In this study, we profiled a series of 25 MB with a 32K BAC array covering 99% of the current assembly of the human genome for the identification of genetic copy number alterations possibly important in MB. Previously known aberrations as well as several novel focally amplified loci could be identified. As expected, the most frequently observed alteration was the combination of 17p loss and 17q gain, which was detected in both high- and standard-risk patients. We also defined minimal overlapping regions of aberrations, including 16 regions of gain and 18 regions of loss in various chromosomes. A few noteworthy narrow amplified loci were identified on autosomes 1 (38.89-41.97 and 84.89-90.76 Mb), 3 (27.64-28.20 and 35.80-43.50 Mb), and 8 (119.66-139.79 Mb), aberrations that were verified with an alternative platform (Illumina 610Q chips). Gene expression levels were also established for these samples using Affymetrix U133Plus2.0 arrays. Several interesting genes encompassed within the amplified regions and presenting with transcript upregulation were identified. These data contribute to the characterization of this malignant childhood brain tumor and confirm its genetic heterogeneity.
Collapse
|
31
|
Inferring gene-phenotype associations via global protein complex network propagation. PLoS One 2011; 6:e21502. [PMID: 21799737 PMCID: PMC3143124 DOI: 10.1371/journal.pone.0021502] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 05/30/2011] [Indexed: 12/05/2022] Open
Abstract
Background Phenotypically similar diseases have been found to be caused by functionally related genes, suggesting a modular organization of the genetic landscape of human diseases that mirrors the modularity observed in biological interaction networks. Protein complexes, as molecular machines that integrate multiple gene products to perform biological functions, express the underlying modular organization of protein-protein interaction networks. As such, protein complexes can be useful for interrogating the networks of phenome and interactome to elucidate gene-phenotype associations of diseases. Methodology/Principal Findings We proposed a technique called RWPCN (Random Walker on Protein Complex Network) for predicting and prioritizing disease genes. The basis of RWPCN is a protein complex network constructed using existing human protein complexes and protein interaction network. To prioritize candidate disease genes for the query disease phenotypes, we compute the associations between the protein complexes and the query phenotypes in their respective protein complex and phenotype networks. We tested RWPCN on predicting gene-phenotype associations using leave-one-out cross-validation; our method was observed to outperform existing approaches. We also applied RWPCN to predict novel disease genes for two representative diseases, namely, Breast Cancer and Diabetes. Conclusions/Significance Guilt-by-association prediction and prioritization of disease genes can be enhanced by fully exploiting the underlying modular organizations of both the disease phenome and the protein interactome. Our RWPCN uses a novel protein complex network as a basis for interrogating the human phenome-interactome network. As the protein complex network can capture the underlying modularity in the biological interaction networks better than simple protein interaction networks, RWPCN was found to be able to detect and prioritize disease genes better than traditional approaches that used only protein-phenotype associations.
Collapse
|
32
|
Montañez-Wiscovich ME, Shelton MD, Seachrist DD, Lozada KL, Johnson E, Miedler JD, Abdul-Karim FW, Visvader JE, Keri RA. Aberrant expression of LMO4 induces centrosome amplification and mitotic spindle abnormalities in breast cancer cells. J Pathol 2010; 222:271-81. [PMID: 20814902 DOI: 10.1002/path.2762] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The LIM-only protein, LMO4, is a transcriptional modulator overexpressed in breast cancer. It is oncogenic in murine mammary epithelium and is required for G2/M progression of ErbB2-dependent cells as well as growth and invasion of other breast cancer cell types. However, the mechanisms underlying the oncogenic activity of LMO4 remain unclear. Herein, we show that LMO4 is expressed in all breast cancer subtypes examined and its expression level correlates with the degree of proliferation of such tumours. In addition, we have determined that LMO4 silencing induces G2/M arrest in cells from various breast cancer subtypes, suggesting that LMO4 action in the cell cycle is not restricted to a single breast cancer subtype. This arrest was accompanied by increased cell death, amplification of centrosomes, and formation of abnormal mitotic spindles. Consistent with its ability to positively and negatively regulate the formation of active transcription complexes, overexpression of LMO4 also resulted in an increase in centrosome number. Centrosome amplification has been shown to prolong the G2/M phase of the cell cycle and induce apoptosis; thus, we conclude that supernumerary centrosomes mediate the G2/M arrest and cell death in LMO4-deficient cells. Furthermore, the correlation of centrosome amplification with genomic instability suggests that the impact of dysregulated LMO4 on the centrosome cycle may promote LMO4-induced tumour formation.
Collapse
|
33
|
Yori JL, Johnson E, Zhou G, Jain MK, Keri RA. Kruppel-like factor 4 inhibits epithelial-to-mesenchymal transition through regulation of E-cadherin gene expression. J Biol Chem 2010; 285:16854-63. [PMID: 20356845 DOI: 10.1074/jbc.m110.114546] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Krüppel-like factor 4 (KLF4) is a transcriptional regulator of proliferation and differentiation in epithelial cells, both during development and tumorigenesis. Although KLF4 functions as a tumor suppressor in several tissues, including the colon, the role of KLF4 in breast cancer is less clear. Here, we show that KLF4 is necessary for maintenance of the epithelial phenotype in non-transformed MCF-10A mammary epithelial cells. KLF4 silencing led to alterations in epithelial cell morphology and migration, indicative of an epithelial-to-mesenchymal transition. Consistent with these changes, decreased levels of KLF4 also resulted in the loss of E-cadherin protein and mRNA. Promoter/reporter analyses revealed decreased E-cadherin promoter activity with KLF4 silencing, while chromatin immunoprecipitation identified endogenous KLF4 binding to the GC-rich/E-box region of this promoter. Furthermore, forced expression of KLF4 in the highly metastatic MDA-MB-231 breast tumor cell line was sufficient to restore E-cadherin expression and suppress migration and invasion. These findings identify E-cadherin as a novel transcriptional target of KLF4. The clear requirement for KLF4 to maintain E-cadherin expression and prevent epithelial-to-mesenchymal transition in mammary epithelial cells supports a metastasis suppressive role for KLF4 in breast cancer.
Collapse
Affiliation(s)
- Jennifer L Yori
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | | | | | | | | |
Collapse
|